메뉴 건너뛰기




Volumn , Issue , 2009, Pages 185-210

Predicting molecular interactions in structural proteomics

Author keywords

[No Author keywords available]

Indexed keywords


EID: 78049464618     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1201/9781420070071     Document Type: Chapter
Times cited : (5)

References (89)
  • 1
    • 35748953417 scopus 로고    scopus 로고
    • Structural genomics: Winning the second half of the game
    • Janin J. 2007. Structural genomics: Winning the second half of the game. Structure 15(11):1347-1349.
    • (2007) Structure , vol.15 , Issue.11 , pp. 1347-1349
    • Janin, J.1
  • 2
    • 37549063951 scopus 로고    scopus 로고
    • PSI has to live and become PCI: Protein Complex Initiative
    • Vakser IA. 2008. PSI has to live and become PCI: Protein Complex Initiative. Structure 16(1):1-3.
    • (2008) Structure , vol.16 , Issue.1 , pp. 1-3
    • Vakser, I.A.1
  • 3
    • 34447286664 scopus 로고    scopus 로고
    • Trp/Met/Phe hot spots in protein-protein interactions: Potential targets in drug design
    • Ma B, Nussinov R. 2007. Trp/Met/Phe hot spots in protein-protein interactions: Potential targets in drug design. Curr Top Med Chem 7(10):999-1005.
    • (2007) Curr Top Med Chem , vol.7 , Issue.10 , pp. 999-1005
    • Ma, B.1    Nussinov, R.2
  • 4
    • 46449113031 scopus 로고    scopus 로고
    • Similar chemistry, but different bond pReferences in inter- versus intra-protein interactions
    • Cohen M, Reichmann D, Neuvirth H, Schreiber G. 2008. Similar chemistry, but different bond pReferences in inter- versus intra-protein interactions. Proteins 72(2):741-753.
    • (2008) Proteins , vol.72 , Issue.2 , pp. 741-753
    • Cohen, M.1    Reichmann, D.2    Neuvirth, H.3    Schreiber, G.4
  • 6
    • 34249930159 scopus 로고    scopus 로고
    • Single-molecule experiments in vitro and in silico
    • Sotomayor M, Schulten K. 2007. Single-molecule experiments in vitro and in silico. Science 316(5828):1144-1148.
    • (2007) Science , vol.316 , Issue.5828 , pp. 1144-1148
    • Sotomayor, M.1    Schulten, K.2
  • 7
    • 33646839120 scopus 로고    scopus 로고
    • Characterization of protein-ligand interaction sites using experimental and computational methods
    • Vajda S, Guarnieri F. 2006. Characterization of protein-ligand interaction sites using experimental and computational methods. Curr Opin Drug Discov Devel 9(3):354-362.
    • (2006) Curr Opin Drug Discov Devel , vol.9 , Issue.3 , pp. 354-362
    • Vajda, S.1    Guarnieri, F.2
  • 8
    • 41949102408 scopus 로고    scopus 로고
    • Predicting 3D structures of protein-protein complexes
    • Vakser IA, Kundrotas P. 2008. Predicting 3D structures of protein-protein complexes. Curr Pharm Biotechnol 9(2):57-66.
    • (2008) Curr Pharm Biotechnol , vol.9 , Issue.2 , pp. 57-66
    • Vakser, I.A.1    Kundrotas, P.2
  • 10
    • 37548998973 scopus 로고    scopus 로고
    • Comparative modeling in structural genomics
    • Moult J. 2008. Comparative modeling in structural genomics. Structure 16(1):14-16.
    • (2008) Structure , vol.16 , Issue.1 , pp. 14-16
    • Moult, J.1
  • 11
    • 10844235653 scopus 로고    scopus 로고
    • Optimal docking area: A new method for predicting protein-protein interaction sites
    • Fernandez-Recio J, Totrov M, Skorodumov C, Abagyan R. 2005. Optimal docking area: A new method for predicting protein-protein interaction sites. Proteins 58(1):134-143.
    • (2005) Proteins , vol.58 , Issue.1 , pp. 134-143
    • Fernandez-Recio, J.1    Totrov, M.2    Skorodumov, C.3    Abagyan, R.4
  • 13
    • 0036149480 scopus 로고    scopus 로고
    • Soft protein-protein docking in internal coordinates
    • Fernández-Recio J, Totrov M, Abagyan R. 2002. Soft protein-protein docking in internal coordinates. Protein Sci 11(2):280-291.
