메뉴 건너뛰기




Volumn 68, Issue 1, 2007, Pages 57-66

Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys

Author keywords

Contact potential; Delauney tessellation (DT); Four body potential; Two body potential

Indexed keywords

ALANINE; AMINO ACID; ARGININE; ASPARAGINE; ASPARTIC ACID; CYSTEINE; GLUTAMIC ACID; GLUTAMINE; GLYCINE; HISTIDINE; ISOLEUCINE; LEUCINE; LYSINE; METHIONINE; PHENYLALANINE; PROLINE; PROTEIN; SERINE; THREONINE; TRYPTOPHAN; TYROSINE; VALINE;

EID: 34249938371     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21362     Document Type: Article
Times cited : (67)

References (46)
  • 3
    • 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
  • 7
    • 0016610491 scopus 로고
    • Computer simulation of protein folding
    • Levitt M, Warshel A. Computer simulation of protein folding. Nature 1975;253:694-698.
    • (1975) Nature , vol.253 , pp. 694-698
    • Levitt, M.1    Warshel, A.2
  • 8
    • 0017157584 scopus 로고
    • A simplified representation of protein conformation for rapid simulation of protein folding
    • Levitt M. A simplified representation of protein conformation for rapid simulation of protein folding. J Mol Biol 1976;104:59-107.
    • (1976) J Mol Biol , vol.104 , pp. 59-107
    • Levitt, M.1
  • 9
    • 33646786723 scopus 로고    scopus 로고
    • Empirical potential function for simplified protein models: Combining contact and local sequence-structure descriptors
    • Zhang J, Chen R, Liang J. Empirical potential function for simplified protein models: combining contact and local sequence-structure descriptors. Proteins 2006;63:949-960.
    • (2006) Proteins , vol.63 , pp. 949-960
    • Zhang, J.1    Chen, R.2    Liang, J.3
  • 10
    • 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;9:925-950.
    • (1976) Macromolecules , vol.9 , pp. 925-950
    • Tanaka, S.1    Scheraga, H.A.2
  • 11
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
    • Miyazawa S, Jernigan RL. Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation. Macromolecules 1985;18:534-552.
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 12
    • 0029919190 scopus 로고    scopus 로고
    • Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
    • Miyazawa S, Jernigan RL. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol 1996;256:623-644.
    • (1996) J Mol Biol , vol.256 , pp. 623-644
    • Miyazawa, S.1    Jernigan, R.L.2
  • 13
    • 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
  • 14
    • 0025008445 scopus 로고
    • Identification of native protein folds amongst a large number of incorrect models - the calculation of low-energy conformations from potentials of mean force
    • Hendlich M, Lackner P, Weitckus S, Floeckner H, Froschauer R, Gottsbacher K, Casari G, Sippl MJ. Identification of native protein folds amongst a large number of incorrect models - the calculation of low-energy conformations from potentials of mean force. J Mol Biol 1990;216:167-180.
    • (1990) J Mol Biol , vol.216 , pp. 167-180
    • Hendlich, M.1    Lackner, P.2    Weitckus, S.3    Floeckner, H.4    Froschauer, R.5    Gottsbacher, K.6    Casari, G.7    Sippl, M.J.8
  • 15
    • 0026785519 scopus 로고
    • Contact potential that recognizes the correct folding of globular proteins
    • Maiorov VN, Crippen GM. Contact potential that recognizes the correct folding of globular proteins. J Mol Biol 1992;277:676-888.
    • (1992) J Mol Biol , vol.277 , pp. 676-888
    • Maiorov, V.N.1    Crippen, G.M.2
  • 16
    • 0030983768 scopus 로고    scopus 로고
    • Derivation and testing of pair potentials for protein folding. When is the quasi-chemical approximation correct?
    • Skolnick J, Jaroszewski L, Kolinski A, Godzik A. Derivation and testing of pair potentials for protein folding. When is the quasi-chemical approximation correct? Protein Sci 1997;6:676-688.
    • (1997) Protein Sci , vol.6 , pp. 676-688
    • Skolnick, J.1    Jaroszewski, L.2    Kolinski, A.3    Godzik, A.4
  • 17
    • 0033970623 scopus 로고    scopus 로고
    • Derivation of protein-specific pair potentials based on weak sequence fragment similarity
    • Skolnick J, Kolinski A, Ortiz A. Derivation of protein-specific pair potentials based on weak sequence fragment similarity. Proteins 2000;38:3-16.
    • (2000) Proteins , vol.38 , pp. 3-16
    • Skolnick, J.1    Kolinski, A.2    Ortiz, A.3
  • 18
    • 0030596063 scopus 로고    scopus 로고
    • How to derive a protein folding potentials? A new approach to an old problem
    • Mirny LA, Shakhnovich EI. How to derive a protein folding potentials? A new approach to an old problem. J Mol Biol 1996;264:1164-1179.
    • (1996) J Mol Biol , vol.264 , pp. 1164-1179
    • Mirny, L.A.1    Shakhnovich, E.I.2
  • 19
    • 0029909384 scopus 로고    scopus 로고
