메뉴 건너뛰기




Volumn 119, Issue 1, 2015, Pages 20-32

In silico design of low molecular weight protein-protein interaction inhibitors: Overall concept and recent advances

Author keywords

Bioinformatics; Chemoinformatics; Compound collection; Focused library; Protein protein interaction inhibitors; Virtual screening

Indexed keywords

LIGAND; MOLECULAR LIBRARY;

EID: 84940891441     PISSN: 00796107     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbiomolbio.2015.02.006     Document Type: Review
Times cited : (54)

References (225)
  • 1
    • 79960153981 scopus 로고    scopus 로고
    • Intramolecular hydrogen bonding to improve membrane permeability and absorption in beyond rule of five chemical space
    • Alex A., Millan D.S., Perez M., Wakenhut F., Whitlock G.A. Intramolecular hydrogen bonding to improve membrane permeability and absorption in beyond rule of five chemical space. Med. Chem. Commun. 2011, 2:669-674.
    • (2011) Med. Chem. Commun. , vol.2 , pp. 669-674
    • Alex, A.1    Millan, D.S.2    Perez, M.3    Wakenhut, F.4    Whitlock, G.A.5
  • 2
    • 84908374552 scopus 로고    scopus 로고
    • Molecular simulations with solvent competition quantify water displaceability and provide accurate interaction maps of protein binding sites
    • Alvarez-Garcia D., Barril X. Molecular simulations with solvent competition quantify water displaceability and provide accurate interaction maps of protein binding sites. J. Med. Chem. 2014, 57:8530-8539.
    • (2014) J. Med. Chem. , vol.57 , pp. 8530-8539
    • Alvarez-Garcia, D.1    Barril, X.2
  • 3
    • 84902077293 scopus 로고    scopus 로고
    • Evolution of protein interactions: from interactomes to interfaces
    • Andreani J., Guerois R. Evolution of protein interactions: from interactomes to interfaces. Arch. Biochem. Biophys. 2014, 554:65-75.
    • (2014) Arch. Biochem. Biophys. , vol.554 , pp. 65-75
    • Andreani, J.1    Guerois, R.2
  • 4
    • 84909587217 scopus 로고    scopus 로고
    • Small-molecule inhibitors of protein-protein interactions: progressing toward the reality
    • Arkin M.R., Tang Y., Wells J.A. Small-molecule inhibitors of protein-protein interactions: progressing toward the reality. Chem. Biol. 2014, 21:1102-1114.
    • (2014) Chem. Biol. , vol.21 , pp. 1102-1114
    • Arkin, M.R.1    Tang, Y.2    Wells, J.A.3
  • 5
    • 3142781225 scopus 로고    scopus 로고
    • Small-molecule inhibitors of protein-protein interactions: progressing towards the dream
    • Arkin M.R., Wells J.A. Small-molecule inhibitors of protein-protein interactions: progressing towards the dream. Nat. Rev. Drug Discov. 2004, 3:301-317.
    • (2004) Nat. Rev. Drug Discov. , vol.3 , pp. 301-317
    • Arkin, M.R.1    Wells, J.A.2
  • 6
    • 33646060435 scopus 로고    scopus 로고
    • Proposed structural models of the prothrombinase (FXa-FVa) complex
    • Autin L., Steen M., Dahlback B., Villoutreix B.O. Proposed structural models of the prothrombinase (FXa-FVa) complex. Proteins 2006, 63:440-450.
    • (2006) Proteins , vol.63 , pp. 440-450
    • Autin, L.1    Steen, M.2    Dahlback, B.3    Villoutreix, B.O.4
  • 7
    • 84875436143 scopus 로고    scopus 로고
    • Inhibition of alpha-helix-mediated protein-protein interactions using designed molecules
    • Azzarito V., Long K., Murphy N.S., Wilson A.J. Inhibition of alpha-helix-mediated protein-protein interactions using designed molecules. Nat. Chem. 2013, 5:161-173.
    • (2013) Nat. Chem. , vol.5 , pp. 161-173
    • Azzarito, V.1    Long, K.2    Murphy, N.S.3    Wilson, A.J.4
  • 8
    • 84888825453 scopus 로고    scopus 로고
    • Coarse-grain modelling of protein-protein interactions
    • Baaden M., Marrink S.J. Coarse-grain modelling of protein-protein interactions. Curr. Opin. Struct. Biol. 2013, 23:878-886.
    • (2013) Curr. Opin. Struct. Biol. , vol.23 , pp. 878-886
    • Baaden, M.1    Marrink, S.J.2
  • 9
    • 84908530414 scopus 로고    scopus 로고
    • Chemistry: chemical con artists foil drug discovery
    • Baell J., Walters M.A. Chemistry: chemical con artists foil drug discovery. Nature 2014, 513:481-483.
    • (2014) Nature , vol.513 , pp. 481-483
    • Baell, J.1    Walters, M.A.2
  • 10
    • 77950571108 scopus 로고    scopus 로고
    • New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays
    • Baell J.B., Holloway G.A. New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays. J. Med. Chem. 2010, 53:2719-2740.
    • (2010) J. Med. Chem. , vol.53 , pp. 2719-2740
    • Baell, J.B.1    Holloway, G.A.2
  • 11
    • 0036835460 scopus 로고    scopus 로고
    • Integration of virtual and high-throughput screening
    • Bajorath J. Integration of virtual and high-throughput screening. Nat. Rev. Drug Discov. 2002, 1:882-894.
    • (2002) Nat. Rev. Drug Discov. , vol.1 , pp. 882-894
    • Bajorath, J.1
  • 13
    • 79954550877 scopus 로고    scopus 로고
    • Mechanisms of chemical carcinogenicity and mutagenicity: a review with implications for predictive toxicology
    • Benigni R., Bossa C. Mechanisms of chemical carcinogenicity and mutagenicity: a review with implications for predictive toxicology. Chem. Rev. 2011, 111:2507-2536.
    • (2011) Chem. Rev. , vol.111 , pp. 2507-2536
    • Benigni, R.1    Bossa, C.2
  • 14
    • 84857733776 scopus 로고    scopus 로고
    • Computational drug design targeting protein-protein interactions
    • Bienstock R.J. Computational drug design targeting protein-protein interactions. Curr. Pharm. Des. 2012, 18:1240-1254.
    • (2012) Curr. Pharm. Des. , vol.18 , pp. 1240-1254
    • Bienstock, R.J.1
  • 15
    • 0032479179 scopus 로고    scopus 로고
    • Anatomy of hot spots in protein interfaces
    • Bogan A.A., Thorn K.S. Anatomy of hot spots in protein interfaces. J. Mol. Biol. 1998, 280:1-9.
    • (1998) J. Mol. Biol. , vol.280 , pp. 1-9
    • Bogan, A.A.1    Thorn, K.S.2
  • 16
    • 84881614684 scopus 로고    scopus 로고
    • Plasma protein binding: from discovery to development
    • Bohnert T., Gan L.S. Plasma protein binding: from discovery to development. J. Pharm. Sci. 2013, 102:2953-2994.
    • (2013) J. Pharm. Sci. , vol.102 , pp. 2953-2994
    • Bohnert, T.1    Gan, L.S.2
  • 17
    • 84908351629 scopus 로고    scopus 로고
    • Evidence of conformational selection driving the formation of ligand binding sites in protein-protein interfaces
    • Bohnuud T., Kozakov D., Vajda S. Evidence of conformational selection driving the formation of ligand binding sites in protein-protein interfaces. PLoS Comput. Biol. 2014, 10:e1003872.
    • (2014) PLoS Comput. Biol. , vol.10 , pp. e1003872
    • Bohnuud, T.1    Kozakov, D.2    Vajda, S.3
  • 18
    • 33744539143 scopus 로고    scopus 로고
    • Chemical database preparation for compound acquisition or virtual screening
    • Bologa C.G., Olah M.M., Oprea T.I. Chemical database preparation for compound acquisition or virtual screening. Methods Mol. Biol. 2006, 316:375-388.
    • (2006) Methods Mol. Biol. , vol.316 , pp. 375-388
    • Bologa, C.G.1    Olah, M.M.2    Oprea, T.I.3
  • 19
    • 33746076877 scopus 로고    scopus 로고
    • Effects of conformational dynamics on predicted protein druggability
    • Brown S.P., Hajduk P.J. Effects of conformational dynamics on predicted protein druggability. ChemMedChem 2006, 1:70-72.
    • (2006) ChemMedChem , vol.1 , pp. 70-72
    • Brown, S.P.1    Hajduk, P.J.2
  • 21
    • 79951960238 scopus 로고    scopus 로고
    • Small-molecule protein-protein interaction inhibitors: therapeutic potential in light of molecular size, chemical space, and ligand binding efficiency considerations
    • Buchwald P. Small-molecule protein-protein interaction inhibitors: therapeutic potential in light of molecular size, chemical space, and ligand binding efficiency considerations. IUBMB Life 2010, 62:724-731.
    • (2010) IUBMB Life , vol.62 , pp. 724-731
    • Buchwald, P.1
  • 22
    • 80052566586 scopus 로고    scopus 로고
    • Assessing helical protein interfaces for inhibitor design
    • Bullock B.N., Jochim A.L., Arora P.S. Assessing helical protein interfaces for inhibitor design. J. Am. Chem. Soc. 2011, 133:14220-14223.
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 14220-14223
    • Bullock, B.N.1    Jochim, A.L.2    Arora, P.S.3
  • 23
    • 67649518035 scopus 로고    scopus 로고
    • Homology modeling in drug discovery: current trends and applications
    • Cavasotto C.N., Phatak S.S. Homology modeling in drug discovery: current trends and applications. Drug Discov. Today 2009, 14:676-683.
    • (2009) Drug Discov. Today , vol.14 , pp. 676-683
    • Cavasotto, C.N.1    Phatak, S.S.2
  • 24
    • 84884586690 scopus 로고    scopus 로고
    • How to design a drug for the disordered proteins?