    • (2002) Protein Sci , vol.11 , Issue.2 , pp. 280-291
    • Fernández-Recio, J.1    Totrov, M.2    Abagyan, R.3
  • 14
    • 57349132441 scopus 로고    scopus 로고
    • Protein-protein docking benchmark version 3. 0
    • Hwang H, Pierce B, Mintseris J, Janin J, Weng Z. 2008. Protein-protein docking benchmark version 3. 0. Proteins 73(3):705-709.
    • (2008) Proteins , vol.73 , Issue.3 , pp. 705-709
    • Hwang, H.1    Pierce, B.2    Mintseris, J.3    Janin, J.4    Weng, Z.5
  • 15
    • 36749060694 scopus 로고    scopus 로고
    • DOCKGROUND system of databases for protein recognition studies: Unbound structures for docking
    • Gao Y, Douguet D, Tovchigrechko A, Vakser IA. 2007. DOCKGROUND system of databases for protein recognition studies: Unbound structures for docking. Proteins 69(4):845-851.
    • (2007) Proteins , vol.69 , Issue.4 , pp. 845-851
    • Gao, Y.1    Douguet, D.2    Tovchigrechko, A.3    Vakser, I.A.4
  • 16
    • 19544390737 scopus 로고    scopus 로고
    • REVCOM: A robust Bayesian method for evolutionary rate estimation
    • Bordner AJ, Abagyan R. 2005. REVCOM: A robust Bayesian method for evolutionary rate estimation. Bioinformatics 21(10):2315-2321.
    • (2005) Bioinformatics , vol.21 , Issue.10 , pp. 2315-2321
    • Bordner, A.J.1    Abagyan, R.2
  • 18
    • 15244355250 scopus 로고    scopus 로고
    • The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking
    • Smith GR, Sternberg MJ, Bates PA. 2005. The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking. J Mol Biol 347(5):1077-1101.
    • (2005) J Mol Biol , vol.347 , Issue.5 , pp. 1077-1101
    • Smith, G.R.1    Sternberg, M.J.2    Bates, P.A.3
  • 20
    • 0029913807 scopus 로고    scopus 로고
    • An evolutionary trace method defines binding surfaces common to protein families
    • Lichtarge O, Bourne HR, Cohen FE. 1996. An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol 257(2):342-358.
    • (1996) J Mol Biol , vol.257 , Issue.2 , pp. 342-358
    • Lichtarge, O.1    Bourne, H.R.2    Cohen, F.E.3
  • 21
    • 2942553723 scopus 로고    scopus 로고
    • Protein-protein interactions; coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking
    • Halperin I, Wolfson H, Nussinov R. 2004. Protein-protein interactions; coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking. Structure (Camb) 12(6):1027-1038.
    • (2004) Structure (Camb) , vol.12 , Issue.6 , pp. 1027-1038
    • Halperin, I.1    Wolfson, H.2    Nussinov, R.3
  • 22
    • 0037609791 scopus 로고    scopus 로고
    • Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces
    • Ma B, Elkayam T, Wolfson H, Nussinov R. 2003. Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc Natl Acad Sci USA 100(10):5772-5777.
    • (2003) Proc Natl Acad Sci USA , vol.100 , Issue.10 , pp. 5772-5777
    • Ma, B.1    Elkayam, T.2    Wolfson, H.3    Nussinov, R.4
  • 23
    • 0037265213 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions from evolutionary information
    • Valencia A, Pazos F. 2003. Prediction of protein-protein interactions from evolutionary information. Methods Biochem Anal 44:411-426.
    • (2003) Methods Biochem Anal , vol.44 , pp. 411-426
    • Valencia, A.1    Pazos, F.2
  • 24
    • 0036468670 scopus 로고    scopus 로고
    • Evolutionary predictions of binding surfaces and interactions
    • Lichtarge O, Sowa ME. 2002. Evolutionary predictions of binding surfaces and interactions. Curr Opin Struct Biol 12(1):21-27.
    • (2002) Curr Opin Struct Biol , vol.12 , Issue.1 , pp. 21-27
    • Lichtarge, O.1    Sowa, M.E.2
  • 25
    • 0035896024 scopus 로고    scopus 로고
    • ConSurf: An algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information
    • Armon A, Graur D, Ben-Tal N. 2001. ConSurf: An algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J Mol Biol 307(1):447-463.
