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Volumn 185, Issue 2, 2014, Pages 193-202

Computational design of protein-small molecule interfaces

Author keywords

Computational interface design; Ligand docking; Protein small molecule interaction; Rosetta; RosettaLigand; Sequence optimization

Indexed keywords

COMPUTATIONAL INTERFACE DESIGN; LIGAND DOCKING; PROTEIN-SMALL MOLECULE INTERACTION; ROSETTA; ROSETTALIGAND; SEQUENCE OPTIMIZATION;

EID: 84894929772     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2013.08.003     Document Type: Article
Times cited : (23)

References (43)
  • 1
    • 2542523113 scopus 로고    scopus 로고
    • Computational design of receptors for an organophosphate surrogate of the nerve agent soman. Proceedings of the National Academy of Sciences of the United States of America 101, 7907-12. Epub 2004 May 17.
    • Allert, M.; Rizk, S. S.; Looger, L. L.; Hellinga, H. W., 2004. Computational design of receptors for an organophosphate surrogate of the nerve agent soman. Proceedings of the National Academy of Sciences of the United States of America 101, 7907-12. Epub 2004 May 17.
    • (2004)
    • Allert, M.1    Rizk, S.S.2    Looger, L.L.3    Hellinga, H.W.4
  • 4
    • 77956532389 scopus 로고    scopus 로고
    • Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs
    • Ashworth J., Taylor G.K., Havranek J.J., Quadri S.A., Stoddard B.L., et al. Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs. Nucleic Acids Res. 2010, 38:5601-5608.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 5601-5608
    • Ashworth, J.1    Taylor, G.K.2    Havranek, J.J.3    Quadri, S.A.4    Stoddard, B.L.5
  • 5
    • 2442680491 scopus 로고    scopus 로고
    • Biosensors for environmental pollutants and food contaminants
    • Baeumner A.J. Biosensors for environmental pollutants and food contaminants. Anal. Bioanal. Chem. 2003, 377:434-445.
    • (2003) Anal. Bioanal. Chem. , vol.377 , pp. 434-445
    • Baeumner, A.J.1
  • 6
    • 58149094776 scopus 로고    scopus 로고
    • RosettaLigand docking with full ligand and receptor flexibility
    • Baker D., Davis I.W. RosettaLigand docking with full ligand and receptor flexibility. J. Mol. Biol. 2009, 385:381-392.
    • (2009) J. Mol. Biol. , vol.385 , pp. 381-392
    • Baker, D.1    Davis, I.W.2
  • 7
    • 40449116114 scopus 로고    scopus 로고
    • De novo computational design of retro-aldol enzymes
    • Baker D., Jiang L., Althoff E.A., Clemente F.R., Doyle L., et al. De novo computational design of retro-aldol enzymes. Science 2008, 319:1387-1391.
    • (2008) Science , vol.319 , pp. 1387-1391
    • Baker, D.1    Jiang, L.2    Althoff, E.A.3    Clemente, F.R.4    Doyle, L.5
  • 9
    • 77954811495 scopus 로고    scopus 로고
    • Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction
    • Baker D., Siegel J.B., Zanghellini A., Lovick H.M., Kiss G., et al. Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science 2010, 329:309-313.
    • (2010) Science , vol.329 , pp. 309-313
    • Baker, D.1    Siegel, J.B.2    Zanghellini, A.3    Lovick, H.M.4    Kiss, G.5
  • 10
    • 84872869954 scopus 로고    scopus 로고
    • Benchmarking ligand-based virtual high-throughput screening with the pubchem database
    • Butkiewicz M., Lowe E.W., Mueller R., Mendenhall J.L., Teixeira P.L., et al. Benchmarking ligand-based virtual high-throughput screening with the pubchem database. Molecules 2013, 18:735-756.
    • (2013) Molecules , vol.18 , pp. 735-756
    • Butkiewicz, M.1    Lowe, E.W.2    Mueller, R.3    Mendenhall, J.L.4    Teixeira, P.L.5
  • 12
    • 67651244131 scopus 로고    scopus 로고
    • Siderocalins: siderophore-binding proteins of the innate immune system
    • Clifton M.C., Corrent C., Strong R.K. Siderocalins: siderophore-binding proteins of the innate immune system. Biometals 2009, 22:557-564.
    • (2009) Biometals , vol.22 , pp. 557-564
    • Clifton, M.C.1    Corrent, C.2    Strong, R.K.3
  • 13
    • 80053596579 scopus 로고    scopus 로고