    • An interative method for extracting energy-like quantities from protein structures
    • Thomas PD, Dill KA. An interative method for extracting energy-like quantities from protein structures. Proc Natl Acad Sci USA 1996;93:11628-11633.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 11628-11633
    • Thomas, P.D.1    Dill, K.A.2
  • 20
    • 0034237798 scopus 로고    scopus 로고
    • On the design and analysis of protein folding potentials
    • Tobi D, Shafran G, Linial N, Elber R. On the design and analysis of protein folding potentials. Proteins 2000;40:71-85.
    • (2000) Proteins , vol.40 , pp. 71-85
    • Tobi, D.1    Shafran, G.2    Linial, N.3    Elber, R.4
  • 21
    • 0035865950 scopus 로고    scopus 로고
    • Learning effective amino acid interactions through iterative stochastic techniques
    • Micheletti C, Seno F, Banavar JR, Maritan A. Learning effective amino acid interactions through iterative stochastic techniques. Proteins 2001;42:422-431.
    • (2001) Proteins , vol.42 , pp. 422-431
    • Micheletti, C.1    Seno, F.2    Banavar, J.R.3    Maritan, A.4
  • 22
    • 0030968991 scopus 로고    scopus 로고
    • Empirical potentials and functions for protein folding and binding
    • Vajda S, Sippl M, Novotny J. Empirical potentials and functions for protein folding and binding. Curr Opin Struct Biol 1997;7:222-228.
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 222-228
    • Vajda, S.1    Sippl, M.2    Novotny, J.3
  • 23
    • 0030584681 scopus 로고    scopus 로고
    • Knowledge-based potentials for protein folding: What can we learn from known protein structures?
    • Godzik A. Knowledge-based potentials for protein folding: what can we learn from known protein structures? Structure 1996;4:363-366.
    • (1996) Structure , vol.4 , pp. 363-366
    • Godzik, A.1
  • 24
    • 0029942661 scopus 로고    scopus 로고
    • Structure-derived potentials and protein simulations
    • Jernigan RL, Bahar I. Structure-derived potentials and protein simulations. Curr Opin Struct Biol 1996;6:195-209.
    • (1996) Curr Opin Struct Biol , vol.6 , pp. 195-209
    • Jernigan, R.L.1    Bahar, I.2
  • 25
    • 0029000696 scopus 로고
    • Knowledge-based potentials for proteins
    • Sippl MJ. Knowledge-based potentials for proteins. Curr Opin Struct Biol 1995;5:229-235.
    • (1995) Curr Opin Struct Biol , vol.5 , pp. 229-235
    • Sippl, M.J.1
  • 26
    • 0033117762 scopus 로고    scopus 로고
    • Designing potential energy functions for protein folding
    • Hao MH, Scheraga HA, Designing potential energy functions for protein folding. Curr Opin Struct Biol 1999;9:184-188.
    • (1999) Curr Opin Struct Biol , vol.9 , pp. 184-188
    • Hao, M.H.1    Scheraga, H.A.2
  • 27
    • 0033566967 scopus 로고    scopus 로고
    • Evaluation of short-range interactions as secondary structure energies for protein fold and sequence recognition
    • Miyazawa S, Jernigan RL. Evaluation of short-range interactions as secondary structure energies for protein fold and sequence recognition. Proteins 199936:347-356.
    • (1999) Proteins , vol.36 , pp. 347-356
    • Miyazawa, S.1    Jernigan, R.L.2
  • 28
    • 0030832809 scopus 로고    scopus 로고
    • Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches
    • Bahar I, Kaplan M, Jernigan RL. Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches. Proteins 1997;29:292-308.
    • (1997) Proteins , vol.29 , pp. 292-308
    • Bahar, I.1    Kaplan, M.2    Jernigan, R.L.3
  • 29
    • 0033867374 scopus 로고    scopus 로고
    • Identifying sequence-structure pairs undetected by sequence alignments
    • Miyazawa S, Jernigan RL. Identifying sequence-structure pairs undetected by sequence alignments. Protein Eng 2000;13:459-475.
    • (2000) Protein Eng , vol.13 , pp. 459-475
    • Miyazawa, S.1    Jernigan, R.L.2
  • 30
    • 0037233452 scopus 로고    scopus 로고
    • Long- and short-range interactions in native protein structures are consistent/minimally frustrated in sequence space
    • Miyazawa S, Jernigan RL. Long- and short-range interactions in native protein structures are consistent/minimally frustrated in sequence space. Proteins 2003;50:35-43.
    • (2003) Proteins , vol.50 , pp. 35-43
    • Miyazawa, S.1    Jernigan, R.L.2
  • 31
    • 22944468214 scopus 로고    scopus 로고
    • How effective for fold recognition is a potential of mean force that includes relative orientations between contacting residues in proteins?
    • Miyazawa S, Jernigan RL. How effective for fold recognition is a potential of mean force that includes relative orientations between contacting residues in proteins? J Chem Phys 2005;22: 024901.
    • (2005) J Chem Phys , vol.22 , pp. 024901
    • Miyazawa, S.1    Jernigan, R.L.2
  • 33
    • 0034141931 scopus 로고    scopus 로고
