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Volumn 70, Issue 4, 2008, Pages 1540-1550

A knowledge-based forcefield for protein-protein interface design

Author keywords

Antibody; Binding energy; Forcefield; Protein design; Protein protein docking

Indexed keywords

ARTICLE; ATOM; BINDING AFFINITY; CALCULATION; FORCE; FORCE FIELD; KNOWLEDGE BASE; MATHEMATICAL ANALYSIS; PERFORMANCE; PRIORITY JOURNAL; PROBABILITY; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION;

EID: 39749180316     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21694     Document Type: Article
Times cited : (14)

References (43)
  • 1
    • 0036468385 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions by docking methods
    • Smith GR, Sternberg MJ. Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol 2002;12:28-35.
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 28-35
    • Smith, G.R.1    Sternberg, M.J.2
  • 3
    • 0038021436 scopus 로고    scopus 로고
    • Assessment of blind predictions of protein-protein interactions: Current status of docking methods
    • Mendez R, Leplae R, Maria LD, Wodak SJ. Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins 2003;52:51-67.
    • (2003) Proteins , vol.52 , pp. 51-67
    • Mendez, R.1    Leplae, R.2    Maria, L.D.3    Wodak, S.J.4
  • 4
    • 1242270553 scopus 로고    scopus 로고
    • Protein-protein docking: Is the glass half-full or half-empty?
    • Vajda S, Camacho CJ. Protein-protein docking: is the glass half-full or half-empty? Trends Biotechnol 2004;22:110-116.
    • (2004) Trends Biotechnol , vol.22 , pp. 110-116
    • Vajda, S.1    Camacho, C.J.2
  • 5
    • 0038526303 scopus 로고    scopus 로고
    • ZDOCK: An initial-stage protein-docking algorithm
    • Chen R, Li L, Weng Z. ZDOCK: an initial-stage protein-docking algorithm. Proteins 2003;52:80-87.
    • (2003) Proteins , vol.52 , pp. 80-87
    • Chen, R.1    Li, L.2    Weng, Z.3
  • 6
    • 0038583687 scopus 로고    scopus 로고
    • Protein-protein docking with a reduced protein model accounting for side-chain flexibility
    • Zacharias M. Protein-protein docking with a reduced protein model accounting for side-chain flexibility. Protein Sci 2003;12:1271-1282.
    • (2003) Protein Sci , vol.12 , pp. 1271-1282
    • Zacharias, M.1
  • 7
    • 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. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 2003;331:281-299.
    • (2003) J Mol Biol , vol.331 , 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
  • 8
    • 23844455986 scopus 로고    scopus 로고
    • Adaptation of a fast fourier transform-based docking algorithm for protein design
    • Huang PS, Love JJ, Mayo SL. Adaptation of a fast fourier transform-based docking algorithm for protein design. J Comput Chem 2005;26:1222-1232.
    • (2005) J Comput Chem , vol.26 , pp. 1222-1232
    • Huang, P.S.1    Love, J.J.2    Mayo, S.L.3
  • 9
    • 0017021957 scopus 로고
    • Medium-and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins
    • Tanaka S, Scheraga HA. Medium-and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. Macromolecules 1976;9:945-950.
    • (1976) Macromolecules , vol.9 , pp. 945-950
    • Tanaka, S.1    Scheraga, H.A.2
  • 10
    • 0025341310 scopus 로고
    • Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of focal structures in globular proteins
    • Sippl MJ. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of focal structures in globular proteins. J Mol Biol 1990;213:859-883.
    • (1990) J Mol Biol , vol.213 , pp. 859-883
    • Sippl, M.J.1
  • 11
    • 0031566950 scopus 로고    scopus 로고
    • Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation
    • Bahar I, Jernigan RL. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J Mol Biol 1997;266:195-214.
    • (1997) J Mol Biol , vol.266 , pp. 195-214
    • Bahar, I.1    Jernigan, R.L.2
  • 12
    • 0035882533 scopus 로고    scopus 로고
    • A distance-dependent atomic knowledge-based potential for improved protein structure selection
    • Lu H, Skolnick J. A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins 2001;44:223-232.
    • (2001) Proteins , vol.44 , pp. 223-232
    • Lu, H.1    Skolnick, J.2
  • 13
    • 24644464131 scopus 로고    scopus 로고
