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Volumn 159, Issue 3, 2012, Pages 123-134

Structure-based computational analysis of protein binding sites for function and druggability prediction

Author keywords

Computational analysis; Druggability; Protein binding sites; Protein function prediction; Protein structure

Indexed keywords

COMPUTATIONAL ANALYSIS; DRUGGABILITY; PROTEIN FUNCTION PREDICTION; PROTEIN STRUCTURES; PROTEIN-BINDING SITES;

EID: 84860838201     PISSN: 01681656     EISSN: 18734863     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2011.12.005     Document Type: Article
Times cited : (101)

References (91)
  • 1
    • 53549133573 scopus 로고    scopus 로고
    • Protein flexibility and mobility in structure-based drug design
    • Ahmed A., Kazemi S., Gohlke H. Protein flexibility and mobility in structure-based drug design. Front. Drug Des. Discov. 2007, 3:455-476.
    • (2007) Front. Drug Des. Discov. , vol.3 , pp. 455-476
    • Ahmed, A.1    Kazemi, S.2    Gohlke, H.3
  • 2
    • 67849116891 scopus 로고    scopus 로고
    • MolLoc: a web tool for the local structural alignment of molecular surfaces
    • Angaran S., Bock M.E., Garutti C., Guerra C. MolLoc: a web tool for the local structural alignment of molecular surfaces. Nucleic Acids Res. 2009, 37:W565-W570.
    • (2009) Nucleic Acids Res. , vol.37
    • Angaran, S.1    Bock, M.E.2    Garutti, C.3    Guerra, C.4
  • 3
    • 67651242479 scopus 로고    scopus 로고
    • BSAlign: a rapid graph-based algorithm for detecting ligand-binding sites in protein structures
    • Aung Z., Tong J.C. BSAlign: a rapid graph-based algorithm for detecting ligand-binding sites in protein structures. Genome Inf. 2008, 21:65-76.
    • (2008) Genome Inf. , vol.21 , pp. 65-76
    • Aung, Z.1    Tong, J.C.2
  • 4
    • 33947201695 scopus 로고    scopus 로고
    • Query3d: a new method for high-throughput analysis of functional residues in protein structures
    • Ausiello G., Via A., Helmer-Citterich M. Query3d: a new method for high-throughput analysis of functional residues in protein structures. BMC Bioinformatics 2005, 6(Suppl. 4):S5.
    • (2005) BMC Bioinformatics , vol.6 , Issue.SUPPL. 4
    • Ausiello, G.1    Via, A.2    Helmer-Citterich, M.3
  • 5
    • 14044266006 scopus 로고    scopus 로고
    • Failure rates in drug discovery and development: will we ever get any better?
    • Fall
    • Bains W. Failure rates in drug discovery and development: will we ever get any better?. Drug Discov. World 2004, (Fall):9-18.
    • (2004) Drug Discov. World , pp. 9-18
    • Bains, W.1
  • 6
    • 0033963089 scopus 로고    scopus 로고
    • The ENZYME database in 2000
    • Bairoch A. The ENZYME database in 2000. Nucleic Acids Res. 2000, 28:304-305.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 304-305
    • Bairoch, A.1
  • 8
    • 0042890523 scopus 로고    scopus 로고
    • Inferring functional relationships of proteins from local sequence and spatial surface patterns
    • Binkowski T.A., Adamian L., Liang J. Inferring functional relationships of proteins from local sequence and spatial surface patterns. J. Mol. Biol. 2003, 332:505-526.
    • (2003) J. Mol. Biol. , vol.332 , pp. 505-526
    • Binkowski, T.A.1    Adamian, L.2    Liang, J.3
  • 9
    • 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
  • 10
    • 3042809615 scopus 로고    scopus 로고
    • Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: an automated all-against-all structural comparison using geometric matching
    • Brakoulias A., Jackson R.M. Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: an automated all-against-all structural comparison using geometric matching. Proteins 2004, 56:250-260.