    • Chen C.Y., Tou W.I. How to design a drug for the disordered proteins?. Drug Discov. Today 2013, 18:910-915.
    • (2013) Drug Discov. Today , vol.18 , pp. 910-915
    • Chen, C.Y.1    Tou, W.I.2
  • 25
    • 84887035754 scopus 로고    scopus 로고
    • Complementarity between in silico and biophysical screening approaches in fragment-based lead discovery against the A(2A) adenosine receptor
    • Chen D., Ranganathan A., AP I.J., Siegal G., Carlsson J. Complementarity between in silico and biophysical screening approaches in fragment-based lead discovery against the A(2A) adenosine receptor. J. Chem. Inf. Model. 2013, 53:2701-2714.
    • (2013) J. Chem. Inf. Model. , vol.53 , pp. 2701-2714
    • Chen, D.1    Ranganathan, A.2    AP, I.J.3    Siegal, G.4    Carlsson, J.5
  • 26
    • 84878306995 scopus 로고    scopus 로고
    • Protein-protein interactions: general trends in the relationship between binding affinity and interfacial buried surface area
    • Chen J., Sawyer N., Regan L. Protein-protein interactions: general trends in the relationship between binding affinity and interfacial buried surface area. Protein Sci. 2013, 22:510-515.
    • (2013) Protein Sci. , vol.22 , pp. 510-515
    • Chen, J.1    Sawyer, N.2    Regan, L.3
  • 27
    • 79955797274 scopus 로고    scopus 로고
    • A critical comparative assessment of predictions of protein-binding sites for biologically relevant organic compounds
    • Chen K., Mizianty M.J., Gao J., Kurgan L. A critical comparative assessment of predictions of protein-binding sites for biologically relevant organic compounds. Structure 2011, 19:613-621.
    • (2011) Structure , vol.19 , pp. 613-621
    • Chen, K.1    Mizianty, M.J.2    Gao, J.3    Kurgan, L.4
  • 30
    • 84930348435 scopus 로고    scopus 로고
    • Targeting protein-protein interactions in hematologic malignancies: still a challenge or a great opportunity for future therapies?
    • Cierpicki T., Grembecka J. Targeting protein-protein interactions in hematologic malignancies: still a challenge or a great opportunity for future therapies?. Immunol. Rev. 2015, 263:279-301.
    • (2015) Immunol. Rev. , vol.263 , pp. 279-301
    • Cierpicki, T.1    Grembecka, J.2
  • 31
    • 0028916599 scopus 로고
    • A hot spot of binding energy in a hormone-receptor interface
    • Clackson T., Wells J.A. A hot spot of binding energy in a hormone-receptor interface. Science 1995, 267:383-386.
    • (1995) Science , vol.267 , pp. 383-386
    • Clackson, T.1    Wells, J.A.2
  • 32
    • 48749127628 scopus 로고    scopus 로고
    • What has virtual screening ever done for drug discovery?
    • Clark D.E. What has virtual screening ever done for drug discovery?. Expert Opin. Drug Discov. 2008, 3:841-851.
    • (2008) Expert Opin. Drug Discov. , vol.3 , pp. 841-851
    • Clark, D.E.1
  • 33
    • 80054928519 scopus 로고    scopus 로고
    • Pocket-space maps to identify novel binding-site conformations in proteins
    • Craig I.R., Pfleger C., Gohlke H., Essex J.W., Spiegel K. Pocket-space maps to identify novel binding-site conformations in proteins. J. Chem. Inf. Model. 2011, 51:2666-2679.
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 2666-2679
    • Craig, I.R.1    Pfleger, C.2    Gohlke, H.3    Essex, J.W.4    Spiegel, K.5
  • 35
    • 73749087803 scopus 로고    scopus 로고
    • Molecular fields in drug discovery: getting old or reaching maturity?
    • Cross S., Cruciani G. Molecular fields in drug discovery: getting old or reaching maturity?. Drug Discov. Today 2010, 15:23-32.
    • (2010) Drug Discov. Today , vol.15 , pp. 23-32
    • Cross, S.1    Cruciani, G.2
  • 36
    • 0033800498 scopus 로고    scopus 로고
    • VolSurf: a new tool for the pharmacokinetic optimization of lead compounds
    • Cruciani G., Pastor M., Guba W. VolSurf: a new tool for the pharmacokinetic optimization of lead compounds. Eur. J. Pharm. Sci. 2000, 11(Suppl. 2):S29-S39.
    • (2000) Eur. J. Pharm. Sci. , vol.11 , pp. S29-S39
    • Cruciani, G.1    Pastor, M.2    Guba, W.3
  • 38
    • 77952541448 scopus 로고    scopus 로고
    • Disrupting protein-protein interactions with non-peptidic, small molecule alpha-helix mimetics
    • Cummings C.G., Hamilton A.D. Disrupting protein-protein interactions with non-peptidic, small molecule alpha-helix mimetics. Curr. Opin. Chem. Biol. 2010, 14:341-346.
    • (2010) Curr. Opin. Chem. Biol. , vol.14 , pp. 341-346
    • Cummings, C.G.1    Hamilton, A.D.2
  • 39
    • 84906764097 scopus 로고    scopus 로고
    • The essential roles of chemistry in high-throughput screening triage
    • Dahlin J.L., Walters M.A. The essential roles of chemistry in high-throughput screening triage. Future Med. Chem. 2014, 6:1265-1290.
    • (2014) Future Med. Chem. , vol.6 , pp. 1265-1290
    • Dahlin, J.L.1    Walters, M.A.2
  • 40
    • 33746058237 scopus 로고    scopus 로고
    • Streamlining lead discovery by aligning in silico and high-throughput screening
    • Davies J.W., Glick M., Jenkins J.L. Streamlining lead discovery by aligning in silico and high-throughput screening. Curr. Opin. Chem. Biol. 2006, 10:343-351.
    • (2006) Curr. Opin. Chem. Biol. , vol.10 , pp. 343-351
    • Davies, J.W.1    Glick, M.2    Jenkins, J.L.3
  • 44
    • 84909586310 scopus 로고    scopus 로고
    • Oral druggable space beyond the rule of 5: insights from drugs and clinical candidates
    • Doak B.C., Over B., Giordanetto F., Kihlberg J. Oral druggable space beyond the rule of 5: insights from drugs and clinical candidates. Chem. Biol. 2014, 21:1115-1142.
    • (2014) Chem. Biol. , vol.21 , pp. 1115-1142
    • Doak, B.C.1    Over, B.2    Giordanetto, F.3    Kihlberg, J.4
  • 45
    • 78651499200 scopus 로고    scopus 로고
    • Systematic error detection in experimental high-throughput screening
    • Dragiev P., Nadon R., Makarenkov V. Systematic error detection in experimental high-throughput screening. BMC Bioinform. 2011, 12:25.
    • (2011) BMC Bioinform. , vol.12 , pp. 25
    • Dragiev, P.1    Nadon, R.2    Makarenkov, V.3
  • 46
    • 79953703975 scopus 로고    scopus 로고
    • Fragment screening to predict druggability (ligandability) and lead discovery success
    • Edfeldt F.N., Folmer R.H., Breeze A.L. Fragment screening to predict druggability (ligandability) and lead discovery success. Drug Discov. Today 2011, 16:284-287.
    • (2011) Drug Discov. Today , vol.16 , pp. 284-287
    • Edfeldt, F.N.1    Folmer, R.H.2    Breeze, A.L.3
  • 47
    • 34548319111 scopus 로고    scopus 로고
    • In silico pharmacology for drug discovery: applications to targets and beyond
    • Ekins S., Mestres J., Testa B. In silico pharmacology for drug discovery: applications to targets and beyond. Br. J. Pharmacol. 2007, 152:21-37.
    • (2007) Br. J. Pharmacol. , vol.152 , pp. 21-37
    • Ekins, S.1    Mestres, J.2    Testa, B.3
  • 48
    • 34548304745 scopus 로고    scopus 로고
    • In silico pharmacology for drug discovery: methods for virtual ligand screening and profiling
    • Ekins S., Mestres J., Testa B. In silico pharmacology for drug discovery: methods for virtual ligand screening and profiling. Br. J. Pharmacol. 2007, 152:9-20.
    • (2007) Br. J. Pharmacol. , vol.152 , pp. 9-20
    • Ekins, S.1    Mestres, J.2    Testa, B.3
  • 50
    • 34547583152 scopus 로고    scopus 로고
    • Transient pockets on protein surfaces involved in protein-protein interaction
    • Eyrisch S., Helms V. Transient pockets on protein surfaces involved in protein-protein interaction. J. Med. Chem. 2007, 50:3457-3464.
    • (2007) J. Med. Chem. , vol.50 , pp. 3457-3464
    • Eyrisch, S.1    Helms, V.2
  • 51
    • 84895491357 scopus 로고    scopus 로고
    • Structure-based design of small-molecule protein-protein interaction modulators: the story so far
    • Falchi F., Caporuscio F., Recanatini M. Structure-based design of small-molecule protein-protein interaction modulators: the story so far. Future Med. Chem. 2014, 6:343-357.
    • (2014) Future Med. Chem. , vol.6 , pp. 343-357
    • Falchi, F.1    Caporuscio, F.2    Recanatini, M.3
  • 52
    • 80255141850 scopus 로고    scopus 로고
    • Evolution of the physicochemical properties of marketed drugs: can history foretell the future?
    • Faller B., Ottaviani G., Ertl P., Berellini G., Collis A. Evolution of the physicochemical properties of marketed drugs: can history foretell the future?. Drug Discov. Today 2011, 16:976-984.
    • (2011) Drug Discov. Today , vol.16 , pp. 976-984
    • Faller, B.1    Ottaviani, G.2    Ertl, P.3    Berellini, G.4    Collis, A.5
  • 54
    • 79960985571 scopus 로고    scopus 로고
    • Structure-based druggability assessment - identifying suitable targets for small molecule therapeutics
    • Fauman E.B., Rai B.K., Huang E.S. Structure-based druggability assessment - identifying suitable targets for small molecule therapeutics. Curr. Opin. Chem. Biol. 2011, 15:463-468.