    • An atomic environment potential for use in protein structure prediction
    • Summa CM, Levitt M, Degrado WF. An atomic environment potential for use in protein structure prediction. J Mol Biol 2005;352:986-1001.
    • (2005) J Mol Biol , vol.352 , pp. 986-1001
    • Summa, C.M.1    Levitt, M.2    Degrado, W.F.3
  • 14
    • 0036667733 scopus 로고    scopus 로고
    • Knowledge-based potential functions in protein design
    • Russ WP, Ranganathan R. Knowledge-based potential functions in protein design. Curr Opin Struct Biol 2002;12:447-452.
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 447-452
    • Russ, W.P.1    Ranganathan, R.2
  • 15
    • 0036838311 scopus 로고    scopus 로고
    • Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
    • Zhou H, Zhou Y. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci 2002;11:2714-2726.
    • (2002) Protein Sci , vol.11 , pp. 2714-2726
    • Zhou, H.1    Zhou, Y.2
  • 16
    • 2642524483 scopus 로고    scopus 로고
    • A physical reference state unifies the structure-derived potential of mean force for protein folding and binding
    • Liu S, Zhang C, Zhou H, Zhou Y. A physical reference state unifies the structure-derived potential of mean force for protein folding and binding. Proteins 2004;56:93-101.
    • (2004) Proteins , vol.56 , pp. 93-101
    • Liu, S.1    Zhang, C.2    Zhou, H.3    Zhou, Y.4
  • 17
    • 0036467249 scopus 로고    scopus 로고
    • Potential of mean force for protein-protein interaction studies
    • Jiang L, Gao Y, Mao F, Liu Z, Lai L. Potential of mean force for protein-protein interaction studies. Proteins 2002;46:190-196.
    • (2002) Proteins , vol.46 , pp. 190-196
    • Jiang, L.1    Gao, Y.2    Mao, F.3    Liu, Z.4    Lai, L.5
  • 18
    • 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 AV, 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
  • 19
    • 0033562633 scopus 로고    scopus 로고
    • Use of pair potentials across protein interfaces in screening predicted docked complexes
    • Moont G, Gabb HA, Sternberg MJ. Use of pair potentials across protein interfaces in screening predicted docked complexes. Proteins 1999;35:364-373.
    • (1999) Proteins , vol.35 , pp. 364-373
    • Moont, G.1    Gabb, H.A.2    Sternberg, M.J.3
  • 20
    • 0037340493 scopus 로고    scopus 로고
    • Development of unified statistical potentials describing protein-protein interactions
    • Lu H, Lu L, Skolnick J. Development of unified statistical potentials describing protein-protein interactions. Biophys J 2003;84:1895-1901.
    • (2003) Biophys J , vol.84 , pp. 1895-1901
    • Lu, H.1    Lu, L.2    Skolnick, J.3
  • 21
    • 1842507022 scopus 로고    scopus 로고
    • A new, structurally non-redundant, diverse data set of protein-protein interfaces and its implications
    • Keskin O, Tsai CJ, Wolfson H, Nussinov R. A new, structurally non-redundant, diverse data set of protein-protein interfaces and its implications. Protein Sci 2004;13:1043-1055.
    • (2004) Protein Sci , vol.13 , pp. 1043-1055
    • Keskin, O.1    Tsai, C.J.2    Wolfson, H.3    Nussinov, R.4
  • 22
    • 39749192264 scopus 로고    scopus 로고
    • DeLano Scientific
    • DeLano W. The PyMOL molecular graphics system. DeLano Scientific, 2002. http://www.pymol.org
    • (2002)
    • DeLano, W.1
  • 23
    • 0042710087 scopus 로고    scopus 로고
    • Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies
    • Massova I, Kollman PA. Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies. J Am Chem Soc 1999;121:8133-8143.
    • (1999) J Am Chem Soc , vol.121 , pp. 8133-8143
    • Massova, I.1    Kollman, P.A.2
  • 24
    • 39749120810 scopus 로고    scopus 로고
    • Williams T, Kelly C. Gnuplot: an interactive plotting program. 2004, version 4.0, acspline option
    • Williams T, Kelly C. Gnuplot: an interactive plotting program. 2004. http://www.gnuplot.info/ version 4.0, "acspline" option.
  • 26
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • Lee B, Richards FM. The interpretation of protein structures: estimation of static accessibility. J Mol Biol 1971;55:379-400.
    • (1971) J Mol Biol , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 27
    • 0034641749 scopus 로고    scopus 로고
    • Native protein sequences are close to optimal for their structures