    • (2004) Proteins , vol.56 , pp. 250-260
    • Brakoulias, A.1    Jackson, R.M.2
  • 11
    • 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
  • 12
    • 38349100452 scopus 로고    scopus 로고
    • A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
    • Brylinski M., Skolnick J. A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:129-134.
    • (2008) Proc. Natl. Acad. Sci. U.S.A. , vol.105 , pp. 129-134
    • Brylinski, M.1    Skolnick, J.2
  • 14
    • 77953587057 scopus 로고    scopus 로고
    • Real-time ligand binding pocket database search using local surface descriptors
    • Chikhi R., Sael L., Kihara D. Real-time ligand binding pocket database search using local surface descriptors. Proteins 2010, 78:2007-2028.
    • (2010) Proteins , vol.78 , pp. 2007-2028
    • Chikhi, R.1    Sael, L.2    Kihara, D.3
  • 16
    • 73349097886 scopus 로고    scopus 로고
    • Rapid comparison of protein binding site surfaces with property encoded shape distributions
    • Das S., Kokardekar A., Breneman C.M. Rapid comparison of protein binding site surfaces with property encoded shape distributions. J. Chem. Inf. Model. 2009, 49:2863-2872.
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 2863-2872
    • Das, S.1    Kokardekar, A.2    Breneman, C.M.3
  • 17
    • 77957857557 scopus 로고    scopus 로고
    • Binding of protein kinase inhibitors to synapsin I inferred from pair-wise binding site similarity measurements
    • De Franchi E., Schalon C., Messa M., Onofri F., Benfenati F., Rognan D. Binding of protein kinase inhibitors to synapsin I inferred from pair-wise binding site similarity measurements. PLoS One 2010, 5:e12214.
    • (2010) PLoS One , vol.5
    • De Franchi, E.1    Schalon, C.2    Messa, M.3    Onofri, F.4    Benfenati, F.5    Rognan, D.6
  • 18
    • 0034308142 scopus 로고    scopus 로고
    • Practical limits of function prediction
    • Devos D., Valencia A. Practical limits of function prediction. Proteins 2000, 41:98-107.
    • (2000) Proteins , vol.41 , pp. 98-107
    • Devos, D.1    Valencia, A.2
  • 20
    • 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
  • 21
    • 35648948885 scopus 로고    scopus 로고
    • Computational protein function prediction: are we making progress?
    • Godzik A., Jambon M., Friedberg I. Computational protein function prediction: are we making progress?. Cell. Mol. Life. Sci. 2007, 64:2505-2511.
    • (2007) Cell. Mol. Life. Sci. , vol.64 , pp. 2505-2511
    • Godzik, A.1    Jambon, M.2    Friedberg, I.3
  • 22
    • 29444457054 scopus 로고    scopus 로고
    • Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships
    • Gold N.D., Jackson R.M. Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships. J. Mol. Biol. 2006, 355:1112-1124.
    • (2006) J. Mol. Biol. , vol.355 , pp. 1112-1124
    • Gold, N.D.1    Jackson, R.M.2
  • 23
    • 33644876699 scopus 로고    scopus 로고
    • SitesBase: a database for structure-based protein-ligand binding site comparisons
    • Gold N.D., Jackson R.M. SitesBase: a database for structure-based protein-ligand binding site comparisons. Nucleic Acids Res. 2006, 34:D231-D234.
    • (2006) Nucleic Acids Res. , vol.34
    • Gold, N.D.1    Jackson, R.M.2
  • 24
    • 84860833498 scopus 로고    scopus 로고
    • Computational strategies and challenges for targeting protein-protein interactions with small molecules
    • In: Luque, F.J., Barril, X. (Eds.), Physico-chemical and computational approaches to drug discovery, in press.
    • Grimme, D., Gonzalez-Ruiz, D., Gohlke, H. Computational strategies and challenges for targeting protein-protein interactions with small molecules. In: Luque, F.J., Barril, X. (Eds.), Physico-chemical and computational approaches to drug discovery, in press.