    • (2011) Curr. Opin. Chem. Biol. , vol.15 , pp. 463-468
    • Fauman, E.B.1    Rai, B.K.2    Huang, E.S.3
  • 55
    • 84886304492 scopus 로고    scopus 로고
    • De-peptidising protein-protein interactions - big jobs for small molecules
    • Fayne D. De-peptidising protein-protein interactions - big jobs for small molecules. Drug Discov. Today Technol. 2013, 10:e467-e474.
    • (2013) Drug Discov. Today Technol. , vol.10 , pp. e467-e474
    • Fayne, D.1
  • 56
    • 84856010726 scopus 로고    scopus 로고
    • Prediction of protein binding sites and hot spots
    • Fernandez-Recio J. Prediction of protein binding sites and hot spots. WIREs Comput. Mol. Sci. 2011, 1:680-698.
    • (2011) WIREs Comput. Mol. Sci. , vol.1 , pp. 680-698
    • Fernandez-Recio, J.1
  • 59
    • 58849145512 scopus 로고    scopus 로고
    • Predicting druggable binding sites at the protein-protein interface
    • Fuller J.C., Burgoyne N.J., Jackson R.M. Predicting druggable binding sites at the protein-protein interface. Drug Discov. Today 2009, 14:155-161.
    • (2009) Drug Discov. Today , vol.14 , pp. 155-161
    • Fuller, J.C.1    Burgoyne, N.J.2    Jackson, R.M.3
  • 60
    • 34248523175 scopus 로고    scopus 로고
    • DFprot: a webtool for predicting local chain deformability
    • Garzon J.I., Kovacs J., Abagyan R., Chacon P. DFprot: a webtool for predicting local chain deformability. Bioinformatics 2007, 23:901-902.
    • (2007) Bioinformatics , vol.23 , pp. 901-902
    • Garzon, J.I.1    Kovacs, J.2    Abagyan, R.3    Chacon, P.4
  • 62
    • 84910596652 scopus 로고    scopus 로고
    • Stabilization of protein-protein interactions by small molecules
    • Giordanetto F., Schafer A., Ottmann C. Stabilization of protein-protein interactions by small molecules. Drug Discov. Today 2014, 19:1812-1821.
    • (2014) Drug Discov. Today , vol.19 , pp. 1812-1821
    • Giordanetto, F.1    Schafer, A.2    Ottmann, C.3
  • 63
    • 39749181550 scopus 로고    scopus 로고
    • Generation of a set of simple, interpretable ADMET rules of thumb
    • Gleeson M.P. Generation of a set of simple, interpretable ADMET rules of thumb. J. Med. Chem. 2008, 51:817-834.
    • (2008) J. Med. Chem. , vol.51 , pp. 817-834
    • Gleeson, M.P.1
  • 64
    • 84883217711 scopus 로고    scopus 로고
    • Structural properties of non-traditional drug targets present new challenges for virtual screening
    • Gowthaman R., Deeds E.J., Karanicolas J. Structural properties of non-traditional drug targets present new challenges for virtual screening. J. Chem. Inf. Model. 2013, 53:2073-2081.
    • (2013) J. Chem. Inf. Model. , vol.53 , pp. 2073-2081
    • Gowthaman, R.1    Deeds, E.J.2    Karanicolas, J.3
  • 65
    • 84866354446 scopus 로고    scopus 로고
    • Protein-protein docking and hot-spot prediction for drug discovery
    • Grosdidier S., Fernandez-Recio J. Protein-protein docking and hot-spot prediction for drug discovery. Curr. Pharm. Des. 2012, 18:4607-4618.
    • (2012) Curr. Pharm. Des. , vol.18 , pp. 4607-4618
    • Grosdidier, S.1    Fernandez-Recio, J.2
  • 66
    • 84886389108 scopus 로고    scopus 로고
    • FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots
    • Grove L.E., Hall D.R., Beglov D., Vajda S., Kozakov D. FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots. Bioinformatics 2013, 29:1218-1219.
    • (2013) Bioinformatics , vol.29 , pp. 1218-1219
    • Grove, L.E.1    Hall, D.R.2    Beglov, D.3    Vajda, S.4    Kozakov, D.5
  • 67
    • 84912041026 scopus 로고    scopus 로고
    • Protein-protein interaction modulator drug discovery: past efforts and future opportunities using a rich source of low- and high-throughput screening assays
    • Gul S., Hadian K. Protein-protein interaction modulator drug discovery: past efforts and future opportunities using a rich source of low- and high-throughput screening assays. Expert Opin. Drug Discov. 2014, 9:1393-1404.
    • (2014) Expert Opin. Drug Discov. , vol.9 , pp. 1393-1404
    • Gul, S.1    Hadian, K.2
  • 68
    • 17144373303 scopus 로고    scopus 로고
    • Druggability indices for protein targets derived from NMR-based screening data
    • Hajduk P.J., Huth J.R., Fesik S.W. Druggability indices for protein targets derived from NMR-based screening data. J. Med. Chem. 2005, 48:2518-2525.
    • (2005) J. Med. Chem. , vol.48 , pp. 2518-2525
    • Hajduk, P.J.1    Huth, J.R.2    Fesik, S.W.3
  • 71
    • 84860359784 scopus 로고    scopus 로고
    • Finding the sweet spot: the role of nature and nurture in medicinal chemistry
    • Hann M.M., Keseru G.M. Finding the sweet spot: the role of nature and nurture in medicinal chemistry. Nat. Rev. Drug Discov. 2012, 11:355-365.
    • (2012) Nat. Rev. Drug Discov. , vol.11 , pp. 355-365
    • Hann, M.M.1    Keseru, G.M.2
  • 72
    • 84926205808 scopus 로고    scopus 로고
    • The re-emergence of natural products for drug discovery in the genomics era
    • Harvey A.L., Edrada-Ebel R., Quinn R.J. The re-emergence of natural products for drug discovery in the genomics era. Nat. Rev. Drug Discov. 2015, 14:111-129.
    • (2015) Nat. Rev. Drug Discov. , vol.14 , pp. 111-129
    • Harvey, A.L.1    Edrada-Ebel, R.2    Quinn, R.J.3
  • 73
    • 84871390611 scopus 로고    scopus 로고
    • The future of virtual compound screening
    • Heikamp K., Bajorath J. The future of virtual compound screening. Chem. Biol. Drug Des. 2013, 81:33-40.
    • (2013) Chem. Biol. Drug Des. , vol.81 , pp. 33-40
    • Heikamp, K.1    Bajorath, J.2
  • 74
    • 67849097355 scopus 로고    scopus 로고
    • SITEHOUND-web: a server for ligand binding site identification in protein structures
    • Hernandez M., Ghersi D., Sanchez R. SITEHOUND-web: a server for ligand binding site identification in protein structures. Nucleic Acids Res. 2009, 37:W413-W416.
    • (2009) Nucleic Acids Res. , vol.37 , pp. W413-W416
    • Hernandez, M.1    Ghersi, D.2    Sanchez, R.3
  • 75
    • 84893018543 scopus 로고    scopus 로고
    • Protein-protein interactions as druggable targets: recent technological advances
    • Higueruelo A.P., Jubb H., Blundell T.L. Protein-protein interactions as druggable targets: recent technological advances. Curr. Opin. Pharmacol. 2013, 13:791-796.
    • (2013) Curr. Opin. Pharmacol. , vol.13 , pp. 791-796
    • Higueruelo, A.P.1    Jubb, H.2    Blundell, T.L.3
  • 76
    • 84885920636 scopus 로고    scopus 로고
    • TIMBAL v2: update of a database holding small molecules modulating protein-protein interactions
    • 2013, bat039
    • Higueruelo A.P., Jubb H., Blundell T.L. TIMBAL v2: update of a database holding small molecules modulating protein-protein interactions. Database (Oxford) 2013, 2013, bat039.
    • (2013) Database (Oxford)
    • Higueruelo, A.P.1    Jubb, H.2    Blundell, T.L.3
  • 79
    • 77956308900 scopus 로고    scopus 로고
    • Binding-site assessment by virtual fragment screening
    • Huang N., Jacobson M.P. Binding-site assessment by virtual fragment screening. PLoS One 2010, 5:e10109.
    • (2010) PLoS One , vol.5 , pp. e10109
    • Huang, N.1    Jacobson, M.P.2
  • 82
    • 4644235643 scopus 로고    scopus 로고
    • Virtual screening in lead discovery and optimization
    • Jain A.N. Virtual screening in lead discovery and optimization. Curr. Opin. Drug Discov. Dev. 2004, 7:396-403.
    • (2004) Curr. Opin. Drug Discov. Dev. , vol.7 , pp. 396-403
    • Jain, A.N.1
  • 83
    • 52649130704 scopus 로고    scopus 로고
    • Protein-protein interaction and quaternary structure
    • Janin J., Bahadur R.P., Chakrabarti P. Protein-protein interaction and quaternary structure. Q. Rev. Biophys. 2008, 41:133-180.
    • (2008) Q. Rev. Biophys. , vol.41 , pp. 133-180
    • Janin, J.1    Bahadur, R.P.2    Chakrabarti, P.3
  • 84
    • 0025123333 scopus 로고
    • The structure of protein-protein recognition sites
    • Janin J., Chothia C. The structure of protein-protein recognition sites. J. Biol. Chem. 1990, 265:16027-16030.
    • (1990) J. Biol. Chem. , vol.265 , pp. 16027-16030
    • Janin, J.1    Chothia, C.2
  • 85
    • 84891850975 scopus 로고    scopus 로고
    • Targeting protein-protein interaction by small molecules
    • Jin L., Wang W., Fang G. Targeting protein-protein interaction by small molecules. Annu. Rev. Pharmacol. Toxicol. 2014, 54:435-456.
