메뉴 건너뛰기




Volumn 5, Issue 8, 2009, Pages

Four distances between pairs of amino acids provide a precise description of their interaction

Author keywords

[No Author keywords available]

Indexed keywords

CHAINS; CRYSTAL STRUCTURE; PROTEINS;

EID: 70049115535     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000470     Document Type: Article
Times cited : (28)

References (66)
  • 1
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Anfinsen CB (1973) Principles that govern the folding of protein chains. Science 181: 223-230.
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 2
    • 0035882533 scopus 로고    scopus 로고
    • A distance-dependent atomic knowledge-based potential for improved protein structure selection
    • DOI 10.1002/prot.1087
    • Lu H, Skolnick J (2001) A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins 44: 223-232. (Pubitemid 32702231)
    • (2001) Proteins: Structure, Function and Genetics , vol.44 , Issue.3 , pp. 223-232
    • Lu, H.1    Skolnick, J.2
  • 3
    • 35348892593 scopus 로고    scopus 로고
    • A knowledge-based potential with an accurate description of local interactions improves discrimination between native and near-native protein conformations
    • DOI 10.1007/s12013-007-0050-5
    • Ferrada E, Vergara IA, Melo F (2007) A knowledge-based potential with an accurate description of local interactions improves discrimination between native and near-native protein conformations. Cell Biochem Biophys 49: 111-124. (Pubitemid 47574996)
    • (2007) Cell Biochemistry and Biophysics , vol.49 , Issue.2 , pp. 111-124
    • Ferrada, E.1    Vergara, I.A.2    Melo, F.3
  • 4
    • 24344479166 scopus 로고    scopus 로고
    • Atomically detailed potentials to recognize native and approximate protein structures
    • DOI 10.1002/prot.20585
    • Qiu J, Elber R (2005) Atomically detailed potentials to recognize native and approximate protein structures. Proteins 61: 44-55. (Pubitemid 41262916)
    • (2005) Proteins: Structure, Function and Genetics , vol.61 , Issue.1 , pp. 44-55
    • Qiu, J.1    Elber, R.2
  • 5
    • 33847673583 scopus 로고    scopus 로고
    • Near-native structure refinement using in vacuo energy minimization
    • Summa CM, Levitt M (2007) Near-native structure refinement using in vacuo energy minimization. Proc Natl Acad Sci U S A 104: 3177-3182.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 3177-3182
    • Summa, C.M.1    Levitt, M.2
  • 6
    • 34250886494 scopus 로고    scopus 로고
    • Nonbonded terms extrapolated from nonlocal knowledge-based energy functions improve error detection in near-native protein structure models
    • DOI 10.1110/ps.062735907
    • Ferrada E, Melo F (2007) Nonbonded terms extrapolated from nonlocal knowledge-based energy functions improve error detection in near-native protein structure models. Protein Sci 16: 1410-1421. (Pubitemid 46984875)
    • (2007) Protein Science , vol.16 , Issue.7 , pp. 1410-1421
    • Ferrada, E.1    Melo, F.2
  • 8
    • 33749578940 scopus 로고    scopus 로고
    • Statistical potential for assessment and prediction of protein structures
    • DOI 10.1110/ps.062416606
    • Shen MY, Sali A (2006) Statistical potential for assessment and prediction of protein structures. Protein Sci 15: 2507-2524. (Pubitemid 44771688)
    • (2006) Protein Science , vol.15 , Issue.11 , pp. 2507-2524
    • Shen, M.-Y.1    Sali, A.2
  • 9
    • 1842861587 scopus 로고    scopus 로고
    • Development of novel statistical potentials for protein fold recognition
    • DOI 10.1016/j.sbi.2004.03.002, PII S0959440X04000351
    • Buchete NV, Straub JE, Thirumalai D (2004) Development of novel statistical potentials for protein fold recognition. Curr Opin Struc Biol 14: 225-232. (Pubitemid 38490789)
    • (2004) Current Opinion in Structural Biology , vol.14 , Issue.2 , pp. 225-232
    • Buchete, N.-V.1    Straub, J.E.2    Thirumalai, D.3
  • 10
    • 39749180316 scopus 로고    scopus 로고
    • A knowledge-based forcefield for protein-protein interface design
    • Clark LA, van Vlijmen HW (2008) A knowledge-based forcefield for protein-protein interface design. Proteins 70: 1540-1550.