    • Grimme, D.1    Gonzalez-Ruiz, D.2    Gohlke, H.3
  • 25
    • 67651005599 scopus 로고    scopus 로고
    • Structural models in the assessment of protein druggability based on HTS data
    • Gupta A., Gupta A.K., Seshari K. Structural models in the assessment of protein druggability based on HTS data. J. Comput. Aided Mol. Des. 2009, 23:583-592.
    • (2009) J. Comput. Aided Mol. Des. , vol.23 , pp. 583-592
    • Gupta, A.1    Gupta, A.K.2    Seshari, K.3
  • 26
    • 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
  • 27
    • 65249117514 scopus 로고    scopus 로고
    • Identifying and characterizing binding sites and assessing druggability
    • Halgren T.A. Identifying and characterizing binding sites and assessing druggability. J. Chem. Inf. Model. 2009, 49:377-389.
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 377-389
    • Halgren, T.A.1
  • 28
    • 0031370977 scopus 로고    scopus 로고
    • LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins
    • Hendlich M., Rippmann F., Barnickel G. LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J. Mol. Graph. Model. 1997, 15:359-363.
    • (1997) J. Mol. Graph. Model. , vol.15 , pp. 359-363
    • Hendlich, M.1    Rippmann, F.2    Barnickel, G.3
  • 29
    • 76649139794 scopus 로고    scopus 로고
    • Computational approaches to identifying and characterizing protein binding sites for ligand design
    • Henrich S., Salo-Ahen O.M.H., Huang B., Rippmann F., Cruciani G., Wade R.C. Computational approaches to identifying and characterizing protein binding sites for ligand design. J. Mol. Recognit. 2009, 23:209-219.
    • (2009) J. Mol. Recognit. , vol.23 , pp. 209-219
    • Henrich, S.1    Salo-Ahen, O.M.H.2    Huang, B.3    Rippmann, F.4    Cruciani, G.5    Wade, R.C.6
  • 30
    • 2942708194 scopus 로고    scopus 로고
    • SURFCOMP: a novel graph-based approach to molecular surface comparison
    • Hofbauer C., Lohninger H., Aszódi A. SURFCOMP: a novel graph-based approach to molecular surface comparison. J. Chem. Inf. Comput. Sci. 2004, 44:837-847.
    • (2004) J. Chem. Inf. Comput. Sci. , vol.44 , pp. 837-847
    • Hofbauer, C.1    Lohninger, H.2    Aszódi, A.3
  • 31
    • 77950423796 scopus 로고    scopus 로고
    • A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction
    • Hoffmann B., Zaslavskiy M., Vert J.P., Stoven V. A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction. BMC Bioinformatics 2010, 11:99.
    • (2010) BMC Bioinformatics , vol.11 , pp. 99
    • Hoffmann, B.1    Zaslavskiy, M.2    Vert, J.P.3    Stoven, V.4
  • 33
    • 79952588669 scopus 로고    scopus 로고
    • Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. Accuracy of binding free energy calculations based on molecular dynamics simulations
    • Hou T., Wang J., Li Y., Wang W. Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. Accuracy of binding free energy calculations based on molecular dynamics simulations. J. Chem. Inf. Model. 2011, 51:69-82.
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 69-82
    • Hou, T.1    Wang, J.2    Li, Y.3    Wang, W.4
  • 34
    • 77956308900 scopus 로고    scopus 로고
    • Binding-site assessment by virtual fragment screening
    • Huang N., Jacobsen M.P. Binding-site assessment by virtual fragment screening. PLoS One 2010, 5:e10109.
    • (2010) PLoS One , vol.5
    • Huang, N.1    Jacobsen, M.P.2
  • 35
    • 3242890667 scopus 로고    scopus 로고
    • PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins
    • Ivanisenko V.A., Pintus S.S., Grigorovich D.A., Kolchanov N.A. PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins. Nucleic Acids Res. 2004, 32:W549-W554.