    • (2001) J Mol Biol , vol.307 , Issue.1 , pp. 447-463
    • Armon, A.1    Graur, D.2    Ben-Tal, N.3
  • 26
    • 2542445427 scopus 로고    scopus 로고
    • ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information
    • Glaser F, Pupko T, Paz I, Bell RE, Bechor-Shental D, Martz E, Ben-Tal N. 2003. ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 19(1):163-164.
    • (2003) Bioinformatics , vol.19 , Issue.1 , pp. 163-164
    • Glaser, F.1    Pupko, T.2    Paz, I.3    Bell, R.E.4    Bechor-Shental, D.5    Martz, E.6    Ben-Tal, N.7
  • 27
    • 0002218484 scopus 로고    scopus 로고
    • Rate4Site: An algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues
    • Pupko T, Bell RE, Mayrose I, Glaser F, Ben-Tal N. 2002. Rate4Site: An algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues Bioinformatics 18(Suppl 1):71-77.
    • (2002) Bioinformatics , vol.18 , pp. 71-77
    • Pupko, T.1    Bell, R.E.2    Mayrose, I.3    Glaser, F.4    Ben-Tal, N.5
  • 28
    • 0037197902 scopus 로고    scopus 로고
    • Interrogating protein interaction networks through structural biology
    • Aloy P, Russell RB. 2002. Interrogating protein interaction networks through structural biology. Proc Natl Acad Sci USA 99(9):5896-5901.
    • (2002) Proc Natl Acad Sci USA , vol.99 , Issue.9 , pp. 5896-5901
    • Aloy, P.1    Russell, R.B.2
  • 29
    • 0042010066 scopus 로고    scopus 로고
    • Asymmetric mutation rates at enzyme-inhibitor interfaces: Implications for the protein-protein docking problem
    • Bradford JR, Westhead DR. 2003. Asymmetric mutation rates at enzyme-inhibitor interfaces: Implications for the protein-protein docking problem. Protein Sci 12(9):2099-2103.
    • (2003) Protein Sci , vol.12 , Issue.9 , pp. 2099-2103
    • Bradford, J.R.1    Westhead, D.R.2
  • 30
    • 0346733329 scopus 로고    scopus 로고
    • Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?
    • Caffrey DR, Somaroo S, Hughes JD, Mintseris J, Huang ES. 2004. Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Sci 13(1):190-202.
    • (2004) Protein Sci , vol.13 , Issue.1 , pp. 190-202
    • Caffrey, D.R.1    Somaroo, S.2    Hughes, J.D.3    Mintseris, J.4    Huang, E.S.5
  • 31
    • 23344451687 scopus 로고    scopus 로고
    • Structure, function, and evolution of transient and obligate protein-protein interactions
    • Mintseris J, Weng Z. 2005. Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci USA 102(31):10930-10935.
    • (2005) Proc Natl Acad Sci USA , vol.102 , Issue.31 , pp. 10930-10935
    • Mintseris, J.1    Weng, Z.2
  • 32
    • 1042275583 scopus 로고    scopus 로고
    • A dissection of specific and nonspecific protein-protein interfaces
    • Bahadur RP, Chakrabarti P, Rodier F, Janin J. 2004. A dissection of specific and nonspecific protein-protein interfaces. J Mol Biol 336(4):943-955.
    • (2004) J Mol Biol , vol.336 , Issue.4 , pp. 943-955
    • Bahadur, R.P.1    Chakrabarti, P.2    Rodier, F.3    Janin, J.4
  • 33
    • 0031565729 scopus 로고    scopus 로고
    • Analysis of protein-protein interaction sites using surface patches
    • Jones S, Thornton JM. 1997. Analysis of protein-protein interaction sites using surface patches. J Mol Biol 272(1):121-132.
    • (1997) J Mol Biol , vol.272 , Issue.1 , pp. 121-132
    • Jones, S.1    Thornton, J.M.2
  • 34
    • 0032522670 scopus 로고    scopus 로고
    • Morphology of protein-protein interfaces
    • Larsen TA, Olson AJ, Goodsell DS. 1998. Morphology of protein-protein interfaces. Structure 6(4):421-427.