    • (2014) Annu. Rev. Pharmacol. Toxicol. , vol.54 , pp. 435-456
    • Jin, L.1    Wang, W.2    Fang, G.3
  • 86
    • 84875984520 scopus 로고    scopus 로고
    • Druggable protein interaction sites are more predisposed to surface pocket formation than the rest of the protein surface
    • Johnson D.K., Karanicolas J. Druggable protein interaction sites are more predisposed to surface pocket formation than the rest of the protein surface. PLoS Comput. Biol. 2013, 9:e1002951.
    • (2013) PLoS Comput. Biol. , vol.9 , pp. e1002951
    • Johnson, D.K.1    Karanicolas, J.2
  • 87
    • 84897404335 scopus 로고    scopus 로고
    • Analyzing protein-protein interactions in the post-interactomic era. Are we ready for the endgame?
    • Johnsson N. Analyzing protein-protein interactions in the post-interactomic era. Are we ready for the endgame?. Biochem. Biophys. Res. Commun. 2014, 445:739-745.
    • (2014) Biochem. Biophys. Res. Commun. , vol.445 , pp. 739-745
    • Johnsson, N.1
  • 89
    • 84940893103 scopus 로고    scopus 로고
    • Flexibility and small pockets at protein-protein interfaces: new insights into druggability
    • Jubb H., Blundell T.L., Ascher D.B. Flexibility and small pockets at protein-protein interfaces: new insights into druggability. Prog. Biophys. Mol. Biol. 2015, 119:2-9.
    • (2015) Prog. Biophys. Mol. Biol. , vol.119 , pp. 2-9
    • Jubb, H.1    Blundell, T.L.2    Ascher, D.B.3
  • 90
  • 91
    • 37349061824 scopus 로고    scopus 로고
    • PocketDepth: a new depth based algorithm for identification of ligand binding sites in proteins
    • Kalidas Y., Chandra N. PocketDepth: a new depth based algorithm for identification of ligand binding sites in proteins. J. Struct. Biol. 2008, 161:31-42.
    • (2008) J. Struct. Biol. , vol.161 , pp. 31-42
    • Kalidas, Y.1    Chandra, N.2
  • 92
    • 38549117345 scopus 로고    scopus 로고
    • Computer-aided drug discovery and development (CADDD): in silico-chemico-biological approach
    • Kapetanovic I.M. Computer-aided drug discovery and development (CADDD): in silico-chemico-biological approach. Chem. Biol. Interact. 2008, 171:165-176.
    • (2008) Chem. Biol. Interact. , vol.171 , pp. 165-176
    • Kapetanovic, I.M.1
  • 93
    • 84874298502 scopus 로고    scopus 로고
    • How far can virtual screening take us in drug discovery?
    • Kar S., Roy K. How far can virtual screening take us in drug discovery?. Expert Opin. Drug Discov. 2013, 8:245-261.
    • (2013) Expert Opin. Drug Discov. , vol.8 , pp. 245-261
    • Kar, S.1    Roy, K.2
  • 94
    • 84883256420 scopus 로고    scopus 로고
    • Future directions for peptide therapeutics development
    • Kaspar A.A., Reichert J.M. Future directions for peptide therapeutics development. Drug Discov. Today 2013, 18:807-817.
    • (2013) Drug Discov. Today , vol.18 , pp. 807-817
    • Kaspar, A.A.1    Reichert, J.M.2
  • 95
    • 84872225092 scopus 로고    scopus 로고
    • On the binding affinity of macromolecular interactions: daring to ask why proteins interact
    • Kastritis P.L., Bonvin A.M. On the binding affinity of macromolecular interactions: daring to ask why proteins interact. J. R. Soc. Interface 2013, 10:20120835.
    • (2013) J. R. Soc. Interface , vol.10 , pp. 20120835
    • Kastritis, P.L.1    Bonvin, A.M.2
  • 96
    • 84897007440 scopus 로고    scopus 로고
    • HADDOCK(2P2I): a biophysical model for predicting the binding affinity of protein-protein interaction inhibitors
    • Kastritis P.L., Rodrigues J.P., Bonvin A.M. HADDOCK(2P2I): a biophysical model for predicting the binding affinity of protein-protein interaction inhibitors. J. Chem. Inf. Model. 2014, 54:826-836.
    • (2014) J. Chem. Inf. Model. , vol.54 , pp. 826-836
    • Kastritis, P.L.1    Rodrigues, J.P.2    Bonvin, A.M.3
  • 97
    • 43149092276 scopus 로고    scopus 로고
    • Principles of protein-protein interactions: what are the preferred ways for proteins to interact?
    • Keskin O., Gursoy A., Ma B., Nussinov R. Principles of protein-protein interactions: what are the preferred ways for proteins to interact?. Chem. Rev. 2008, 108:1225-1244.
    • (2008) Chem. Rev. , vol.108 , pp. 1225-1244
    • Keskin, O.1    Gursoy, A.2    Ma, B.3    Nussinov, R.4
  • 98
    • 84883418471 scopus 로고    scopus 로고
    • Predicting binding within disordered protein regions to structurally characterised peptide-binding domains
    • Khan W., Duffy F., Pollastri G., Shields D.C., Mooney C. Predicting binding within disordered protein regions to structurally characterised peptide-binding domains. PLoS One 2013, 8:e72838.
    • (2013) PLoS One , vol.8 , pp. e72838
    • Khan, W.1    Duffy, F.2    Pollastri, G.3    Shields, D.C.4    Mooney, C.5
  • 99
    • 84910033683 scopus 로고    scopus 로고
    • An overview of FDA-approved biologics medicines
    • Kinch M.S. An overview of FDA-approved biologics medicines. Drug Discov. Today 2014, S1359-S6446.
    • (2014) Drug Discov. Today , pp. S1359-S6446
    • Kinch, M.S.1
  • 100
    • 84910681711 scopus 로고    scopus 로고
    • The rise (and decline?) of biotechnology
    • Kinch M.S. The rise (and decline?) of biotechnology. Drug Discov. Today 2014, 19:1686-1690.
    • (2014) Drug Discov. Today , vol.19 , pp. 1686-1690
    • Kinch, M.S.1
  • 101
    • 84864133078 scopus 로고    scopus 로고
    • Small-molecule inhibitor starting points learned from protein-protein interaction inhibitor structure
    • Koes D.R., Camacho C.J. Small-molecule inhibitor starting points learned from protein-protein interaction inhibitor structure. Bioinformatics 2012, 28:784-791.
    • (2012) Bioinformatics , vol.28 , pp. 784-791
    • Koes, D.R.1    Camacho, C.J.2
  • 103
    • 84870030186 scopus 로고    scopus 로고
    • How good are state-of-the-art docking tools in predicting ligand binding modes in protein-protein interfaces?
    • Kruger D.M., Jessen G., Gohlke H. How good are state-of-the-art docking tools in predicting ligand binding modes in protein-protein interfaces?. J. Chem. Inf. Model. 2012, 52:2807-2811.
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 2807-2811
    • Kruger, D.M.1    Jessen, G.2    Gohlke, H.3
  • 105
    • 84872225145 scopus 로고    scopus 로고
    • Compound activity prediction using models of binding pockets or ligand properties in 3D
    • Kufareva I., Chen Y.C., Ilatovskiy A.V., Abagyan R. Compound activity prediction using models of binding pockets or ligand properties in 3D. Curr. Top. Med. Chem. 2012, 12:1869-1882.
    • (2012) Curr. Top. Med. Chem. , vol.12 , pp. 1869-1882
    • Kufareva, I.1    Chen, Y.C.2    Ilatovskiy, A.V.3    Abagyan, R.4
  • 106
    • 84856370676 scopus 로고    scopus 로고
    • Pocketome: an encyclopedia of small-molecule binding sites in 4D
    • Kufareva I., Ilatovskiy A.V., Abagyan R. Pocketome: an encyclopedia of small-molecule binding sites in 4D. Nucleic Acids Res. 2012, 40:D535-D540.
    • (2012) Nucleic Acids Res. , vol.40 , pp. D535-D540
    • Kufareva, I.1    Ilatovskiy, A.V.2    Abagyan, R.3
  • 107
    • 84884587933 scopus 로고    scopus 로고
    • IPPI-DB: a manually curated and interactive database of small non-peptide inhibitors of protein-protein interactions
    • Labbe C.M., Laconde G., Kuenemann M.A., Villoutreix B.O., Sperandio O. iPPI-DB: a manually curated and interactive database of small non-peptide inhibitors of protein-protein interactions. Drug Discov. Today 2013, 18:958-968.
    • (2013) Drug Discov. Today , vol.18 , pp. 958-968
    • Labbe, C.M.1    Laconde, G.2    Kuenemann, M.A.3    Villoutreix, B.O.4    Sperandio, O.5
  • 108
    • 84908371409 scopus 로고    scopus 로고
    • Protein-protein interactions and genetic diseases: the interactome
    • Lage K. Protein-protein interactions and genetic diseases: the interactome. Biochim. Biophys. Acta 2014, 1842:1971-1980.
    • (2014) Biochim. Biophys. Acta , vol.1842 , pp. 1971-1980
    • Lage, K.1
  • 110
    • 84863598108 scopus 로고    scopus 로고
    • Bioinformatics and variability in drug response: a protein structural perspective
    • Lahti J.L., Tang G.W., Capriotti E., Liu T., Altman R.B. Bioinformatics and variability in drug response: a protein structural perspective. J. R. Soc. Interface 2012, 9:1409-1437.
    • (2012) J. R. Soc. Interface , vol.9 , pp. 1409-1437
    • Lahti, J.L.1    Tang, G.W.2    Capriotti, E.3    Liu, T.4    Altman, R.B.5
  • 112
    • 18744394070 scopus 로고    scopus 로고
    • Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites
    • Laurie A.T., Jackson R.M. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 2005, 21:1908-1916.
    • (2005) Bioinformatics , vol.21 , pp. 1908-1916
    • Laurie, A.T.1    Jackson, R.M.2
  • 113
    • 67649422714 scopus 로고    scopus 로고
    • Fpocket: an open source platform for ligand pocket detection
    • Le Guilloux V., Schmidtke P., Tuffery P. Fpocket: an open source platform for ligand pocket detection. BMC Bioinform. 2009, 10:168.