    • (2004) Nucleic Acids Res. , vol.32
    • Ivanisenko, V.A.1    Pintus, S.S.2    Grigorovich, D.A.3    Kolchanov, N.A.4
  • 36
    • 0037661398 scopus 로고    scopus 로고
    • A new bioinformatic approach to detect common 3D sites in protein structures
    • Jambon M., Imberty A., Deleage G., Geourjon C. A new bioinformatic approach to detect common 3D sites in protein structures. Proteins 2003, 52:137-145.
    • (2003) Proteins , vol.52 , pp. 137-145
    • Jambon, M.1    Imberty, A.2    Deleage, G.3    Geourjon, C.4
  • 40
  • 41
    • 65249170904 scopus 로고    scopus 로고
    • Binding site similarity analysis for the functional classification of the protein kinase family
    • Kinnings S.L., Jackson R.M. Binding site similarity analysis for the functional classification of the protein kinase family. J. Chem. Inf. Model. 2009, 49:318-329.
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 318-329
    • Kinnings, S.L.1    Jackson, R.M.2
  • 42
    • 68249144628 scopus 로고    scopus 로고
    • Drug discovery using chemical systems biology: repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis
    • Kinnings S.L., Liu N., Buchmeier N., Tonge P.J., Xie L., Bourne P.E. Drug discovery using chemical systems biology: repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis. PloS Comput. Biol. 2009, 5:e1000423.
    • (2009) PloS Comput. Biol. , vol.5
    • Kinnings, S.L.1    Liu, N.2    Buchmeier, N.3    Tonge, P.J.4    Xie, L.5    Bourne, P.E.6
  • 43
    • 0036288284 scopus 로고    scopus 로고
    • Identification of protein functions from a molecular surface database, eF-site
    • Kinoshita K., Furui J., Nakamura H. Identification of protein functions from a molecular surface database, eF-site. J. Struct. Funct. Genomics 2001, 2:9-22.
    • (2001) J. Struct. Funct. Genomics , vol.2 , pp. 9-22
    • Kinoshita, K.1    Furui, J.2    Nakamura, H.3
  • 44
    • 34547587452 scopus 로고    scopus 로고
    • EF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape
    • Kinoshita K., Murakami Y., Nakamura H. eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape. Nucleic Acids Res. 2007, 35:W398-W402.
    • (2007) Nucleic Acids Res. , vol.35
    • Kinoshita, K.1    Murakami, Y.2    Nakamura, H.3
  • 45
    • 77952849162 scopus 로고    scopus 로고
    • ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment
    • Konc J., Janezic D. ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment. Bioinformatics 2010, 26:1160-1168.
    • (2010) Bioinformatics , vol.26 , pp. 1160-1168
    • Konc, J.1    Janezic, D.2
  • 46
    • 82355186340 scopus 로고    scopus 로고
    • DrugPred: a structure-based approach to predict protein druggability developed using an extensive nonredundant data set
    • Krasowski A., Muthas D., Sarkar A., Schmitt S., Brenk R. DrugPred: a structure-based approach to predict protein druggability developed using an extensive nonredundant data set. J. Chem. Inf. Model. 2011, 51:2829-2842.
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 2829-2842
    • Krasowski, A.1    Muthas, D.2    Sarkar, A.3    Schmitt, S.4    Brenk, R.5
  • 47
    • 0028881975 scopus 로고
    • SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions
    • 323-330, 307-308
    • Laskowski R.A. SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J. Mol. Graph. 1995, 13. 323-330, 307-308.
    • (1995) J. Mol. Graph. , vol.13
    • Laskowski, R.A.1
  • 49
    • 22544441094 scopus 로고    scopus 로고
    • ProFunc: a server for predicting protein function from 3D structure
    • Laskowski R.A., Watson J.D., Thornton J.M. ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res. 2005, 33:W89-W93.