    • Can a pairwise contact potentials stabilize native protein folds against decoys obtained by threading?
    • Vendruscolo M, Najmanovich R Domany E. Can a pairwise contact potentials stabilize native protein folds against decoys obtained by threading? Proteins 2000;38:134-148.
    • (2000) Proteins , vol.38 , pp. 134-148
    • Vendruscolo, M.1    Najmanovich, R.2    Domany, E.3
  • 34
    • 0035943455 scopus 로고    scopus 로고
    • Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations
    • Cater CW, Jr, LeFebvre BC, Cammer SA, Tropsha A, Edgell MH. Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations. J Mol Biol 2001;311:625-638.
    • (2001) J Mol Biol , vol.311 , pp. 625-638
    • Cater Jr, C.W.1    LeFebvre, B.C.2    Cammer, S.A.3    Tropsha, A.4    Edgell, M.H.5
  • 35
    • 0033005899 scopus 로고    scopus 로고
    • Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes
    • Betancourt MR, Thirumalai D. Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes. Protein Sci 1999;8:361-369.
    • (1999) Protein Sci , vol.8 , pp. 361-369
    • Betancourt, M.R.1    Thirumalai, D.2
  • 36
    • 0030806961 scopus 로고    scopus 로고
    • Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment
    • Munson PJ, Singh RK. Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment. Protein Sci 1997;6:1467-1481.
    • (1997) Protein Sci , vol.6 , pp. 1467-1481
    • Munson, P.J.1    Singh, R.K.2
  • 37
    • 19544391428 scopus 로고    scopus 로고
    • Geometric cooperativity and anticooperativity of three-body interactions in native proteins
    • Li X, Liang J. Geometric cooperativity and anticooperativity of three-body interactions in native proteins. Proteins 2005;60: 46-65.
    • (2005) Proteins , vol.60 , pp. 46-65
    • Li, X.1    Liang, J.2
  • 38
    • 0042889108 scopus 로고    scopus 로고
    • Development of a four-body statistical pseudo-potential to discriminate native from nonnative protein conformations
    • Krishnamoorthy B, Tropsha A. Development of a four-body statistical pseudo-potential to discriminate native from nonnative protein conformations. Bioinformatics 2003;19:1540-1548.
    • (2003) Bioinformatics , vol.19 , pp. 1540-1548
    • Krishnamoorthy, B.1    Tropsha, A.2
  • 39
    • 33847261239 scopus 로고    scopus 로고
    • The dominant role of side-chain backbone interactions in structural realization of amino acid code. ChiRotor: A side-chain prediction algorithm based on side-chain backbone interactions
    • Spassov VZ, Yan L, Flook PK. The dominant role of side-chain backbone interactions in structural realization of amino acid code. ChiRotor: A side-chain prediction algorithm based on side-chain backbone interactions. Protein Sci 2007;16:1-13.
    • (2007) Protein Sci , vol.16 , pp. 1-13
    • Spassov, V.Z.1    Yan, L.2    Flook, P.K.3
  • 40
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: A protein sequence culling server
    • Wang G, Dunbrack RL, Jr. PISCES: a protein sequence culling server. Bioinformatics 2003;19:1589-1591.
    • (2003) Bioinformatics , vol.19 , pp. 1589-1591
    • Wang, G.1    Dunbrack Jr, R.L.2
  • 42
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 1988;85:2444-2448.
    • (1988) Proc Natl Acad Sci USA , vol.85 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 43
    • 0000243829 scopus 로고
    • PROCHECK: A program to check the stereochemical quality of protein structures
    • Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 1993;26:283-291.
    • (1993) J Appl Cryst , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 44
    • 34249937756 scopus 로고    scopus 로고
    • Hubbard SJ, Thornton JM. NACCESS, Computer Program, Department of Biochemistry and Molecular Biology, University College London, London; 1993.
    • Hubbard SJ, Thornton JM. NACCESS, Computer Program, Department of Biochemistry and Molecular Biology, University College London, London; 1993.
  • 45
    • 0033853177 scopus 로고    scopus 로고
    • Decoys 'R' Us: A database of incorrect conformations to improve protein structure prediction
    • Samudrala R, Levitt M. Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction. Protein Sci 2000;9:1399-1401.
    • (2000) Protein Sci , vol.9 , pp. 1399-1401
    • Samudrala, R.1    Levitt, M.2
  • 46
    • 0032612579 scopus 로고    scopus 로고
    • Simon KT, Bonneau R, Ruczinski I, Baker D. Ab Initio protein structure prediction of CASPIII targets using ROSETTA. Proteins: Struct Funct Genet 1999;3:171-176. Also available at http://depts.washington.edu/bakerpg/decoys/
    • Simon KT, Bonneau R, Ruczinski I, Baker D. Ab Initio protein structure prediction of CASPIII targets using ROSETTA. Proteins: Struct Funct Genet 1999;3:171-176. Also available at http://depts.washington.edu/bakerpg/decoys/


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.