    • Design of native-like proteins through an exposure-dependent environment potential
    • DeLuca S., Dorr B., Meiler J. Design of native-like proteins through an exposure-dependent environment potential. Biochemistry-US 2011, 50:8521-8528.
    • (2011) Biochemistry-US , vol.50 , pp. 8521-8528
    • DeLuca, S.1    Dorr, B.2    Meiler, J.3
  • 14
    • 80053333972 scopus 로고    scopus 로고
    • CSAR benchmark exercise of 2010: selection of the protein-ligand complexes
    • Dunbar J.B., Smith R.D., Yang C.Y., Ung P.M.U., Lexa K.W., et al. CSAR benchmark exercise of 2010: selection of the protein-ligand complexes. J. Chem. Inf. Model. 2011, 51:2036-2046.
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 2036-2046
    • Dunbar, J.B.1    Smith, R.D.2    Yang, C.Y.3    Ung, P.M.U.4    Lexa, K.W.5
  • 15
    • 0034609833 scopus 로고    scopus 로고
    • Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties
    • Ertl P., Rohde B., Selzer P. Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties. J. Med. Chem. 2000, 43:3714-3717.
    • (2000) J. Med. Chem. , vol.43 , pp. 3714-3717
    • Ertl, P.1    Rohde, B.2    Selzer, P.3
  • 16
    • 79956017135 scopus 로고    scopus 로고
    • Computational design of proteins targeting the conserved stem region of influenza hemagglutinin
    • Fleishman S.J., Whitehead T.A., Ekiert D.C., Dreyfus C., Corn J.E., et al. Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science 2011, 332:816-821.
    • (2011) Science , vol.332 , pp. 816-821
    • Fleishman, S.J.1    Whitehead, T.A.2    Ekiert, D.C.3    Dreyfus, C.4    Corn, J.E.5
  • 19
    • 84874028898 scopus 로고    scopus 로고
    • OSPREY: protein design with ensembles, flexibility, and provable algorithms
    • Gainza P., Roberts K.E., Georgiev I., Lilien R.H., Keedy D.A., et al. OSPREY: protein design with ensembles, flexibility, and provable algorithms. Methods Enzymol. 2013, 523:87-107.
    • (2013) Methods Enzymol. , vol.523 , pp. 87-107
    • Gainza, P.1    Roberts, K.E.2    Georgiev, I.3    Lilien, R.H.4    Keedy, D.A.5
  • 20
    • 46449106372 scopus 로고    scopus 로고
    • The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles
    • Georgiev I., Lilien R.H., Donald B.R. The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles. J. Comput. Chem. 2008, 29:1527-1542.
    • (2008) J. Comput. Chem. , vol.29 , pp. 1527-1542
    • Georgiev, I.1    Lilien, R.H.2    Donald, B.R.3
  • 21
    • 37749004225 scopus 로고    scopus 로고
    • Protein therapeutics: a summary and pharmacological classification
    • Golan D.E., Leader B., Baca Q.J. Protein therapeutics: a summary and pharmacological classification. Nat. Rev. Drug Discovery 2008, 7:21-39.
    • (2008) Nat. Rev. Drug Discovery , vol.7 , pp. 21-39
    • Golan, D.E.1    Leader, B.2    Baca, Q.J.3
  • 22
    • 84871034932 scopus 로고    scopus 로고
    • Dead-end elimination with perturbations (DEEPer): a provable protein design algorithm with continuous sidechain and backbone flexibility
    • Hallen M.A., Keedy D.A., Donald B.R. Dead-end elimination with perturbations (DEEPer): a provable protein design algorithm with continuous sidechain and backbone flexibility. Proteins 2013, 81:18-39.
    • (2013) Proteins , vol.81 , pp. 18-39
    • Hallen, M.A.1    Keedy, D.A.2    Donald, B.R.3
  • 23
    • 70350053005 scopus 로고    scopus 로고
    • Key protein-design papers challenged
    • Hayden E.C. Key protein-design papers challenged. Nature 2009, 461:859.
    • (2009) Nature , vol.461 , pp. 859
    • Hayden, E.C.1
  • 26
    • 68049140791 scopus 로고    scopus 로고
    • Starving the addiction: new opportunities for durable suppression of AR signaling in prostate cancer
    • Knudsen K.E., Scher H.I. Starving the addiction: new opportunities for durable suppression of AR signaling in prostate cancer. Clin. Cancer Res. 2009, 15:4792-4798.
    • (2009) Clin. Cancer Res. , vol.15 , pp. 4792-4798
    • Knudsen, K.E.1    Scher, H.I.2
  • 27
    • 0037470581 scopus 로고    scopus 로고