    • (2008) Proteins , vol.70 , pp. 1540-1550
    • Clark, L.A.1    Van Vlijmen, H.W.2
  • 11
    • 36749008025 scopus 로고    scopus 로고
    • A knowledge-based potential function predicts the specificity and relative binding energy of RNA-binding proteins
    • DOI 10.1111/j.1742-4658.2007.06155.x
    • Zheng S, Robertson TA, Varani G (2007) A knowledge-based potential function predicts the specificity and relative binding energy of RNA-binding proteins. Febs J 274: 6378-6391. (Pubitemid 350215927)
    • (2007) FEBS Journal , vol.274 , Issue.24 , pp. 6378-6391
    • Zheng, S.1    Robertson, T.A.2    Varani, G.3
  • 12
    • 34547614501 scopus 로고    scopus 로고
    • A novel empirical free energy function that explains and predicts protein-protein binding affinities
    • DOI 10.1016/j.bpc.2007.05.021, PII S0301462207001536
    • Audie J, Scarlata S (2007) A novel empirical free energy function that explains and predicts protein-protein binding affinities. Biophys Chem 129: 198-211. (Pubitemid 47202023)
    • (2007) Biophysical Chemistry , vol.129 , Issue.2-3 , pp. 198-211
    • Audie, J.1    Scarlata, S.2
  • 13
    • 2642524483 scopus 로고    scopus 로고
    • A physical reference state unifies the structure-derived potential of mean force for protein folding and binding
    • DOI 10.1002/prot.20019
    • Liu S, Zhang C, Zhou H, Zhou Y (2004) A physical reference state unifies the structure-derived potential of mean force for protein folding and binding. Proteins 56: 93-101. (Pubitemid 38720841)
    • (2004) Proteins: Structure, Function and Genetics , vol.56 , Issue.1 , pp. 93-101
    • Liu, S.1    Zhang, C.2    Zhou, H.3    Zhou, Y.4
  • 14
    • 33845976703 scopus 로고    scopus 로고
    • An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure
    • Robertson TA, Varani G (2007) An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure. Proteins 66: 359-374.
    • (2007) Proteins , vol.66 , pp. 359-374
    • Robertson, T.A.1    Varani, G.2
  • 15
    • 0030968991 scopus 로고    scopus 로고
    • Empirical potentials and functions for protein folding and binding
    • DOI 10.1016/S0959-440X(97)80029-2
    • Vajda S, Sippl M, Novotny J (1997) Empirical potentials and functions for protein folding and binding. Curr Opin Struct Biol 7: 222-228. (Pubitemid 27156721)
    • (1997) Current Opinion in Structural Biology , vol.7 , Issue.2 , pp. 222-228
    • Vajda, S.1    Sippl, M.2    Novotny, J.3
  • 16
    • 0034645763 scopus 로고    scopus 로고
    • Knowledge-based scoring function to predict protein-ligand interactions
    • DOI 10.1006/jmbi.1999.3371
    • Gohlke H, Hendlich M, Klebe G (2000) Knowledge-based scoring function to predict protein-ligand interactions. J Mol Biol 295: 337-356. (Pubitemid 30045364)
    • (2000) Journal of Molecular Biology , vol.295 , Issue.2 , pp. 337-356
    • Gohlke, H.1    Hendlich, M.2    Klebe, G.3
  • 17
    • 34547599808 scopus 로고    scopus 로고
    • MODPROPEP: A program for knowledge-based modeling of protein-peptide complexes
    • Kumar N, Mohanty D (2007) MODPROPEP: a program for knowledge-based modeling of protein-peptide complexes. Nucleic Acids Res 35: W549-W555.
    • (2007) Nucleic Acids Res , vol.35
    • Kumar, N.1    Mohanty, D.2
  • 19
    • 57649232774 scopus 로고    scopus 로고
    • Prediction of specific protein-DNA recognition by knowledge-based two-body and three-body interaction potentials
    • Zhao G, Carson MB, Lu H (2007) Prediction of specific protein-DNA recognition by knowledge-based two-body and three-body interaction potentials. Conf Proc IEEE Eng Med Biol Soc 2007: 5017-5020.