    • (1998) Structure , vol.6 , Issue.4 , pp. 421-427
    • Larsen, T.A.1    Olson, A.J.2    Goodsell, D.S.3
  • 35
    • 0003187567 scopus 로고    scopus 로고
    • The atomic structure of protein-protein recognition sites
    • Conte LL, Chothia C, Janin J. 1999. The atomic structure of protein-protein recognition sites. J Mol Biol 285(5):2177-2198.
    • (1999) J Mol Biol , vol.285 , Issue.5 , pp. 2177-2198
    • Conte, L.L.1    Chothia, C.2    Janin, J.3
  • 36
    • 0030580057 scopus 로고    scopus 로고
    • Antibody-antigen interactions: Contact analysis and binding site topography
    • MacCallum RM, Martin AC, Thornton JM. 1996. Antibody-antigen interactions: Contact analysis and binding site topography. J Mol Biol 262(5):732-745.
    • (1996) J Mol Biol , vol.262 , Issue.5 , pp. 732-745
    • Maccallum, R.M.1    Martin, A.C.2    Thornton, J.M.3
  • 37
    • 0037474541 scopus 로고    scopus 로고
    • Structural characterisation and functional significance of transient protein-protein interactions
    • Nooren IM, Thornton JM. 2003. Structural characterisation and functional significance of transient protein-protein interactions. J Mol Biol 325(5):991-1018.
    • (2003) J Mol Biol , vol.325 , Issue.5 , pp. 991-1018
    • Nooren, I.M.1    Thornton, J.M.2
  • 38
    • 0037229456 scopus 로고    scopus 로고
    • Rost B. Analysing six types of protein-protein interfaces
    • Ofran Y, Rost B. Analysing six types of protein-protein interfaces. 2003. J Mol Biol 325(2):377-387.
    • (2003) J Mol Biol , vol.325 , Issue.2 , pp. 377-387
    • Ofran, Y.1
  • 40
    • 1842405464 scopus 로고    scopus 로고
    • Studies of protein-protein interfaces: A statistical analysis of the hydrophobic effect
    • Tsai CJ, Lin SL, Wolfson HJ, Nussinov R. 1997. Studies of protein-protein interfaces: A statistical analysis of the hydrophobic effect. Protein Sci 16(1):53-64.
    • (1997) Protein Sci , vol.16 , Issue.1 , pp. 53-64
    • Tsai, C.J.1    Lin, S.L.2    Wolfson, H.J.3    Nussinov, R.4
  • 41
    • 0028332007 scopus 로고
    • A role for surface hydrophobicity in protein-protein recognition
    • Young L, Jernigan RL, Covell DG. 1994. A role for surface hydrophobicity in protein-protein recognition. Protein Sci 3(5):717-729.
    • (1994) Protein Sci , vol.3 , Issue.5 , pp. 717-729
    • Young, L.1    Jernigan, R.L.2    Covell, D.G.3
  • 42
    • 0030028728 scopus 로고    scopus 로고
    • Principles of protein-protein interactions
    • Jones S, Thornton JM. 1996. Principles of protein-protein interactions. Proc Natl Acad Sci USA 93(1):13-20.
    • (1996) Proc Natl Acad Sci USA , vol.93 , Issue.1 , pp. 13-20
    • Jones, S.1    Thornton, J.M.2
  • 43
    • 0041312697 scopus 로고    scopus 로고
    • Diversity of protein-protein interactions
    • Nooren IM, Thornton JM. 2003. Diversity of protein-protein interactions. EMBO J 22(14):3486-3492.
    • (2003) EMBO J , vol.22 , Issue.14 , pp. 3486-3492
    • Nooren, I.M.1    Thornton, J.M.2
  • 44
    • 0032479179 scopus 로고    scopus 로고
    • Anatomy of hot spots in protein interfaces
    • Bogan AA, Thorn KS. 1998. Anatomy of hot spots in protein interfaces. J Mol Biol 280(1):1-9.
    • (1998) J Mol Biol , vol.280 , Issue.1 , pp. 1-9
    • Bogan, A.A.1    Thorn, K.S.2
  • 45
    • 0028916599 scopus 로고
    • A hot spot of binding energy in a hormone-receptor interface
    • Clackson T, Wells JA. 1995. A hot spot of binding energy in a hormone-receptor interface. Science 267(5196):383-386.