    • (2005) Nucleic Acids Res. , vol.33
    • Laskowski, R.A.1    Watson, J.D.2    Thornton, J.M.3
  • 50
    • 33749506205 scopus 로고    scopus 로고
    • Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening
    • Laurie A.T.R., Jackson R.M. Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening. Curr. Protein Pept. Sci. 2006, 7:395-406.
    • (2006) Curr. Protein Pept. Sci. , vol.7 , pp. 395-406
    • Laurie, A.T.R.1    Jackson, R.M.2
  • 51
    • 0031687653 scopus 로고    scopus 로고
    • Anatomy of protein pockets and cavities: measurements of binding site geometry and implications for ligand design
    • Liang J., Edelsbrunner H., Woodward H. Anatomy of protein pockets and cavities: measurements of binding site geometry and implications for ligand design. Protein Sci. 1998, 7:1884-1897.
    • (1998) Protein Sci. , vol.7 , pp. 1884-1897
    • Liang, J.1    Edelsbrunner, H.2    Woodward, H.3
  • 53
    • 27744495232 scopus 로고    scopus 로고
    • Get ready to GO! A biologist's guide to the Gene Ontology
    • Lomax J. Get ready to GO! A biologist's guide to the Gene Ontology. Brief Bioinform. 2005, 6:298-304.
    • (2005) Brief Bioinform. , vol.6 , pp. 298-304
    • Lomax, J.1
  • 54
    • 0033642945 scopus 로고    scopus 로고
    • Structural stability of binding sites: consequences for binding affinity and allosteric effects
    • Luque I., Freire E. Structural stability of binding sites: consequences for binding affinity and allosteric effects. Proteins Suppl. 2000, 4:63-71.
    • (2000) Proteins Suppl. , vol.4 , pp. 63-71
    • Luque, I.1    Freire, E.2
  • 55
    • 0036147568 scopus 로고    scopus 로고
    • Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations
    • Ma B., Shatsky M., Wolfson H.J.M., Nussinov R. Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci. 2002, 11:184-197.
    • (2002) Protein Sci. , vol.11 , pp. 184-197
    • Ma, B.1    Shatsky, M.2    Wolfson, H.J.M.3    Nussinov, R.4
  • 56
    • 63249114018 scopus 로고    scopus 로고
    • Vicinity analysis: a methodology for the identification of similar protein active sites
    • McGready A., Stevens A., Lipkin M., Hudson B.D., Whitley D.C., Ford M.G. Vicinity analysis: a methodology for the identification of similar protein active sites. J. Mol. Model. 2009, 15:489-498.
    • (2009) J. Mol. Model. , vol.15 , pp. 489-498
    • McGready, A.1    Stevens, A.2    Lipkin, M.3    Hudson, B.D.4    Whitley, D.C.5    Ford, M.G.6
  • 57
    • 84857291408 scopus 로고    scopus 로고
    • Hot spots and transient pockets: predicting the determinants of small-molecule binding to a protein-protein interface
    • doi:10.1021/ci200322s
    • Metz, A., Pfleger, C., Kopitz, H., Pfeiffer-Marek, S., Baringhaus, K.-H., Gohlke, H., 2011. Hot spots and transient pockets: predicting the determinants of small-molecule binding to a protein-protein interface. J. Chem. Inf. Model., doi:10.1021/ci200322s.
    • (2011) J. Chem. Inf. Model.
    • Metz, A.1    Pfleger, C.2    Kopitz, H.3    Pfeiffer-Marek, S.4    Baringhaus, K.-H.5    Gohlke, H.6
  • 58
    • 0141482410 scopus 로고    scopus 로고
    • Common Structural Cliques: a tool for protein structure and function
    • Milik M., Szalma S., Olszewski K.A. Common Structural Cliques: a tool for protein structure and function. Protein Eng. 2003, 16:543-552.