    • (2007) Conf Proc IEEE Eng Med Biol Soc , vol.2007 , pp. 5017-5020
    • Zhao, G.1    Carson, M.B.2    Lu, H.3
  • 20
    • 27844505722 scopus 로고    scopus 로고
    • Advances in protein structure prediction and de novo protein design: A review
    • DOI 10.1016/j.ces.2005.04.009, PII S0009250905002988, Biomolecular Engineering
    • Floudas CA, Fung HK, McAllister SR, Monnigmann M, Rajgaria R (2006) Advances in protein structure prediction and de novo protein design: A review. Chem Eng Sci 61: 966-988. (Pubitemid 41655853)
    • (2006) Chemical Engineering Science , vol.61 , Issue.3 , pp. 966-988
    • Floudas, C.A.1    Fung, H.K.2    McAllister, S.R.3    Monnigmann, M.4    Rajgaria, R.5
  • 21
    • 0029563695 scopus 로고
    • Are database-derived potentials valid for scoring both forward and inverted protein folding?
    • Rooman MJ, Wodak SJ (1995) Are database-derived potentials valid for scoring both forward and inverted protein folding? Protein Eng 8: 849-858.
    • (1995) Protein Eng , vol.8 , pp. 849-858
    • Rooman, M.J.1    Wodak, S.J.2
  • 22
    • 10244245448 scopus 로고    scopus 로고
    • Developing optimal non-linear scoring function for protein design
    • DOI 10.1093/bioinformatics/bth369
    • Hu CY, Li X, Liang J (2004) Developing optimal non-linear scoring function for protein design. Bioinformatics 20: 3080-3098. (Pubitemid 39619199)
    • (2004) Bioinformatics , vol.20 , Issue.17 , pp. 3080-3098
    • Hu, C.1    Li, X.2    Liang, J.3
  • 24
    • 33645855864 scopus 로고    scopus 로고
    • Potential functions for hydrogen bonds in protein structure prediction and design
    • Morozov AV, Kortemme T (2006) Potential functions for hydrogen bonds in protein structure prediction and design. Adv Protein Chem 72: 1-+.
    • (2006) Adv Protein Chem , vol.72
    • Morozov, A.V.1    Kortemme, T.2
  • 25
    • 1242294472 scopus 로고    scopus 로고
    • Can contact potentials reliably predict stability of proteins?
    • Khatun J, Khare SD, Dokholyan NV (2004) Can contact potentials reliably predict stability of proteins? J Mol Biol 336: 1223-1238.
    • (2004) J Mol Biol , vol.336 , pp. 1223-1238
    • Khatun, J.1    Khare, S.D.2    Dokholyan, N.V.3
  • 26
    • 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
    • DOI 10.1110/ps.0217002
    • Zhou H, Zhou Y (2002) Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci 11: 2714-2726. (Pubitemid 35191145)
    • (2002) Protein Science , vol.11 , Issue.11 , pp. 2714-2726
    • Zhou, H.1    Zhou, Y.2
  • 27
    • 11844265970 scopus 로고    scopus 로고
    • Protein sequence randomization: Efficient estimation of protein stability using knowledge-based potentials
    • DOI 10.1016/j.jmb.2004.11.012, PII S002228360401438X
    • Wiederstein M, Sippl MJ (2005) Protein sequence randomization: efficient estimation of protein stability using knowledge-based potentials. J Mol Biol 345: 1199-1212. (Pubitemid 40092234)
    • (2005) Journal of Molecular Biology , vol.345 , Issue.5 , pp. 1199-1212
    • Wiederstein, M.1    Sippl, M.J.2
  • 28
    • 33749234779 scopus 로고    scopus 로고
    • What is a desirable statistical energy function for proteins and how can it be obtained?
    • Zhou Y, Zhou H, Zhang C, Liu S (2006) What is a desirable statistical energy function for proteins and how can it be obtained? Cell Biochem Biophys 46: 165-174.
    • (2006) Cell Biochem Biophys , vol.46 , pp. 165-174
    • Zhou, Y.1    Zhou, H.2    Zhang, C.3    Liu, S.4
  • 29
    • 34250309666 scopus 로고    scopus 로고
    • A free-rotating and self-avoiding chain model for deriving statistical potentials based on protein structures
    • DOI 10.1529/biophysj.106.102152
    • Cheng J, Pei JF, Lai LH (2007) A free-rotating and self-avoiding chain model for deriving statistical potentials based on protein structures. Biophys J 92: 3868-3877. (Pubitemid 46910573)
    • (2007) Biophysical Journal , vol.92 , Issue.11 , pp. 3868-3877
    • Cheng, J.1    Pei, J.2    Lai, L.3
  • 30
    • 0033117762 scopus 로고    scopus 로고
    • Designing potential energy functions for protein folding
    • DOI 10.1016/S0959-440X(99)80026-8
    • Hao MH, Scheraga HA (1999) Designing potential energy functions for protein folding. Curr Opin Struc Biol 9: 184-188. (Pubitemid 29452896)
    • (1999) Current Opinion in Structural Biology , vol.9 , Issue.2 , pp. 184-188
    • Hao, M.-H.1    Scheraga, H.A.2
  • 31
    • 14144256681 scopus 로고    scopus 로고
    • Energy functions for protein design: Adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity
    • DOI 10.1016/j.jmb.2004.12.019
    • Pokala N, Handel TM (2005) Energy functions for protein design: Adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity. J Mol Biol 347: 203-227. (Pubitemid 40283639)
    • (2005) Journal of Molecular Biology , vol.347 , Issue.1 , pp. 203-227
    • Pokala, N.1    Handel, T.M.2
  • 32
    • 0001064488 scopus 로고    scopus 로고
    • Statistical potentials extracted from protein structures: Are these meaningful potentials?