    • (2009) BMC Bioinform. , vol.10 , pp. 168
    • Le, G.V.1    Schmidtke, P.2    Tuffery, P.3
  • 114
    • 80053471789 scopus 로고    scopus 로고
    • The influence of the 'organizational factor' on compound quality in drug discovery
    • Leeson P.D., St-Gallay S.A. The influence of the 'organizational factor' on compound quality in drug discovery. Nat. Rev. Drug Discov. 2011, 10:749-765.
    • (2011) Nat. Rev. Drug Discov. , vol.10 , pp. 749-765
    • Leeson, P.D.1    St-Gallay, S.A.2
  • 115
    • 77953504480 scopus 로고    scopus 로고
    • In silico prediction of binding sites on proteins
    • Leis S., Schneider S., Zacharias M. In silico prediction of binding sites on proteins. Curr. Med. Chem. 2010, 17:1550-1562.
    • (2010) Curr. Med. Chem. , vol.17 , pp. 1550-1562
    • Leis, S.1    Schneider, S.2    Zacharias, M.3
  • 116
    • 77957921373 scopus 로고    scopus 로고
    • A simple definition of structural regions in proteins and its use in analyzing interface evolution
    • Levy E.D. A simple definition of structural regions in proteins and its use in analyzing interface evolution. J. Mol. Biol. 2010, 403:660-670.
    • (2010) J. Mol. Biol. , vol.403 , pp. 660-670
    • Levy, E.D.1
  • 117
    • 84901596602 scopus 로고    scopus 로고
    • Computational method to identify druggable binding sites that target protein-protein interactions
    • Li H., Kasam V., Tautermann C.S., Seeliger D., Vaidehi N. Computational method to identify druggable binding sites that target protein-protein interactions. J. Chem. Inf. Model. 2014, 54:1391-1400.
    • (2014) J. Chem. Inf. Model. , vol.54 , pp. 1391-1400
    • Li, H.1    Kasam, V.2    Tautermann, C.S.3    Seeliger, D.4    Vaidehi, N.5
  • 118
    • 0035289779 scopus 로고    scopus 로고
    • Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
    • Lipinski C.A., Lombardo F., Dominy B.W., Feeney P.J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev. 2001, 46:3-26.
    • (2001) Adv. Drug Deliv. Rev. , vol.46 , pp. 3-26
    • Lipinski, C.A.1    Lombardo, F.2    Dominy, B.W.3    Feeney, P.J.4
  • 119
    • 84897460110 scopus 로고    scopus 로고
    • Fragment-based identification of an inducible binding site on cell surface receptor CD44 for the design of protein-carbohydrate interaction inhibitors
    • Liu L.K., Finzel B.C. Fragment-based identification of an inducible binding site on cell surface receptor CD44 for the design of protein-carbohydrate interaction inhibitors. J. Med. Chem. 2014, 57:2714-2725.
    • (2014) J. Med. Chem. , vol.57 , pp. 2714-2725
    • Liu, L.K.1    Finzel, B.C.2
  • 120
    • 33846108633 scopus 로고    scopus 로고
    • BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities
    • Liu T., Lin Y., Wen X., Jorissen R.N., Gilson M.K. BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res. 2007, 35:D198-D201.
    • (2007) Nucleic Acids Res. , vol.35 , pp. D198-D201
    • Liu, T.1    Lin, Y.2    Wen, X.3    Jorissen, R.N.4    Gilson, M.K.5
  • 121
    • 84888851991 scopus 로고    scopus 로고
    • Peptide docking and structure-based characterization of peptide binding: from knowledge to know-how
    • London N., Raveh B., Schueler-Furman O. Peptide docking and structure-based characterization of peptide binding: from knowledge to know-how. Curr. Opin. Struct. Biol. 2013, 23:894-902.
    • (2013) Curr. Opin. Struct. Biol. , vol.23 , pp. 894-902
    • London, N.1    Raveh, B.2    Schueler-Furman, O.3
  • 122
    • 71049126548 scopus 로고    scopus 로고
    • Escape from flatland: increasing saturation as an approach to improving clinical success
    • Lovering F., Bikker J., Humblet C. Escape from flatland: increasing saturation as an approach to improving clinical success. J. Med. Chem. 2009, 52:6752-6756.
    • (2009) J. Med. Chem. , vol.52 , pp. 6752-6756
    • Lovering, F.1    Bikker, J.2    Humblet, C.3
  • 123
    • 84905454868 scopus 로고    scopus 로고
    • Structure-based druggability assessment of the mammalian structural proteome with inclusion of light protein flexibility
    • Loving K.A., Lin A., Cheng A.C. Structure-based druggability assessment of the mammalian structural proteome with inclusion of light protein flexibility. PLoS Comput. Biol. 2014, 10:e1003741.
    • (2014) PLoS Comput. Biol. , vol.10 , pp. e1003741
    • Loving, K.A.1    Lin, A.2    Cheng, A.C.3
  • 124
    • 84902833898 scopus 로고    scopus 로고
    • Druggable orthosteric and allosteric hot spots to target protein-protein interactions
    • Ma B., Nussinov R. Druggable orthosteric and allosteric hot spots to target protein-protein interactions. Curr. Pharm. Des. 2014, 20:1293-1301.
    • (2014) Curr. Pharm. Des. , vol.20 , pp. 1293-1301
    • Ma, B.1    Nussinov, R.2
  • 126
    • 84871365798 scopus 로고    scopus 로고
    • Expanding the number of 'druggable' targets: non-enzymes and protein-protein interactions
    • Makley L.N., Gestwicki J.E. Expanding the number of 'druggable' targets: non-enzymes and protein-protein interactions. Chem. Biol. Drug Des. 2013, 81:22-32.
    • (2013) Chem. Biol. Drug Des. , vol.81 , pp. 22-32
    • Makley, L.N.1    Gestwicki, J.E.2
  • 129
    • 35348821202 scopus 로고    scopus 로고
    • Virtual screening strategies in drug discovery
    • McInnes C. Virtual screening strategies in drug discovery. Curr. Opin. Chem. Biol. 2007, 11:494-502.
    • (2007) Curr. Opin. Chem. Biol. , vol.11 , pp. 494-502
    • McInnes, C.1
  • 130
    • 84879940511 scopus 로고    scopus 로고
    • Can emerging drug classes improve R&D productivity?
    • Meier C., Cairns-Smith S., Schulze U. Can emerging drug classes improve R&D productivity?. Drug Discov. Today 2013, 18:607-609.
    • (2013) Drug Discov. Today , vol.18 , pp. 607-609
    • Meier, C.1    Cairns-Smith, S.2    Schulze, U.3
  • 131
    • 84856383832 scopus 로고    scopus 로고
    • Privileged scaffolds or promiscuous binders: a comparative study on rhodanines and related heterocycles in medicinal chemistry
    • Mendgen T., Steuer C., Klein C.D. Privileged scaffolds or promiscuous binders: a comparative study on rhodanines and related heterocycles in medicinal chemistry. J. Med. Chem. 2012, 55:743-753.
    • (2012) J. Med. Chem. , vol.55 , pp. 743-753
    • Mendgen, T.1    Steuer, C.2    Klein, C.D.3
  • 132
    • 84857291408 scopus 로고    scopus 로고
    • Hot spots and transient pockets: predicting the determinants of small-molecule binding to a protein-protein interface
    • Metz A., Pfleger C., Kopitz H., Pfeiffer-Marek S., Baringhaus K.H., Gohlke H. Hot spots and transient pockets: predicting the determinants of small-molecule binding to a protein-protein interface. J. Chem. Inf. Model. 2012, 52:120-133.
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 120-133
    • Metz, A.1    Pfleger, C.2    Kopitz, H.3    Pfeiffer-Marek, S.4    Baringhaus, K.H.5    Gohlke, H.6
  • 134
    • 84875421001 scopus 로고    scopus 로고
    • Locating sweet spots for screening hits and evaluating pan-assay interference filters from the performance analysis of two lead-like libraries
    • Mok N.Y., Maxe S., Brenk R. Locating sweet spots for screening hits and evaluating pan-assay interference filters from the performance analysis of two lead-like libraries. J. Chem. Inf. Model. 2013, 53:534-544.
    • (2013) J. Chem. Inf. Model. , vol.53 , pp. 534-544
    • Mok, N.Y.1    Maxe, S.2    Brenk, R.3
  • 136
    • 79960990847 scopus 로고    scopus 로고
    • Chemical and structural lessons from recent successes in protein-protein interaction inhibition (2P2I)
    • Morelli X., Bourgeas R., Roche P. Chemical and structural lessons from recent successes in protein-protein interaction inhibition (2P2I). Curr. Opin. Chem. Biol. 2011, 15:475-481.
    • (2011) Curr. Opin. Chem. Biol. , vol.15 , pp. 475-481
    • Morelli, X.1    Bourgeas, R.2    Roche, P.3
  • 139
    • 84857712365 scopus 로고    scopus 로고
    • Protein-protein interaction inhibitors get into the groove
    • Mullard A. Protein-protein interaction inhibitors get into the groove. Nat. Rev. Drug Discov. 2012, 11:173-175.
    • (2012) Nat. Rev. Drug Discov. , vol.11 , pp. 173-175
    • Mullard, A.1
  • 140
    • 84879866133 scopus 로고    scopus 로고
    • A critical assessment of modeling safety-related drug attrition
    • Muthas D., Boyer S., Hasselgren C. A critical assessment of modeling safety-related drug attrition. MedChemComm 2013, 4:1058-1065.
    • (2013) MedChemComm , vol.4 , pp. 1058-1065
    • Muthas, D.1    Boyer, S.2    Hasselgren, C.3
  • 141
    • 33646757492 scopus 로고    scopus 로고
    • On the nature of cavities on protein surfaces: application to the identification of drug-binding sites
    • Nayal M., Honig B. On the nature of cavities on protein surfaces: application to the identification of drug-binding sites. Proteins 2006, 63:892-906.