    • (2003) Protein Eng. , vol.16 , pp. 543-552
    • Milik, M.1    Szalma, S.2    Olszewski, K.A.3
  • 59
    • 77956040404 scopus 로고    scopus 로고
    • Predicting polypharmacology by binding site similarity: from kinases to the protein universe
    • Milletti F., Vulpetti A. Predicting polypharmacology by binding site similarity: from kinases to the protein universe. J. Chem. Inf. Model. 2010, 50:1418-1431.
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 1418-1431
    • Milletti, F.1    Vulpetti, A.2
  • 60
    • 44949110143 scopus 로고    scopus 로고
    • Method for comparing the structures of protein ligand-binding sites and application for predicting protein-drug interactions
    • Minai R., Matsuo Y., Onuki H., Hirota H. Method for comparing the structures of protein ligand-binding sites and application for predicting protein-drug interactions. Proteins 2008, 72:367-381.
    • (2008) Proteins , vol.72 , pp. 367-381
    • Minai, R.1    Matsuo, Y.2    Onuki, H.3    Hirota, H.4
  • 61
    • 49649083383 scopus 로고    scopus 로고
    • Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites
    • Najmanovich R., Kurbatova N., Thornton J. Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites. Bioinformatics 2008, 24:i105-i111.
    • (2008) Bioinformatics , vol.24
    • Najmanovich, R.1    Kurbatova, N.2    Thornton, J.3
  • 62
    • 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
  • 63
    • 0036603905 scopus 로고    scopus 로고
    • Chemical space navigation in lead discovery
    • Oprea T. Chemical space navigation in lead discovery. Curr. Opin. Chem. Biol. 2002, 6:384-389.
    • (2002) Curr. Opin. Chem. Biol. , vol.6 , pp. 384-389
    • Oprea, T.1
  • 64
    • 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
  • 65
    • 33748271948 scopus 로고    scopus 로고
    • Comparison of protein active site structures for functional annotation of proteins and drug design
    • Powers R., Copeland J.C., Germer K., Mercier K.A., Ramanathan V., Revesz P. Comparison of protein active site structures for functional annotation of proteins and drug design. Proteins 2006, 65:124-135.
    • (2006) Proteins , vol.65 , pp. 124-135
    • Powers, R.1    Copeland, J.C.2    Germer, K.3    Mercier, K.A.4    Ramanathan, V.5    Revesz, P.6
  • 66
    • 79251536512 scopus 로고    scopus 로고
    • Searching the protein structure database for ligand-binding site similarities using CPASS v.2
    • Powers R., Copeland J.C., Stark J.L., Caprez A., Guru A., Swanson D. Searching the protein structure database for ligand-binding site similarities using CPASS v.2. BMC Res. Notes 2011, 4:17.
    • (2011) BMC Res. Notes , vol.4 , pp. 17
    • Powers, R.1    Copeland, J.C.2    Stark, J.L.3    Caprez, A.4    Guru, A.5    Swanson, D.6
  • 67
    • 62549146620 scopus 로고    scopus 로고
    • Protein function prediction - the power of multiplicity
    • Rentzsch R., Orengo C.A. Protein function prediction - the power of multiplicity. Trends Biotechnol. 2009, 27:210-219.
    • (2009) Trends Biotechnol. , vol.27 , pp. 210-219
    • Rentzsch, R.1    Orengo, C.A.2
  • 68
    • 78650986186 scopus 로고    scopus 로고
    • Binding ligand prediction for proteins using partial matching of local surface patches
    • Sael L., Kihara D. Binding ligand prediction for proteins using partial matching of local surface patches. Int. J. Mol. Sci. 2010, 11:5009-5026.
    • (2010) Int. J. Mol. Sci. , vol.11 , pp. 5009-5026
    • Sael, L.1    Kihara, D.2
  • 70
    • 44349119204 scopus 로고    scopus 로고
    • A simple and fuzzy method to align and compare druggable ligand-binding sites
    • Schalon C., Surgand J.-S., Kellenberger E., Rognan D. A simple and fuzzy method to align and compare druggable ligand-binding sites. Proteins 2008, 71:1755-1778.