    • Ben-Naim A (1997) Statistical potentials extracted from protein structures: Are these meaningful potentials? Journal of Chemical Physics 107.
    • (1997) Journal of Chemical Physics , pp. 107
    • Ben-Naim, A.1
  • 33
    • 0029976427 scopus 로고    scopus 로고
    • Statistical potentials extracted from protein structures: How accurate are they?
    • Thomas PD, Dill KA (1996) Statistical potentials extracted from protein structures: how accurate are they? J Mol Biol 257: 457-469.
    • (1996) J Mol Biol , vol.257 , pp. 457-469
    • Thomas, P.D.1    Dill, K.A.2
  • 35
    • 0036667733 scopus 로고    scopus 로고
    • Knowledge-based potential functions in protein design
    • Russ WP, Ranganathan R (2002) Knowledge-based potential functions in protein design. Curr Opin Struct Biol 12: 447-452.
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 447-452
    • Russ, W.P.1    Ranganathan, R.2
  • 37
    • 34249938371 scopus 로고    scopus 로고
    • Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys
    • DOI 10.1002/prot.21362
    • Feng Y, Kloczkowski A, Jernigan RL (2007) Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys. Proteins 68: 57-66. (Pubitemid 46876534)
    • (2007) Proteins: Structure, Function and Genetics , vol.68 , Issue.1 , pp. 57-66
    • Feng, Y.1    Kloczkowski, A.2    Jernigan, R.L.3
  • 38
    • 0035943455 scopus 로고    scopus 로고
    • Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations
    • DOI 10.1006/jmbi.2001.4906
    • Carter CW, LeFebvre BC, Cammer SA, Tropsha A, Edgell MH (2001) Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations. J Mol Biol 311: 625-638. (Pubitemid 32803725)
    • (2001) Journal of Molecular Biology , vol.311 , Issue.4 , pp. 625-638
    • Carter Jr., C.W.1    Lefebvre, B.C.2    Cammer, S.A.3    Tropsha, A.4    Edgell, M.H.5
  • 39
    • 16344396587 scopus 로고    scopus 로고
    • A multibody, whole-residue potential for protein structures, with testing by Monte Carlo simulated annealing
    • Mayewski S (2005) A multibody, whole-residue potential for protein structures, with testing by Monte Carlo simulated annealing. Proteins 59: 152-169.
    • (2005) Proteins , vol.59 , pp. 152-169
    • Mayewski, S.1
  • 40
    • 24644464131 scopus 로고    scopus 로고
    • An atomic environment potential for use in protein structure prediction
    • DOI 10.1016/j.jmb.2005.07.054, PII S0022283605008557
    • Summa CM, Levitt M, DeGrado WF (2005) An atomic environment potential for use in protein structure prediction. J Mol Biol 352: 986-1001. (Pubitemid 41267083)
    • (2005) Journal of Molecular Biology , vol.352 , Issue.4 , pp. 986-1001
    • Summa, C.M.1    Levitt, M.2    Degrado, W.F.3
  • 42
    • 0025341310 scopus 로고
    • Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins
    • Sippl MJ (1990) Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol 213: 859-883.
    • (1990) J Mol Biol , vol.213 , pp. 859-883
    • Sippl, M.J.1
  • 43
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal-structures - Quasi-chemical approximation
    • Miyazawa S, Jernigan RL (1985) Estimation of effective interresidue contact energies from protein crystal-structures - quasi-chemical approximation. Macromolecules 18: 534-552.
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 44
    • 0017021957 scopus 로고
    • Medium- And long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins
    • Tanaka S, Scheraga HA (1976) Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. Macromolecules 9: 945-950.