    • (1995) Science , vol.267 , Issue.5196 , pp. 383-386
    • Clackson, T.1    Wells, J.A.2
  • 46
  • 47
    • 0036468396 scopus 로고    scopus 로고
    • Protein-protein association kinetics and protein docking
    • Camacho CJ, Vajda S. 2002. Protein-protein association kinetics and protein docking. Curr Opin Struct Biol 12(1):36-40.
    • (2002) Curr Opin Struct Biol , vol.12 , Issue.1 , pp. 36-40
    • Camacho, C.J.1    Vajda, S.2
  • 48
    • 0036306236 scopus 로고    scopus 로고
    • On the role of electrostatic interactions in the design of protein-protein interfaces
    • Sheinerman FB, Honig B. 2002. On the role of electrostatic interactions in the design of protein-protein interfaces. J Mol Biol 318(1):161-177.
    • (2002) J Mol Biol , vol.318 , Issue.1 , pp. 161-177
    • Sheinerman, F.B.1    Honig, B.2
  • 49
    • 0031565725 scopus 로고    scopus 로고
    • Prediction of protein-protein interaction sites using patch analysis
    • Jones S, Thornton JM. 1997. Prediction of protein-protein interaction sites using patch analysis. J Mol Biol 272(1):133-143.
    • (1997) J Mol Biol , vol.272 , Issue.1 , pp. 133-143
    • Jones, S.1    Thornton, J.M.2
  • 50
    • 0030997363 scopus 로고    scopus 로고
    • Hydrophobic patches on protein subunit interfaces: Characteristics and prediction
    • Lijnzaad P, Argos P. 1997. Hydrophobic patches on protein subunit interfaces: Characteristics and prediction. Proteins 28(3):333-343.
    • (1997) Proteins , vol.28 , Issue.3 , pp. 333-343
    • Lijnzaad, P.1    Argos, P.2
  • 51
    • 1542390499 scopus 로고    scopus 로고
    • Identification of protein-protein interaction sites from docking energy landscapes
    • Fernández-Recio J, Totrov M, Abagyan R. 2004. Identification of protein-protein interaction sites from docking energy landscapes. J Mol Biol 335(3):843-865.
    • (2004) J Mol Biol , vol.335 , Issue.3 , pp. 843-865
    • Fernández-Recio, J.1    Totrov, M.2    Abagyan, R.3
  • 52
    • 33947360625 scopus 로고    scopus 로고
    • PIER: Protein interface recognition for structural proteomics
    • Kufareva I, Budagyan L, Raush E, Totrov M, Abagyan R. 2007. PIER: Protein interface recognition for structural proteomics. Proteins 67(2):400-417.
    • (2007) Proteins , vol.67 , Issue.2 , pp. 400-417
    • Kufareva, I.1    Budagyan, L.2    Raush, E.3    Totrov, M.4    Abagyan, R.5
  • 53
    • 11144325691 scopus 로고
    • Partial least squares regression: A tutorial
    • Geladi P, Kowalski B. 1986. Partial least squares regression: A tutorial. Analytica Chimica Acta 185:1-17.
    • (1986) Analytica Chimica Acta , vol.185 , pp. 1-17
    • Geladi, P.1    Kowalski, B.2
  • 54
    • 84872115717 scopus 로고    scopus 로고
    • Pleckstrin homology (PH) domains and phosphoinositides
    • Lemmon MA. 2007. Pleckstrin homology (PH) domains and phosphoinositides. Biochem Soc Symp 74:81-93.
    • (2007) Biochem Soc Symp , vol.74 , pp. 81-93
    • Lemmon, M.A.1
  • 55
    • 38549092474 scopus 로고    scopus 로고
    • Membrane recognition by phospholipid-binding domains
    • Lemmon MA. 2008. Membrane recognition by phospholipid-binding domains. Nat Rev Mol Cell Biol 9(2):99-111.
    • (2008) Nat Rev Mol Cell Biol , vol.9 , Issue.2 , pp. 99-111
    • Lemmon, M.A.1
  • 58
    • 1842861590 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions: The CAPRI experiment, its evaluation and implications
    • Wodak SJ, Méndez R. 2004. Prediction of protein-protein interactions: The CAPRI experiment, its evaluation and implications. Curr Opin Struct Biol 14(2):242-249.