    • (2008) Proteins , vol.71 , pp. 1755-1778
    • Schalon, C.1    Surgand, J.-S.2    Kellenberger, E.3    Rognan, D.4
  • 71
    • 77955397914 scopus 로고    scopus 로고
    • Understanding and predicting druggability. A high-throughput method for detection of drug binding sites
    • Schmidtke P., Barril X. Understanding and predicting druggability. A high-throughput method for detection of drug binding sites. J. Med. Chem. 2010, 53:5858-5867.
    • (2010) J. Med. Chem. , vol.53 , pp. 5858-5867
    • Schmidtke, P.1    Barril, X.2
  • 73
    • 0036406643 scopus 로고    scopus 로고
    • A new method to detect related function among proteins independent of sequence and fold homology
    • Schmitt S., Kuhn D., Klebe G. A new method to detect related function among proteins independent of sequence and fold homology. J. Mol. Biol. 2002, 323:387-406.
    • (2002) J. Mol. Biol. , vol.323 , pp. 387-406
    • Schmitt, S.1    Kuhn, D.2    Klebe, G.3
  • 74
    • 65449159794 scopus 로고    scopus 로고
    • Binding site detection and druggability index from first principles
    • Seco J., Luque J., Barril X. Binding site detection and druggability index from first principles. J. Med. Chem. 2009, 52:2363-2371.
    • (2009) J. Med. Chem. , vol.52 , pp. 2363-2371
    • Seco, J.1    Luque, J.2    Barril, X.3
  • 75
    • 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., Hooloway 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    Hooloway, M.K.3    Cornell, W.D.4    Gao, Y.-D.5
  • 76
    • 2442614144 scopus 로고    scopus 로고
    • Recognition of functional sites in protein structures
    • Shulman-Peleg A., Nussinov R., Wolfson H.J. Recognition of functional sites in protein structures. J. Mol. Biol. 2004, 339:607-633.
    • (2004) J. Mol. Biol. , vol.339 , pp. 607-633
    • Shulman-Peleg, A.1    Nussinov, R.2    Wolfson, H.J.3
  • 77
    • 48449092564 scopus 로고    scopus 로고
    • MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions
    • Shulman-Peleg A., Shatsky M., Nussinov R., Wolfson H.J. MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions. Nucleic Acids Res. 2008, 36:W260-W264.
    • (2008) Nucleic Acids Res. , vol.36
    • Shulman-Peleg, A.1    Shatsky, M.2    Nussinov, R.3    Wolfson, H.J.4
  • 78
    • 80051567982 scopus 로고    scopus 로고
    • Surface-based protein binding pocket similarity
    • Spitzer R., Cleves A.E., Jain A.N. Surface-based protein binding pocket similarity. Proteins 2011, 79:2746-2763.
    • (2011) Proteins , vol.79 , pp. 2746-2763
    • Spitzer, R.1    Cleves, A.E.2    Jain, A.N.3
  • 79
    • 0041620372 scopus 로고    scopus 로고
    • Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures
    • Stark A. Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures. Nucleic Acids Res. 2003, 31:3341-3344.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3341-3344
    • Stark, A.1
  • 80
    • 0033621104 scopus 로고    scopus 로고
    • Folding and binding cascades: shifts in energy landscapes
    • Tsai C.-J., Ma B., Nussinov R. Folding and binding cascades: shifts in energy landscapes. Proc. Natl. Acad. Sci. U.S.A. 1999, 96:9970-9972.
    • (1999) Proc. Natl. Acad. Sci. U.S.A. , vol.96 , pp. 9970-9972
    • Tsai, C.-J.1    Ma, B.2    Nussinov, R.3
  • 81
    • 61649106689 scopus 로고    scopus 로고
    • Predicting protein function and binding profile via matching of local evolutionary and geometric surface patterns
    • Tseng Y.Y., Dundas J., Liang J. Predicting protein function and binding profile via matching of local evolutionary and geometric surface patterns. J. Mol. Biol. 2009, 387:451-464.