    • (1976) Macromolecules , vol.9 , pp. 945-950
    • Tanaka, S.1    Scheraga, H.A.2
  • 45
    • 0031582083 scopus 로고    scopus 로고
    • Novel knowledge-based mean force potential at atomic
    • DOI 10.1006/jmbi.1996.0868
    • Melo F, Feytmans E (1997) Novel knowledge-based mean force potential at atomic level. J Mol Biol 267: 207-222. (Pubitemid 27149749)
    • (1997) Journal of Molecular Biology , vol.267 , Issue.1 , pp. 207-222
    • Melo, F.1    Feytmans, E.2
  • 46
    • 33745152349 scopus 로고    scopus 로고
    • Protein Refolding in Silico with Atom-based Statistical Potentials and Conformational Search Using a Simple Genetic Algorithm
    • DOI 10.1016/j.jmb.2006.04.033, PII S0022283606004979
    • Fang Q, Shortle D (2006) Protein refolding in silico with atom-based statistical potentials and conformational search using a simple genetic algorithm. J Mol Biol 359: 1456-1467. (Pubitemid 43903493)
    • (2006) Journal of Molecular Biology , vol.359 , Issue.5 , pp. 1456-1467
    • Fang, Q.1    Shortle, D.2
  • 47
    • 33744906496 scopus 로고    scopus 로고
    • A new generation of statistical potentials for proteins
    • DOI 10.1529/biophysj.105.079434
    • Dehouck Y, Gilis D, Rooman M (2006) A new generation of statistical potentials for proteins. Biophys J 90: 4010-4017. (Pubitemid 43846117)
    • (2006) Biophysical Journal , vol.90 , Issue.11 , pp. 4010-4017
    • Dehouck, Y.1    Gilis, D.2    Rooman, M.3
  • 48
    • 0028072364 scopus 로고
    • Pseudodihedrals: Simplified protein backbone representation with knowledge-based energy
    • DeWitte RS, Shakhnovich EI (1994) Pseudodihedrals: simplified protein backbone representation with knowledge-based energy. Protein Sci 3: 1570-1581.
    • (1994) Protein Sci , vol.3 , pp. 1570-1581
    • Dewitte, R.S.1    Shakhnovich, E.I.2
  • 49
    • 0034308163 scopus 로고    scopus 로고
    • Distance-dependent, pair potential for protein folding: Results from linear optimization
    • Tobi D, Elber R (2000) Distance-dependent, pair potential for protein folding: Results from linear optimization. Proteins 41: 40-46.
    • (2000) Proteins , vol.41 , pp. 40-46
    • Tobi, D.1    Elber, R.2
  • 50
    • 33745634606 scopus 로고    scopus 로고
    • Geometric filtering of pairwise atomic interactions applied to the design of efficient statistical potentials
    • DOI 10.1016/j.cagd.2006.03.002, PII S0167839606000240
    • Zomorodian A, Guibas L, Koehl P (2006) Geometric filtering of pairwise atomic interactions applied to the design of efficient statistical potentials. Comput Aided Geom D 23: 531-544. (Pubitemid 43993829)
    • (2006) Computer Aided Geometric Design , vol.23 , Issue.6 , pp. 531-544
    • Zomorodian, A.1    Guibas, L.2    Koehl, P.3
  • 51
    • 42449129569 scopus 로고    scopus 로고
    • Information and discrimination in pairwise contact potentials
    • Solis AD, Rackovsky S (2008) Information and discrimination in pairwise contact potentials. Proteins 71: 1071-1087.
    • (2008) Proteins , vol.71 , pp. 1071-1087
    • Solis, A.D.1    Rackovsky, S.2
  • 52
    • 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 (1999) Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes. Protein Sci 8: 361-369.