    • (2004) Curr Opin Struct Biol , vol.14 , Issue.2 , pp. 242-249
    • Wodak, S.J.1    Méndez, R.2
  • 59
    • 41949099167 scopus 로고    scopus 로고
    • Recognition-induced conformational changes in protein-protein docking
    • Lensink MF, Mendez R. 2008. Recognition-induced conformational changes in protein-protein docking. Curr Pharm Biotechnol 9(2):77-86.
    • (2008) Curr Pharm Biotechnol , vol.9 , Issue.2 , pp. 77-86
    • Lensink, M.F.1    Mendez, R.2
  • 60
    • 33745298429 scopus 로고    scopus 로고
    • Rational design of inhibitors that bind to inactive kinase conformations
    • Liu Y, Gray NS. 2006. Rational design of inhibitors that bind to inactive kinase conformations. Nat Chem Biol 2(7):358-364.
    • (2006) Nat Chem Biol , vol.2 , Issue.7 , pp. 358-364
    • Liu, Y.1    Gray, N.S.2
  • 62
    • 0035037143 scopus 로고    scopus 로고
    • A proposed structural model for amyloid fibril elongation: Domain swapping forms an interdigitating beta-structure polymer
    • Sinha N, Tsai CJ, Nussinov R. 2001. A proposed structural model for amyloid fibril elongation: Domain swapping forms an interdigitating beta-structure polymer. Protein Eng 14(2):93-103.
    • (2001) Protein Eng , vol.14 , Issue.2 , pp. 93-103
    • Sinha, N.1    Tsai, C.J.2    Nussinov, R.3
  • 63
    • 41949131198 scopus 로고    scopus 로고
    • Sequence and structural determinants of strand swapping in cadherin domains: Do all cadherins bind through the same adhesive interface?
    • Posy S, Shapiro L, Honig B. 2008. Sequence and structural determinants of strand swapping in cadherin domains: Do all cadherins bind through the same adhesive interface? J Mol Biol 378(4):952-966.
    • (2008) J Mol Biol , vol.378 , Issue.4 , pp. 952-966
    • Posy, S.1    Shapiro, L.2    Honig, B.3
  • 64
    • 41949111630 scopus 로고    scopus 로고
    • Recent progress and future directions in protein-protein docking
    • Ritchie DW. 2008. Recent progress and future directions in protein-protein docking. Curr Protein Pept Sci 9(1):1-15.
    • (2008) Curr Protein Pept Sci , vol.9 , Issue.1 , pp. 1-15
    • Ritchie, D.W.1
  • 65
    • 21644447570 scopus 로고    scopus 로고
    • Improving CAPRI predictions: Optimized desolvation for rigid-body docking
    • Fernandez-Recio J, Abagyan R, Totrov M. 2005. Improving CAPRI predictions: Optimized desolvation for rigid-body docking. Proteins 60(2):308-313.
    • (2005) Proteins , vol.60 , Issue.2 , pp. 308-313
    • Fernandez-Recio, J.1    Abagyan, R.2    Totrov, M.3
  • 66
    • 0028410583 scopus 로고
    • Detailed ab initio prediction of lysozyme-antibody complex with 1.6 A accuracy
    • Totrov M, Abagyan R. 1994. Detailed ab initio prediction of lysozyme-antibody complex with 1.6 A accuracy. Nat Struct Biol 1(4):259-263.
    • (1994) Nat Struct Biol , vol.1 , Issue.4 , pp. 259-263
    • Totrov, M.1    Abagyan, R.2
  • 67
    • 0027955787 scopus 로고
    • Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins
    • Abagyan R, Totrov M. 1994. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J Mol Biol 235(3):983-1002.
    • (1994) J Mol Biol , vol.235 , Issue.3 , pp. 983-1002
    • Abagyan, R.1    Totrov, M.2
  • 68
    • 50549092426 scopus 로고    scopus 로고
    • Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions
    • Ritchie DW, Kozakov D, Vajda S. 2008. Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions. Bioinformatics 24(17):1865-1873.
    • (2008) Bioinformatics , vol.24 , Issue.17 , pp. 1865-1873
    • Ritchie, D.W.1    Kozakov, D.2    Vajda, S.3
  • 69
    • 0036606483 scopus 로고    scopus 로고
    • Principles of docking: An overview of search algorithms and a guide to scoring functions
    • Halperin I, Ma B, Wolfson H, Nussinov R. 2002. Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins 47(4):409-443.