    • (2006) Proteins , vol.63 , pp. 892-906
    • Nayal, M.1    Honig, B.2
  • 143
    • 34648833340 scopus 로고    scopus 로고
    • Prediction of protein-protein interaction inhibitors by chemoinformatics and machine learning methods
    • Neugebauer A., Hartmann R.W., Klein C.D. Prediction of protein-protein interaction inhibitors by chemoinformatics and machine learning methods. J. Med. Chem. 2007, 50:4665-4668.
    • (2007) J. Med. Chem. , vol.50 , pp. 4665-4668
    • Neugebauer, A.1    Hartmann, R.W.2    Klein, C.D.3
  • 144
    • 84892802037 scopus 로고    scopus 로고
    • Protein-protein interactions: switch from classical methods to proteomics and bioinformatics-based approaches
    • Ngounou Wetie A.G., Sokolowska I., Woods A.G., Roy U., Deinhardt K., Darie C.C. Protein-protein interactions: switch from classical methods to proteomics and bioinformatics-based approaches. Cell. Mol. Life Sci. 2014, 71:205-228.
    • (2014) Cell. Mol. Life Sci. , vol.71 , pp. 205-228
    • Ngounou, W.A.G.1    Sokolowska, I.2    Woods, A.G.3    Roy, U.4    Deinhardt, K.5    Darie, C.C.6
  • 145
    • 0041312697 scopus 로고    scopus 로고
    • Diversity of protein-protein interactions
    • Nooren I.M., Thornton J.M. Diversity of protein-protein interactions. EMBO J. 2003, 22:3486-3492.
    • (2003) EMBO J. , vol.22 , pp. 3486-3492
    • Nooren, I.M.1    Thornton, J.M.2
  • 148
  • 150
    • 77955517509 scopus 로고    scopus 로고
    • Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery
    • Perot S., Sperandio O., Miteva M.A., Camproux A.C., Villoutreix B.O. Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery. Drug Discov. Today 2010, 15:656-667.
    • (2010) Drug Discov. Today , vol.15 , pp. 656-667
    • Perot, S.1    Sperandio, O.2    Miteva, M.A.3    Camproux, A.C.4    Villoutreix, B.O.5
  • 151
    • 84901979488 scopus 로고    scopus 로고
    • Structural bioinformatics of the interactome
    • Petrey D., Honig B. Structural bioinformatics of the interactome. Annu. Rev. Biophys. 2014, 43:193-210.
    • (2014) Annu. Rev. Biophys. , vol.43 , pp. 193-210
    • Petrey, D.1    Honig, B.2
  • 152
    • 84916623136 scopus 로고    scopus 로고
    • Fragment-based docking: development of the CHARMMing web user interface as a platform for computer-aided drug design
    • Pevzner Y., Frugier E., Schalk V., Caflisch A., Woodcock H.L. Fragment-based docking: development of the CHARMMing web user interface as a platform for computer-aided drug design. J. Chem. Inf. Model. 2014, 54:2612-2620.
    • (2014) J. Chem. Inf. Model. , vol.54 , pp. 2612-2620
    • Pevzner, Y.1    Frugier, E.2    Schalk, V.3    Caflisch, A.4    Woodcock, H.L.5
  • 154
    • 84861729758 scopus 로고    scopus 로고
    • E-Drug3D: 3D structure collections dedicated to drug repurposing and fragment-based drug design
    • Pihan E., Colliandre L., Guichou J.F., Douguet D. e-Drug3D: 3D structure collections dedicated to drug repurposing and fragment-based drug design. Bioinformatics 2012, 28:1540-1541.
    • (2012) Bioinformatics , vol.28 , pp. 1540-1541
    • Pihan, E.1    Colliandre, L.2    Guichou, J.F.3    Douguet, D.4
  • 155
    • 84908060372 scopus 로고    scopus 로고
    • Polyphony: superposition independent methods for ensemble-based drug discovery
    • Pitt W.R., Montalvao R.W., Blundell T.L. Polyphony: superposition independent methods for ensemble-based drug discovery. BMC Bioinform. 2014, 15:324.
    • (2014) BMC Bioinform. , vol.15 , pp. 324
    • Pitt, W.R.1    Montalvao, R.W.2    Blundell, T.L.3
  • 156
    • 84884675983 scopus 로고    scopus 로고
    • Estimation of the size of drug-like chemical space based on GDB-17 data
    • Polishchuk P.G., Madzhidov T.I., Varnek A. Estimation of the size of drug-like chemical space based on GDB-17 data. J. Comput. Aided Mol. Des. 2013, 27:675-679.
    • (2013) J. Comput. Aided Mol. Des. , vol.27 , pp. 675-679
    • Polishchuk, P.G.1    Madzhidov, T.I.2    Varnek, A.3
  • 157
    • 84926442979 scopus 로고    scopus 로고
    • Homology model of human prothrombinase based on the crystal structure of pseutarin C
    • Pomowski A., Ustok F.I., Huntington J.A. Homology model of human prothrombinase based on the crystal structure of pseutarin C. Biol. Chem. 2014, 395:1233-1241.
    • (2014) Biol. Chem. , vol.395 , pp. 1233-1241
    • Pomowski, A.1    Ustok, F.I.2    Huntington, J.A.3
  • 159
    • 46749095500 scopus 로고    scopus 로고
    • From virtuality to reality - virtual screening in lead discovery and lead optimization: a medicinal chemistry perspective
    • Rester U. From virtuality to reality - virtual screening in lead discovery and lead optimization: a medicinal chemistry perspective. Curr. Opin. Drug Discov. Dev. 2008, 11:559-568.
    • (2008) Curr. Opin. Drug Discov. Dev. , vol.11 , pp. 559-568
    • Rester, U.1
  • 160
    • 84925393362 scopus 로고    scopus 로고
    • The chemical space project
    • (in press)
    • Reymond J.L. The chemical space project. Acc. Chem. Res. 2015, (in press).
    • (2015) Acc. Chem. Res.
    • Reymond, J.L.1
  • 162
    • 84859468933 scopus 로고    scopus 로고
    • Analysis of structure-based virtual screening studies and characterization of identified active compounds
    • Ripphausen P., Stumpfe D., Bajorath J. Analysis of structure-based virtual screening studies and characterization of identified active compounds. Future Med. Chem. 2012, 4:603-613.
    • (2012) Future Med. Chem. , vol.4 , pp. 603-613
    • Ripphausen, P.1    Stumpfe, D.2    Bajorath, J.3
  • 163
    • 70350409235 scopus 로고    scopus 로고
    • The impact of aromatic ring count on compound developability - are too many aromatic rings a liability in drug design?
    • Ritchie T.J., Macdonald S.J. The impact of aromatic ring count on compound developability - are too many aromatic rings a liability in drug design?. Drug Discov. Today 2009, 14:1011-1020.
    • (2009) Drug Discov. Today , vol.14 , pp. 1011-1020
    • Ritchie, T.J.1    Macdonald, S.J.2
  • 164
    • 84920462422 scopus 로고    scopus 로고
    • Rational design of protein-protein interaction inhibitors
    • Rognan D. Rational design of protein-protein interaction inhibitors. MedChemComm 2015, 6:51-60.
    • (2015) MedChemComm , vol.6 , pp. 51-60
    • Rognan, D.1
  • 165
    • 84869987352 scopus 로고    scopus 로고
    • Enumeration of 166 billion organic small molecules in the chemical universe database GDB-17
    • Ruddigkeit L., van Deursen R., Blum L.C., Reymond J.L. Enumeration of 166 billion organic small molecules in the chemical universe database GDB-17. J. Chem. Inf. Model. 2012, 52:2864-2875.
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 2864-2875
    • Ruddigkeit, L.1    van Deursen, R.2    Blum, L.C.3    Reymond, J.L.4
  • 166
    • 75749093371 scopus 로고    scopus 로고
    • Recipes for the selection of experimental protein conformations for virtual screening
    • Rueda M., Bottegoni G., Abagyan R. Recipes for the selection of experimental protein conformations for virtual screening. J. Chem. Inf. Model. 2010, 50:186-193.
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 186-193
    • Rueda, M.1    Bottegoni, G.2    Abagyan, R.3
  • 167
    • 0030979125 scopus 로고    scopus 로고
    • Automatic identification and representation of protein binding sites for molecular docking
    • Ruppert J., Welch W., Jain A.N. Automatic identification and representation of protein binding sites for molecular docking. Protein Sci. 1997, 6:524-533.
    • (1997) Protein Sci. , vol.6 , pp. 524-533
    • Ruppert, J.1    Welch, W.2    Jain, A.N.3
  • 168
    • 82255164267 scopus 로고    scopus 로고
    • MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories
    • Schmidtke P., Bidon-Chanal A., Luque F.J., Barril X. MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories. Bioinformatics 2011, 27:3276-3285.
    • (2011) Bioinformatics , vol.27 , pp. 3276-3285
    • Schmidtke, P.1    Bidon-Chanal, A.2    Luque, F.J.3    Barril, X.4
  • 169
    • 77950503976 scopus 로고    scopus 로고
    • Virtual screening: an endless staircase?
    • Schneider G. Virtual screening: an endless staircase?. Nat. Rev. Drug Discov. 2010, 9:273-276.
    • (2010) Nat. Rev. Drug Discov. , vol.9 , pp. 273-276
    • Schneider, G.1
  • 170
    • 79961045182 scopus 로고    scopus 로고
    • Thermodynamics-based drug design: strategies for inhibiting protein-protein interactions
    • Schon A., Lam S.Y., Freire E. Thermodynamics-based drug design: strategies for inhibiting protein-protein interactions. Future Med. Chem. 2011, 3:1129-1137.