    • (1999) Protein Sci , vol.8 , pp. 361-369
    • Betancourt, M.R.1    Thirumalai, D.2
  • 53
    • 34247281977 scopus 로고    scopus 로고
    • Effects of amino acid composition, finite size of proteins, and sparse statistics on distance-dependent statistical pair potentials
    • DOI 10.1002/prot.21279
    • Rykunov D, Fiser A (2007) Effects of amino acid composition, finite size of proteins, and sparse statistics on distance-dependent statistical pair potentials. Proteins 67: 559-568. (Pubitemid 46625573)
    • (2007) Proteins: Structure, Function and Genetics , vol.67 , Issue.3 , pp. 559-568
    • Rykunov, D.1    Fiser, A.2
  • 54
    • 0032080720 scopus 로고    scopus 로고
    • Influence of protein structure databases on the predictive power of statistical pair potentials
    • DOI 10.1002/(SICI)1097-0134(19980501)31:2<139::AID-PROT4>3.0.CO;2-H
    • Furuichi E, Koehl P (1998) Influence of protein structure databases on the predictive power of statistical pair potentials. Proteins 31: 139-149. (Pubitemid 28198706)
    • (1998) Proteins: Structure, Function and Genetics , vol.31 , Issue.2 , pp. 139-149
    • Furuichi, E.1    Koehl, P.2
  • 55
    • 0031794714 scopus 로고    scopus 로고
    • Determinants of side chain conformational preferences in protein structures
    • Samudrala R, Moult J (1998) Determinants of side chain conformational preferences in protein structures. Protein Eng 11: 991-997. (Pubitemid 28548492)
    • (1998) Protein Engineering , vol.11 , Issue.11 , pp. 991-997
    • Samudrala, R.1    Moult, J.2
  • 56
    • 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 HY, Zhou YQ (2002) Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci 11: 2714-2726.
    • (2002) Protein Sci , vol.11 , pp. 2714-2726
    • Zhou, H.Y.1    Zhou, Y.Q.2
  • 57
    • 0036145846 scopus 로고    scopus 로고
    • Statistical potentials for fold assessment
    • Melo F, Sanchez R, Sali A (2002) Statistical potentials for fold assessment. Protein Sci 11: 430-448.
    • (2002) Protein Sci , vol.11 , pp. 430-448
    • Melo, F.1    Sanchez, R.2    Sali, A.3
  • 58
    • 0030023960 scopus 로고    scopus 로고
    • Protein folding by a biased Monte Carlo procedure in the dihedral angle space
    • Lee B, Kurochkina N, Kang HS (1996) Protein folding by a biased Monte Carlo procedure in the dihedral angle space. FASEB J 10: 119-125. (Pubitemid 26035514)
    • (1996) FASEB Journal , vol.10 , Issue.1 , pp. 119-125
    • Lee, B.1    Kurochkina, N.2    Kang, H.S.3
  • 59
    • 38049051121 scopus 로고    scopus 로고
    • OPUS-PSP: An orientation-dependent statistical all-atom potential derived from side-chain packing
    • Lu M, Dousis AD, Ma J (2008) OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing. J Mol Biol 376: 288-301.
    • (2008) J Mol Biol , vol.376 , pp. 288-301
    • Lu, M.1    Dousis, A.D.2    Ma, J.3
  • 61
    • 0033562633 scopus 로고    scopus 로고
    • Use of pair potentials across protein interfaces in screening predicted docked complexes
    • DOI 10.1002/(SICI)1097-0134(19990515)35:3<364::AID-PROT11>3.0.CO;2- 4
    • Moont G, Gabb HA, Sternberg MJ (1999) Use of pair potentials across protein interfaces in screening predicted docked complexes. Proteins 35: 364-373. (Pubitemid 29200974)
    • (1999) Proteins: Structure, Function and Genetics , vol.35 , Issue.3 , pp. 364-373
    • Moont, G.1    Gabb, H.A.2    Sternberg, M.J.E.3
  • 62
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: A protein sequence culling server
    • DOI 10.1093/bioinformatics/btg224
    • Wang G, Dunbrack RLJ (2003) PISCES: a protein sequence culling server. Bioinformatics 19: 1589-1591. (Pubitemid 37038881)
    • (2003) Bioinformatics , vol.19 , Issue.12 , pp. 1589-1591
    • Wang, G.1    Dunbrack Jr., R.L.2
  • 65
    • 0001504410 scopus 로고
    • Abbreviations and symbols for description of conformation of polypeptide chains - Tentative rules (1969)
    • IUPAC-IUB commission on biochemical nomenclature
    • IUPAC-IUB commission on biochemical nomenclature (1970) Abbreviations and symbols for description of conformation of polypeptide chains - tentative rules (1969). JBC 245: 6489-6497.
    • (1970) JBC , vol.245 , pp. 6489-6497
  • 66
    • 0037470581 scopus 로고    scopus 로고
    • An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes
    • DOI 10.1016/S0022-2836(03)00021-4
    • Kortemme T, Morozov AV, Baker D (2003) An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J Mol Biol 326: 1239-1259. (Pubitemid 36263395)
    • (2003) Journal of Molecular Biology , vol.326 , Issue.4 , pp. 1239-1259
    • Kortemme, T.1    Morozov, A.V.2    Baker, D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.