    • (2002) Proteins , vol.47 , Issue.4 , pp. 409-443
    • Halperin, I.1    Ma, B.2    Wolfson, H.3    Nussinov, R.4
  • 70
    • 0036468385 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions by docking methods
    • Smith GR, Sternberg MJ. 2002. Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol 12(1):28-35.
    • (2002) Curr Opin Struct Biol , vol.12 , Issue.1 , pp. 28-35
    • Smith, G.R.1    Sternberg, M.J.2
  • 71
    • 0038021436 scopus 로고    scopus 로고
    • Assessment of blind predictions of protein-protein interactions: Current status of docking methods
    • Méndez R, Leplae R, Maria LD, Wodak SJ. 2003. Assessment of blind predictions of protein-protein interactions: Current status of docking methods. Proteins 52(1):51-67.
    • (2003) Proteins , vol.52 , Issue.1 , pp. 51-67
    • Méndez, R.1    Leplae, R.2    Maria, L.D.3    Wodak, S.J.4
  • 72
    • 21644469377 scopus 로고    scopus 로고
    • Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures
    • Méndez R, Leplae R, Lensink MF, Wodak SJ. 2005. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins 60(2):150-169.
    • (2005) Proteins , vol.60 , Issue.2 , pp. 150-169
    • Méndez, R.1    Leplae, R.2    Lensink, M.F.3    Wodak, S.J.4
  • 73
    • 0038161052 scopus 로고    scopus 로고
    • Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
    • Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. 2003. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 331(1):281-299.
    • (2003) J Mol Biol , vol.331 , Issue.1 , pp. 281-299
    • Gray, J.J.1    Moughon, S.2    Wang, C.3    Schueler-Furman, O.4    Kuhlman, B.5    Rohl, C.A.6    Baker, D.7
  • 74
    • 36749045652 scopus 로고    scopus 로고
    • Protein-protein docking: Progress in CAPRI rounds 6-12 using a combination of methods: The introduction of steered solvated molecular dynamics
    • Heifetz A, Pal S, Smith GR. 2007. Protein-protein docking: Progress in CAPRI rounds 6-12 using a combination of methods: The introduction of steered solvated molecular dynamics. Proteins 69(4):816-822.
    • (2007) Proteins , vol.69 , Issue.4 , pp. 816-822
    • Heifetz, A.1    Pal, S.2    Smith, G.R.3
  • 75
    • 36749082073 scopus 로고    scopus 로고
    • A holistic approach to protein docking
    • Qin S, Zhou H-X. 2007. A holistic approach to protein docking. Proteins 69(4):743-749.
    • (2007) Proteins , vol.69 , Issue.4 , pp. 743-749
    • Qin, S.1    Zhou, H.-X.2
  • 76
    • 44349160733 scopus 로고    scopus 로고
    • Protein-protein docking by simulating the process of association subject to biochemical constraints
    • Motiejunas D, Gabdoulline R, Wang T, Feldman-Salit A, Johann T, Winn PJ, Wade RC. 2008. Protein-protein docking by simulating the process of association subject to biochemical constraints. Proteins 71(4):1955-1969.
    • (2008) Proteins , vol.71 , Issue.4 , pp. 1955-1969
    • Motiejunas, D.1    Gabdoulline, R.2    Wang, T.3    Feldman-Salit, A.4    Johann, T.5    Winn, P.J.6    Wade, R.C.7
  • 77
    • 0036510961 scopus 로고    scopus 로고
    • Identification and mapping of small-molecule binding sites in proteins: Computational tools for structure-based drug design
    • Sotriffer C, Klebe G. 2002. Identification and mapping of small-molecule binding sites in proteins: Computational tools for structure-based drug design. Farmaco 57(3):243-251.
    • (2002) Farmaco , vol.57 , Issue.3 , pp. 243-251
    • Sotriffer, C.1    Klebe, G.2
  • 79
    • 21044444449 scopus 로고    scopus 로고
    • Pocketome via comprehensive identification and classification of ligand binding envelopes
    • An J, Totrov M, Abagyan R. 2005. Pocketome via comprehensive identification and classification of ligand binding envelopes. Mol Cell Proteomics 4(6):752-761.
    • (2005) Mol Cell Proteomics , vol.4 , Issue.6 , pp. 752-761
    • An, J.1    Totrov, M.2    Abagyan, R.3
  • 80
    • 47249102090 scopus 로고    scopus 로고
    • A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)
    • Bottegoni G, Kufareva I, Totrov M, Abagyan R. 2008. A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). J Comput Aided Mol Des 22(5):311-325.