    • (2011) Future Med. Chem. , vol.3 , pp. 1129-1137
    • Schon, A.1    Lam, S.Y.2    Freire, E.3
  • 173
    • 78649523910 scopus 로고    scopus 로고
    • Drug-like density: a method of quantifying the "bindability" of a protein target based on a very large set of pockets and drug-like ligands from the protein data bank
    • Sheridan R.P., Maiorov V.N., Holloway M.K., Cornell W.D., Gao Y.D. Drug-like density: a method of quantifying the "bindability" of a protein target based on a very large set of pockets and drug-like ligands from the protein data bank. J. Chem. Inf. Model. 2010, 50:2029-2040.
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 2029-2040
    • Sheridan, R.P.1    Maiorov, V.N.2    Holloway, M.K.3    Cornell, W.D.4    Gao, Y.D.5
  • 174
    • 11144323163 scopus 로고    scopus 로고
    • Virtual screening of chemical libraries
    • Shoichet B.K. Virtual screening of chemical libraries. Nature 2004, 432:862-865.
    • (2004) Nature , vol.432 , pp. 862-865
    • Shoichet, B.K.1
  • 175
    • 84878553777 scopus 로고    scopus 로고
    • Are predicted protein structures of any value for binding site prediction and virtual ligand screening?
    • Skolnick J., Zhou H., Gao M. Are predicted protein structures of any value for binding site prediction and virtual ligand screening?. Curr. Opin. Struct. Biol. 2013, 23:191-197.
    • (2013) Curr. Opin. Struct. Biol. , vol.23 , pp. 191-197
    • Skolnick, J.1    Zhou, H.2    Gao, M.3
  • 176
    • 84874517756 scopus 로고    scopus 로고
    • Features of protein-protein interactions that translate into potent inhibitors: topology, surface area and affinity
    • Smith M.C., Gestwicki J.E. Features of protein-protein interactions that translate into potent inhibitors: topology, surface area and affinity. Expert Rev. Mol. Med. 2012, 14:e16.
    • (2012) Expert Rev. Mol. Med. , vol.14 , pp. e16
    • Smith, M.C.1    Gestwicki, J.E.2
  • 177
    • 78649867646 scopus 로고    scopus 로고
    • Accounting for induced-fit effects in docking: what is possible and what is not?
    • Sotriffer C.A. Accounting for induced-fit effects in docking: what is possible and what is not?. Curr. Top. Med. Chem. 2011, 11:179-191.
    • (2011) Curr. Top. Med. Chem. , vol.11 , pp. 179-191
    • Sotriffer, C.A.1
  • 178
    • 77955627131 scopus 로고    scopus 로고
    • How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis
    • Sperandio O., Mouawad L., Pinto E., Villoutreix B.O., Perahia D., Miteva M.A. How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis. Eur. Biophys. J. 2010, 39:1365-1372.
    • (2010) Eur. Biophys. J. , vol.39 , pp. 1365-1372
    • Sperandio, O.1    Mouawad, L.2    Pinto, E.3    Villoutreix, B.O.4    Perahia, D.5    Miteva, M.A.6
  • 181
    • 84905100973 scopus 로고    scopus 로고
    • Discovery of novel inhibitors of vascular endothelial growth factor-A-neuropilin-1 interaction by structure-based virtual screening
    • Starzec A., Miteva M.A., Ladam P., Villoutreix B.O., Perret G.Y. Discovery of novel inhibitors of vascular endothelial growth factor-A-neuropilin-1 interaction by structure-based virtual screening. Bioorg. Med. Chem. 2014, 22:4042-4048.
    • (2014) Bioorg. Med. Chem. , vol.22 , pp. 4042-4048
    • Starzec, A.1    Miteva, M.A.2    Ladam, P.3    Villoutreix, B.O.4    Perret, G.Y.5
  • 183
    • 84924077519 scopus 로고    scopus 로고
    • An overview of recent advances in structural bioinformatics of protein-protein interactions and a guide to their principles
    • Sudha G., Nussinov R., Srinivasan N. An overview of recent advances in structural bioinformatics of protein-protein interactions and a guide to their principles. Prog. Biophys. Mol. Biol. 2014, 116:141-150.
    • (2014) Prog. Biophys. Mol. Biol. , vol.116 , pp. 141-150
    • Sudha, G.1    Nussinov, R.2    Srinivasan, N.3
  • 184
    • 80051798254 scopus 로고    scopus 로고
    • Fragment-based lead discovery: challenges and opportunities
    • Sun C., Petros A.M., Hajduk P.J. Fragment-based lead discovery: challenges and opportunities. J. Comput. Aided Mol. Des. 2011, 25:607-610.
    • (2011) J. Comput. Aided Mol. Des. , vol.25 , pp. 607-610
    • Sun, C.1    Petros, A.M.2    Hajduk, P.J.3
  • 185
    • 84856389159 scopus 로고    scopus 로고
    • Structural biology and drug discovery of difficult targets: the limits of ligandability
    • Surade S., Blundell T.L. Structural biology and drug discovery of difficult targets: the limits of ligandability. Chem. Biol. 2012, 19:42-50.
    • (2012) Chem. Biol. , vol.19 , pp. 42-50
    • Surade, S.1    Blundell, T.L.2
  • 186
    • 84876709135 scopus 로고    scopus 로고
    • Allo-network drugs: extension of the allosteric drug concept to protein- protein interaction and signaling networks
    • Szilagyi A., Nussinov R., Csermely P. Allo-network drugs: extension of the allosteric drug concept to protein- protein interaction and signaling networks. Curr. Top. Med. Chem. 2013, 13:64-77.
    • (2013) Curr. Top. Med. Chem. , vol.13 , pp. 64-77
    • Szilagyi, A.1    Nussinov, R.2    Csermely, P.3
  • 187
    • 84856385436 scopus 로고    scopus 로고
    • Established and emerging trends in computational drug discovery in the structural genomics era
    • Taboureau O., Baell J.B., Fernandez-Recio J., Villoutreix B.O. Established and emerging trends in computational drug discovery in the structural genomics era. Chem. Biol. 2012, 19:29-41.
    • (2012) Chem. Biol. , vol.19 , pp. 29-41
    • Taboureau, O.1    Baell, J.B.2    Fernandez-Recio, J.3    Villoutreix, B.O.4
  • 188
    • 84855812283 scopus 로고    scopus 로고
    • Modulating protein-protein interactions with small molecules: the importance of binding hotspots
    • Thangudu R.R., Bryant S.H., Panchenko A.R., Madej T. Modulating protein-protein interactions with small molecules: the importance of binding hotspots. J. Mol. Biol. 2012, 415:443-453.
    • (2012) J. Mol. Biol. , vol.415 , pp. 443-453
    • Thangudu, R.R.1    Bryant, S.H.2    Panchenko, A.R.3    Madej, T.4
  • 191
    • 41949132916 scopus 로고    scopus 로고
    • Flexible ligand docking to multiple receptor conformations: a practical alternative
    • Totrov M., Abagyan R. Flexible ligand docking to multiple receptor conformations: a practical alternative. Curr. Opin. Struct. Biol. 2008, 18:178-184.
    • (2008) Curr. Opin. Struct. Biol. , vol.18 , pp. 178-184
    • Totrov, M.1    Abagyan, R.2
  • 192
    • 84881251398 scopus 로고    scopus 로고
    • Structure-based target druggability assessment
    • Trosset J.Y., Vodovar N. Structure-based target druggability assessment. Methods Mol. Biol. 2013, 986:141-164.
    • (2013) Methods Mol. Biol. , vol.986 , pp. 141-164
    • Trosset, J.Y.1    Vodovar, N.2
  • 193
    • 84866388293 scopus 로고    scopus 로고
    • Druggability of dynamic protein-protein interfaces
    • Ulucan O., Eyrisch S., Helms V. Druggability of dynamic protein-protein interfaces. Curr. Pharm. Des. 2012, 18:4599-4606.
    • (2012) Curr. Pharm. Des. , vol.18 , pp. 4599-4606
    • Ulucan, O.1    Eyrisch, S.2    Helms, V.3
  • 194
    • 84901364194 scopus 로고    scopus 로고
    • Chemical, target, and bioactive properties of allosteric modulation
    • van Westen G.J., Gaulton A., Overington J.P. Chemical, target, and bioactive properties of allosteric modulation. PLoS Comput. Biol. 2014, 10:e1003559.
    • (2014) PLoS Comput. Biol. , vol.10 , pp. e1003559
    • van, W.G.J.1    Gaulton, A.2    Overington, J.P.3
  • 195
  • 196
    • 84878948028 scopus 로고    scopus 로고
    • Determinants and associated factors influencing medication adherence and persistence to oral anticancer drugs: a systematic review
    • Verbrugghe M., Verhaeghe S., Lauwaert K., Beeckman D., Van Hecke A. Determinants and associated factors influencing medication adherence and persistence to oral anticancer drugs: a systematic review. Cancer Treat. Rev. 2013, 39:610-621.
    • (2013) Cancer Treat. Rev. , vol.39 , pp. 610-621
    • Verbrugghe, M.1    Verhaeghe, S.2    Lauwaert, K.3    Beeckman, D.4    Van Hecke, A.5
  • 200
    • 79959306961 scopus 로고    scopus 로고
    • Tyrosine kinase syk non-enzymatic inhibitors and potential anti-allergic drug-like compounds discovered by virtual and in vitro screening
    • Villoutreix B.O., Laconde G., Lagorce D., Martineau P., Miteva M.A., Dariavach P. Tyrosine kinase syk non-enzymatic inhibitors and potential anti-allergic drug-like compounds discovered by virtual and in vitro screening. PLoS One 2011, 6:e21117.
    • (2011) PLoS One , vol.6 , pp. e21117
    • Villoutreix, B.O.1    Laconde, G.2    Lagorce, D.3    Martineau, P.4    Miteva, M.A.5    Dariavach, P.6
  • 201
    • 84886950237 scopus 로고    scopus 로고
    • One hundred thousand mouse clicks down the road: selected online resources supporting drug discovery collected over a decade
    • Villoutreix B.O., Lagorce D., Labbe C.M., Sperandio O., Miteva M.A. One hundred thousand mouse clicks down the road: selected online resources supporting drug discovery collected over a decade. Drug Discov. Today 2013, 18:1081-1089.