    • Kuhlman B, Baker D. Native protein sequences are close to optimal for their structures. Proc Natl Acad Sci USA 2000;97:10383-10388.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 10383-10388
    • Kuhlman, B.1    Baker, D.2
  • 28
    • 39749118953 scopus 로고    scopus 로고
    • Rosetta software package version 2.1. Available from the University of Washington, Seattle. 2006
    • Rosetta software package version 2.1. Available from the University of Washington, Seattle. 2006. http://www.rosettacommons.org/
  • 29
    • 0035342450 scopus 로고    scopus 로고
    • Residue frequencies and pairing preferences at protein-protein interfaces
    • Glaser F, Steinberg DM, Vakser IA, Ben-Tal N. Residue frequencies and pairing preferences at protein-protein interfaces. Proteins 2001;43:89-102.
    • (2001) Proteins , vol.43 , pp. 89-102
    • Glaser, F.1    Steinberg, D.M.2    Vakser, I.A.3    Ben-Tal, N.4
  • 30
    • 0003187567 scopus 로고    scopus 로고
    • The atomic structure of protein-protein recognition sites
    • Lo Conte L, Chothia C, Janin J. The atomic structure of protein-protein recognition sites. J Mol Biol 1999;285:2177-2198.
    • (1999) J Mol Biol , vol.285 , pp. 2177-2198
    • Lo Conte, L.1    Chothia, C.2    Janin, J.3
  • 31
    • 33745323376 scopus 로고    scopus 로고
    • Trends in antibody sequence changes during the somatic hypermutation process
    • Clark LA, Ganesan S, Papp S, Van Vlijmen HW. Trends in antibody sequence changes during the somatic hypermutation process. J Immunol 2006;177:333-340.
    • (2006) J Immunol , vol.177 , pp. 333-340
    • Clark, L.A.1    Ganesan, S.2    Papp, S.3    Van Vlijmen, H.W.4
  • 32
    • 0030005250 scopus 로고    scopus 로고
    • Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides
    • Wimley WC, Creamer TP, White SH. Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides. Biochemistry 1996;35:5109-5124.
    • (1996) Biochemistry , vol.35 , pp. 5109-5124
    • Wimley, W.C.1    Creamer, T.P.2    White, S.H.3
  • 33
    • 0033405041 scopus 로고    scopus 로고
    • Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48g7
    • Chong LT, Duan Y, Wang L, Massova I, Kollman PA. Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48g7. Proc Natl Acad Sci USA 1999;96:14330-14335.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 14330-14335
    • Chong, L.T.1    Duan, Y.2    Wang, L.3    Massova, I.4    Kollman, P.A.5
  • 35
    • 0034900495 scopus 로고    scopus 로고
    • Free energy decomposition of protein-protein interactions
    • Noskov SY, Lim C. Free energy decomposition of protein-protein interactions. Biophys J 2001;81:737-750.
    • (2001) Biophys J , vol.81 , pp. 737-750
    • Noskov, S.Y.1    Lim, C.2
  • 37
    • 0000372879 scopus 로고    scopus 로고
    • Protein-protein interactions: Interface structure, binding thermodynamics, and mutational analysis
    • Stites WE. Protein-protein interactions: interface structure, binding thermodynamics, and mutational analysis. Chem Rev 1997;97:1233-1250.
    • (1997) Chem Rev , vol.97 , pp. 1233-1250
    • Stites, W.E.1
  • 40
    • 0035896029 scopus 로고    scopus 로고
    • Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: Implications for protein design and structural genomics
    • Looger LL, Hellinga HW. Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics. J Mol Biol 2001;307:429-445.
    • (2001) J Mol Biol , vol.307 , pp. 429-445
    • Looger, L.L.1    Hellinga, H.W.2
  • 41
    • 0027764344 scopus 로고
    • Protein sequence alignments: A strategy for the hierarchical analysis of residue conservation
    • Livingstone CD, Barton GJ. Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation. Comput Appl Biosci 1993;9:745-756.
    • (1993) Comput Appl Biosci , vol.9 , pp. 745-756
    • Livingstone, C.D.1    Barton, G.J.2
  • 42
    • 0030762021 scopus 로고    scopus 로고
    • Coupling backbone flexibility and amino acid sequence selection in protein design
    • Su A, Mayo SL. Coupling backbone flexibility and amino acid sequence selection in protein design. Protein Sci 1997;6:1701-1707.
    • (1997) Protein Sci , vol.6 , pp. 1701-1707
    • Su, A.1    Mayo, S.L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.