    • (2009) J. Mol. Biol. , vol.387 , pp. 451-464
    • Tseng, Y.Y.1    Dundas, J.2    Liang, J.3
  • 82
    • 75549090058 scopus 로고    scopus 로고
    • FPOP: footprinting functional pockets of proteins by comparative spatial patterns
    • Tseng Y.Y., Chen Z.J., Li W.H. fPOP: footprinting functional pockets of proteins by comparative spatial patterns. Nucleic Acids Res. 2009, 38:D288-D295.
    • (2009) Nucleic Acids Res. , vol.38
    • Tseng, Y.Y.1    Chen, Z.J.2    Li, W.H.3
  • 83
    • 0028301575 scopus 로고
    • Amino acid preferences at protein binding sites
    • Villar H.O., Kauvar L.M. Amino acid preferences at protein binding sites. FEBS Lett. 1994, 349:125-130.
    • (1994) FEBS Lett. , vol.349 , pp. 125-130
    • Villar, H.O.1    Kauvar, L.M.2
  • 84
    • 78649499434 scopus 로고    scopus 로고
    • Analyzing the topology of active sites: on the prediction of pockets and subpockets
    • Volkamer A., Griewel A., Grombacher T., Rarey M. Analyzing the topology of active sites: on the prediction of pockets and subpockets. J. Chem. Inf. Model. 2010, 50:2041-2052.
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 2041-2052
    • Volkamer, A.1    Griewel, A.2    Grombacher, T.3    Rarey, M.4
  • 85
    • 66349094968 scopus 로고    scopus 로고
    • Prediction of sub-cavity binding preferences using an adaptive physicochemical structure representation
    • Wallach I., Lilien R.H. Prediction of sub-cavity binding preferences using an adaptive physicochemical structure representation. Bioinformatics 2009, 25:i296-i304.
    • (2009) Bioinformatics , vol.25
    • Wallach, I.1    Lilien, R.H.2
  • 86
    • 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
  • 87
    • 75749155406 scopus 로고    scopus 로고
    • Alignment-free ultra-high-throughput comparison of druggable protein-ligand binding sites
    • Weill N., Rognan D. Alignment-free ultra-high-throughput comparison of druggable protein-ligand binding sites. J. Chem. Inf. Model. 2010, 50:123-135.
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 123-135
    • Weill, N.1    Rognan, D.2
  • 88
    • 60349119258 scopus 로고    scopus 로고
    • Form follows function: shape analysis of protein cavities for receptor-based drug design
    • Weisel M., Proschak E., Kriegl J.M., Schneider G. Form follows function: shape analysis of protein cavities for receptor-based drug design. Proteomics 2009, 9:451-459.
    • (2009) Proteomics , vol.9 , pp. 451-459
    • Weisel, M.1    Proschak, E.2    Kriegl, J.M.3    Schneider, G.4
  • 89
    • 44449139387 scopus 로고    scopus 로고
    • Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments
    • Xie L., Bourne P.E. Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:5441-5446.
    • (2008) Proc. Natl. Acad. Sci. U.S.A. , vol.105 , pp. 5441-5446
    • Xie, L.1    Bourne, P.E.2
  • 90
    • 60649117152 scopus 로고    scopus 로고
    • PocketMatch: a new algorithm to compare binding sites in protein structures
    • Yeturu K., Chandra N. PocketMatch: a new algorithm to compare binding sites in protein structures. BMC Bioinformatics 2008, 9:543.
    • (2008) BMC Bioinformatics , vol.9 , pp. 543
    • Yeturu, K.1    Chandra, N.2
  • 91
    • 79960739917 scopus 로고    scopus 로고
    • PocketAlign: a novel algorithm for aligning binding sites in protein structures
    • Yeturu K., Chandra N.R. PocketAlign: a novel algorithm for aligning binding sites in protein structures. J. Chem. Inf. Model. 2011, 51:1725-1736.
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 1725-1736
    • Yeturu, K.1    Chandra, N.R.2


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