    • (2013) Drug Discov. Today , vol.18 , pp. 1081-1089
    • Villoutreix, B.O.1    Lagorce, D.2    Labbe, C.M.3    Sperandio, O.4    Miteva, M.A.5
  • 203
    • 77951290766 scopus 로고    scopus 로고
    • In silico studies of blood coagulation proteins: from mosaic proteases to nonenzymatic cofactor inhibitors
    • Villoutreix B.O., Sperandio O. In silico studies of blood coagulation proteins: from mosaic proteases to nonenzymatic cofactor inhibitors. Curr. Opin. Struct. Biol. 2010, 20:168-179.
    • (2010) Curr. Opin. Struct. Biol. , vol.20 , pp. 168-179
    • Villoutreix, B.O.1    Sperandio, O.2
  • 204
    • 84878773643 scopus 로고    scopus 로고
    • Protein interface pharmacophore mapping tools for small molecule protein: protein interaction inhibitor discovery
    • Voet A., Banwell E.F., Sahu K.K., Heddle J.G., Zhang K.Y. Protein interface pharmacophore mapping tools for small molecule protein: protein interaction inhibitor discovery. Curr. Top. Med. Chem. 2013, 13:989-1001.
    • (2013) Curr. Top. Med. Chem. , vol.13 , pp. 989-1001
    • Voet, A.1    Banwell, E.F.2    Sahu, K.K.3    Heddle, J.G.4    Zhang, K.Y.5
  • 206
    • 2542530042 scopus 로고    scopus 로고
    • The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures
    • Wang R., Fang X., Lu Y., Wang S. The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures. J. Med. Chem. 2004, 47:2977-2980.
    • (2004) J. Med. Chem. , vol.47 , pp. 2977-2980
    • Wang, R.1    Fang, X.2    Lu, Y.3    Wang, S.4
  • 207
    • 81855166104 scopus 로고    scopus 로고
    • Druggability assessment of protein-protein interfaces
    • Wanner J., Fry D.C., Peng Z., Roberts J. Druggability assessment of protein-protein interfaces. Future Med. Chem. 2011, 3:2021-2038.
    • (2011) Future Med. Chem. , vol.3 , pp. 2021-2038
    • Wanner, J.1    Fry, D.C.2    Peng, Z.3    Roberts, J.4
  • 208
    • 84906346249 scopus 로고    scopus 로고
    • What does the aromatic ring number mean for drug design?
    • Ward S.E., Beswick P. What does the aromatic ring number mean for drug design?. Expert Opin. Drug Discov. 2014, 9:995-1003.
    • (2014) Expert Opin. Drug Discov. , vol.9 , pp. 995-1003
    • Ward, S.E.1    Beswick, P.2
  • 209
    • 84939970800 scopus 로고    scopus 로고
    • Structure-based inhibition of protein-protein interactions
    • (in press)
    • Watkins A.M., Arora P.S. Structure-based inhibition of protein-protein interactions. Eur. J. Med. Chem. 2015, (in press).
    • (2015) Eur. J. Med. Chem.
    • Watkins, A.M.1    Arora, P.S.2
  • 210
    • 37249004920 scopus 로고    scopus 로고
    • Reaching for high-hanging fruit in drug discovery at protein-protein interfaces
    • Wells J.A., McClendon C.L. Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 2007, 450:1001-1009.
    • (2007) Nature , vol.450 , pp. 1001-1009
    • Wells, J.A.1    McClendon, C.L.2
  • 211
    • 79958701058 scopus 로고    scopus 로고
    • Growing PAINS in academic drug discovery
    • Whitty A. Growing PAINS in academic drug discovery. Future Med. Chem. 2011, 3:797-801.
    • (2011) Future Med. Chem. , vol.3 , pp. 797-801
    • Whitty, A.1
  • 212
    • 70450169243 scopus 로고    scopus 로고
    • Inhibition of protein-protein interactions using designed molecules
    • Wilson A.J. Inhibition of protein-protein interactions using designed molecules. Chem. Soc. Rev. 2009, 38:3289-3300.
    • (2009) Chem. Soc. Rev. , vol.38 , pp. 3289-3300
    • Wilson, A.J.1
  • 213
    • 84870810902 scopus 로고    scopus 로고
    • Biophysical and computational fragment-based approaches to targeting protein-protein interactions: applications in structure-guided drug discovery
    • Winter A., Higueruelo A.P., Marsh M., Sigurdardottir A., Pitt W.R., Blundell T.L. Biophysical and computational fragment-based approaches to targeting protein-protein interactions: applications in structure-guided drug discovery. Q. Rev. Biophys. 2012, 45:383-426.
    • (2012) Q. Rev. Biophys. , vol.45 , pp. 383-426
    • Winter, A.1    Higueruelo, A.P.2    Marsh, M.3    Sigurdardottir, A.4    Pitt, W.R.5    Blundell, T.L.6
  • 215
    • 73349117207 scopus 로고    scopus 로고
    • Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin
    • Wlodarski T., Zagrovic B. Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:19346-19351.
    • (2009) Proc. Natl. Acad. Sci. U. S. A. , vol.106 , pp. 19346-19351
    • Wlodarski, T.1    Zagrovic, B.2
  • 216
    • 84921775709 scopus 로고    scopus 로고
    • Methods for predicting protein-ligand binding sites
    • Xie Z.R., Hwang M.J. Methods for predicting protein-ligand binding sites. Methods Mol. Biol. 2015, 1215:383-398.
    • (2015) Methods Mol. Biol. , vol.1215 , pp. 383-398
    • Xie, Z.R.1    Hwang, M.J.2
  • 217
    • 0442279524 scopus 로고    scopus 로고
    • Solution conformations of wild-type and mutated Bak BH3 peptides via dynamical conformational sampling and implication to their binding to antiapoptotic Bcl-2 proteins
    • Yang C.-Y., Nikolovska-Coleska Z., Li P., Roller P., Wang S. Solution conformations of wild-type and mutated Bak BH3 peptides via dynamical conformational sampling and implication to their binding to antiapoptotic Bcl-2 proteins. J. Phys. Chem. B 2004, 108:1467-1477.
    • (2004) J. Phys. Chem. B , vol.108 , pp. 1467-1477
    • Yang, C.-Y.1    Nikolovska-Coleska, Z.2    Li, P.3    Roller, P.4    Wang, S.5
  • 219
    • 84865494461 scopus 로고    scopus 로고
    • Relationship between hot spot residues and ligand binding hot spots in protein-protein interfaces
    • Zerbe B.S., Hall D.R., Vajda S., Whitty A., Kozakov D. Relationship between hot spot residues and ligand binding hot spots in protein-protein interfaces. J. Chem. Inf. Model. 2012, 52:2236-2244.
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 2236-2244
    • Zerbe, B.S.1    Hall, D.R.2    Vajda, S.3    Whitty, A.4    Kozakov, D.5
  • 220
    • 79960395595 scopus 로고    scopus 로고
    • Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction
    • Zhang Z., Li Y., Lin B., Schroeder M., Huang B. Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction. Bioinformatics 2011, 27:2083-2088.
    • (2011) Bioinformatics , vol.27 , pp. 2083-2088
    • Zhang, Z.1    Li, Y.2    Lin, B.3    Schroeder, M.4    Huang, B.5
  • 221
    • 84906727867 scopus 로고    scopus 로고
    • Focused chemical libraries - design and enrichment: an example of protein-protein interaction chemical space
    • Zhang X., Betzi S., Morelli X., Roche P. Focused chemical libraries - design and enrichment: an example of protein-protein interaction chemical space. Future Med. Chem. 2014, 6:1291-1307.
    • (2014) Future Med. Chem. , vol.6 , pp. 1291-1307
    • Zhang, X.1    Betzi, S.2    Morelli, X.3    Roche, P.4
  • 222
    • 84908626312 scopus 로고    scopus 로고
    • Rational design of small-molecule stabilizers of spermine synthase dimer by virtual screening and free energy-based approach
    • Zhang Z., Martiny V., Lagorce D., Ikeguchi Y., Alexov E., Miteva M.A. Rational design of small-molecule stabilizers of spermine synthase dimer by virtual screening and free energy-based approach. PLoS One 2014, 9:e110884.
    • (2014) PLoS One , vol.9 , pp. e110884
    • Zhang, Z.1    Martiny, V.2    Lagorce, D.3    Ikeguchi, Y.4    Alexov, E.5    Miteva, M.A.6
  • 223
    • 79851514658 scopus 로고    scopus 로고
    • Lead optimization in the nondrug-like space
    • Zhao H. Lead optimization in the nondrug-like space. Drug Discov. Today 2011, 16:158-163.
    • (2011) Drug Discov. Today , vol.16 , pp. 158-163
    • Zhao, H.1
  • 224
    • 84871940431 scopus 로고    scopus 로고
    • Pocket-based drug design: exploring pocket space
    • Zheng X., Gan L., Wang E., Wang J. Pocket-based drug design: exploring pocket space. AAPS J. 2012, 15:228-241.
    • (2012) AAPS J. , vol.15 , pp. 228-241
    • Zheng, X.1    Gan, L.2    Wang, E.3    Wang, J.4
  • 225
    • 84884237765 scopus 로고    scopus 로고
    • Hit identification and optimization in virtual screening: practical recommendations based on a critical literature analysis
    • Zhu T., Cao S., Su P.C., Patel R., Shah D., Chokshi H.B., Szukala R., Johnson M.E., Hevener K.E. Hit identification and optimization in virtual screening: practical recommendations based on a critical literature analysis. J. Med. Chem. 2013, 56:6560-6572.
    • (2013) J. Med. Chem. , vol.56 , pp. 6560-6572
    • Zhu, T.1    Cao, S.2    Su, P.C.3    Patel, R.4    Shah, D.5    Chokshi, H.B.6    Szukala, R.7    Johnson, M.E.8    Hevener, K.E.9


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.