    • An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes
    • Kortemme T., Morozov A.V., Baker D. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J. Mol. Biol. 2003, 326:1239-1259.
    • (2003) J. Mol. Biol. , vol.326 , pp. 1239-1259
    • Kortemme, T.1    Morozov, A.V.2    Baker, D.3
  • 29
    • 33750056673 scopus 로고    scopus 로고
    • RosettaLigand: protein-small molecule docking with full side-chain flexibility
    • Meiler J., Baker D. RosettaLigand: protein-small molecule docking with full side-chain flexibility. Proteins 2006, 65:538-548.
    • (2006) Proteins , vol.65 , pp. 538-548
    • Meiler, J.1    Baker, D.2
  • 30
    • 59849093622 scopus 로고    scopus 로고
    • Structural determinants of species-selective substrate recognition in human and Drosaphila serotonin transporters revealed through computational docking studies
    • Meiler J., Kaufmann K.W., Dawson E.S., Henry L.K., Field J.R., et al. Structural determinants of species-selective substrate recognition in human and Drosaphila serotonin transporters revealed through computational docking studies. Proteins 2009, 74:630-642.
    • (2009) Proteins , vol.74 , pp. 630-642
    • Meiler, J.1    Kaufmann, K.W.2    Dawson, E.S.3    Henry, L.K.4    Field, J.R.5
  • 33
  • 34
  • 35
    • 34548838274 scopus 로고    scopus 로고
    • Phage display for engineering and analyzing protein interaction interfaces
    • Sidhu S.S., Koide S. Phage display for engineering and analyzing protein interaction interfaces. Curr. Opin. Struct. Biol. 2007, 17:481-487.
    • (2007) Curr. Opin. Struct. Biol. , vol.17 , pp. 481-487
    • Sidhu, S.S.1    Koide, S.2
  • 37
    • 77954811495 scopus 로고    scopus 로고
    • Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction
    • Siegel J.B., Zanghellini A., Lovick H.M., Kiss G., Lambert A.R., et al. Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science 2010, 329:309-313.
    • (2010) Science , vol.329 , pp. 309-313
    • Siegel, J.B.1    Zanghellini, A.2    Lovick, H.M.3    Kiss, G.4    Lambert, A.R.5
  • 38
    • 33644949935 scopus 로고    scopus 로고
    • Recapitulation and design of protein binding peptide structures and sequences
    • Sood V.D., Baker D. Recapitulation and design of protein binding peptide structures and sequences. J. Mol. Biol. 2006, 357:917-927.
    • (2006) J. Mol. Biol. , vol.357 , pp. 917-927
    • Sood, V.D.1    Baker, D.2
  • 39
    • 84855858058 scopus 로고    scopus 로고
    • Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design
    • Wang L., Althoff E.A., Bolduc J., Jiang L., Moody J., et al. Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design. J. Mol. Biol. 2012, 415:615-625.
    • (2012) J. Mol. Biol. , vol.415 , pp. 615-625
    • Wang, L.1    Althoff, E.A.2    Bolduc, J.3    Jiang, L.4    Moody, J.5
  • 40
    • 0036139210 scopus 로고    scopus 로고
    • Protein therapeutics: promises and challenges for the 21st century
    • Weng Z.P., DeLisi C. Protein therapeutics: promises and challenges for the 21st century. Trends Biotechnol. 2002, 20:29-35.
    • (2002) Trends Biotechnol. , vol.20 , pp. 29-35
    • Weng, Z.P.1    DeLisi, C.2
  • 41
    • 0036628547 scopus 로고    scopus 로고
    • Novel methods for the prediction of log P, pK(a), and log D
    • Xing L., Glen R.C. Novel methods for the prediction of log P, pK(a), and log D. J. Chem. Inf. Comput. Sci. 2002, 42:796-805.
    • (2002) J. Chem. Inf. Comput. Sci. , vol.42 , pp. 796-805
    • Xing, L.1    Glen, R.C.2
  • 43
    • 32044465761 scopus 로고    scopus 로고
    • Complete reaction cycle of a cocaine catalytic antibody at atomic resolution
    • Zhu X., Dickerson T.J., Rogers C.J., Kaufmann G.F., Mee J.M., et al. Complete reaction cycle of a cocaine catalytic antibody at atomic resolution. Structure 2006, 14:205-216.
    • (2006) Structure , vol.14 , pp. 205-216
    • Zhu, X.1    Dickerson, T.J.2    Rogers, C.J.3    Kaufmann, G.F.4    Mee, J.M.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.