    • (2008) J Comput Aided Mol Des , vol.22 , Issue.5 , pp. 311-325
    • Bottegoni, G.1    Kufareva, I.2    Totrov, M.3    Abagyan, R.4
  • 81
    • 41349095752 scopus 로고    scopus 로고
    • New method for the assessment of all drug-like pockets across a structural genome
    • Nicola G, Smith CA, Abagyan R. 2008. New method for the assessment of all drug-like pockets across a structural genome. J Comput Biol 15(3):231-240.
    • (2008) J Comput Biol , vol.15 , Issue.3 , pp. 231-240
    • Nicola, G.1    Smith, C.A.2    Abagyan, R.3
  • 82
    • 33749506205 scopus 로고    scopus 로고
    • Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening
    • Laurie ATR, Jackson RM. 2006. Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening. Curr Protein Pept Sci 7(5):395-406.
    • (2006) Curr Protein Pept Sci , vol.7 , Issue.5 , pp. 395-406
    • Laurie, A.1    Jackson, R.M.2
  • 83
    • 0031302358 scopus 로고    scopus 로고
    • Flexible protein-ligand docking by global energy optimization in internal coordinates
    • Totrov M, Abagyan R. 1997. Flexible protein-ligand docking by global energy optimization in internal coordinates. Proteins 29(Suppl 1):215-220.
    • (1997) Proteins , vol.29 , pp. 215-220
    • Totrov, M.1    Abagyan, R.2
  • 84
    • 41949132916 scopus 로고    scopus 로고
    • Flexible ligand docking to multiple receptor conformations: A practical alternative
    • Totrov M, Abagyan R. 2008. Flexible ligand docking to multiple receptor conformations: A practical alternative. Curr Opin Struct Biol 18(2):178-184.
    • (2008) Curr Opin Struct Biol , vol.18 , Issue.2 , pp. 178-184
    • Totrov, M.1    Abagyan, R.2
  • 85
    • 0027185404 scopus 로고
    • A method to configure protein side-chains from the main-chain trace in homology modelling
    • Eisenmenger F, Argos P, Abagyan R. 1993. A method to configure protein side-chains from the main-chain trace in homology modelling. J Mol Biol 231(3):849-860.
    • (1993) J Mol Biol , vol.231 , Issue.3 , pp. 849-860
    • Eisenmenger, F.1    Argos, P.2    Abagyan, R.3
  • 86
    • 31544450787 scopus 로고    scopus 로고
    • Novel procedure for modeling ligand/receptor induced fit effects
    • Sherman W, Day T, Jacobson MP, Friesner RA, Farid R. 2006. Novel procedure for modeling ligand/receptor induced fit effects. J Med Chem 49(2):534-553.
    • (2006) J Med Chem , vol.49 , Issue.2 , pp. 534-553
    • Sherman, W.1    Day, T.2    Jacobson, M.P.3    Friesner, R.A.4    Farid, R.5
  • 87
    • 0033137131 scopus 로고    scopus 로고
    • Prediction of the binding energy for small molecules, peptides and proteins
    • Schapira M, Totrov M, Abagyan R. 1999. Prediction of the binding energy for small molecules, peptides and proteins. J Mol Recog 12(3):177-190.
    • (1999) J Mol Recog , vol.12 , Issue.3 , pp. 177-190
    • Schapira, M.1    Totrov, M.2    Abagyan, R.3
  • 88
    • 60549086155 scopus 로고    scopus 로고
    • Four-dimensional docking: A fast and accurate account of discrete receptor flexibility in ligand docking
    • Bottegoni G, Kufareva I, Totrov M, Abagyan R. 2009. Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking. Journal of Medicinal Chemistry 52(2):397-406.
    • (2009) Journal of Medicinal Chemistry , vol.52 , Issue.2 , pp. 397-406
    • Bottegoni, G.1    Kufareva, I.2    Totrov, M.3    Abagyan, R.4
  • 89
    • 58149102648 scopus 로고    scopus 로고
    • Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states
    • Kufareva I, Abagyan R. 2008. Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states. Journal of Medicinal Chemistry 51(24):7921-7932.
    • (2008) Journal of Medicinal Chemistry , vol.51 , Issue.24 , pp. 7921-7932
    • Kufareva, I.1    Abagyan, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.