메뉴 건너뛰기




Volumn 352, Issue 4, 2005, Pages 986-1001

An atomic environment potential for use in protein structure prediction

Author keywords

Environment potential; Protein structure prediction; Statistical atomic potential

Indexed keywords

ARTICLE; ATOM; DERIVATIZATION; ENERGY TRANSFER; MICROENVIRONMENT; PREDICTION; PRIORITY JOURNAL; PROBABILITY; PROTEIN FUNCTION; PROTEIN STRUCTURE;

EID: 24644464131     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.07.054     Document Type: Article
Times cited : (52)

References (60)
  • 1
    • 0032835617 scopus 로고    scopus 로고
    • De novo design and structural characterization of proteins and metalloproteins
    • W.F. DeGrado, C.M. Summa, V. Pavone, F. Nastri, and A. Lombardi De novo design and structural characterization of proteins and metalloproteins Annu. Rev. Biochem. 68 1999 779 819
    • (1999) Annu. Rev. Biochem. , vol.68 , pp. 779-819
    • Degrado, W.F.1    Summa, C.M.2    Pavone, V.3    Nastri, F.4    Lombardi, A.5
  • 3
    • 0036667734 scopus 로고    scopus 로고
    • Combinatorial protein design
    • J.G. Saven Combinatorial protein design Curr. Opin. Struct. Biol. 12 2002 453 458
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 453-458
    • Saven, J.G.1
  • 4
    • 1042298843 scopus 로고    scopus 로고
    • Computational design of protein-protein interactions
    • T. Kortemme, and D. Baker Computational design of protein-protein interactions Curr. Opin. Chem. Biol. 8 2004 91 97
    • (2004) Curr. Opin. Chem. Biol. , vol.8 , pp. 91-97
    • Kortemme, T.1    Baker, D.2
  • 5
    • 0001686478 scopus 로고    scopus 로고
    • Radical performance enhancements for combinatorial optimization algorithms based on the dead-end elimination theorem
    • D.B. Gordon, and S.L. Mayo Radical performance enhancements for combinatorial optimization algorithms based on the dead-end elimination theorem J. Comp. Chem. 19 1998 1505 1514
    • (1998) J. Comp. Chem. , vol.19 , pp. 1505-1514
    • Gordon, D.B.1    Mayo, S.L.2
  • 8
    • 0034985005 scopus 로고    scopus 로고
    • Ab initio protein structure prediction: Progress and prospects
    • R. Bonneau, and D. Baker Ab initio protein structure prediction: progress and prospects Annu. Rev. Biophys. Biomol. Struct. 30 2001 173 189
    • (2001) Annu. Rev. Biophys. Biomol. Struct. , vol.30 , pp. 173-189
    • Bonneau, R.1    Baker, D.2
  • 9
    • 0034031680 scopus 로고    scopus 로고
    • Effective energy functions for protein structure prediction
    • T. Laziridis, and M. Karplus Effective energy functions for protein structure prediction Curr. Opin. Struct. Biol. 10 2000 139 145
    • (2000) Curr. Opin. Struct. Biol. , vol.10 , pp. 139-145
    • Laziridis, T.1    Karplus, M.2
  • 10
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
    • S. Miyazawa, and R.L. Jernigan Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation Macromolecules 18 1985 534 552
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 12
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known three-dimensional structure
    • J.U. Bowie, R. Luthy, and D. Eisenberg A method to identify protein sequences that fold into a known three-dimensional structure Science 253 1991 164 170
    • (1991) Science , vol.253 , pp. 164-170
    • Bowie, J.U.1    Luthy, R.2    Eisenberg, D.3
  • 13
    • 0029775624 scopus 로고    scopus 로고
    • Clusters of charged residues in protein 3-dimensional structures
    • S. Karlin, and Z.Y. Zhu Clusters of charged residues in protein 3-dimensional structures Proc. Natl Acad. Sci. USA 93 1996 8350 8355
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 8350-8355
    • Karlin, S.1    Zhu, Z.Y.2
  • 14
    • 0029738719 scopus 로고    scopus 로고
    • Characterizations of diverse residue clusters in protein 3-dimensional structures
    • S. Karlin, and Z.Y. Zhu Characterizations of diverse residue clusters in protein 3-dimensional structures Proc. Natl Acad. Sci. USA 93 1996 8344 8349
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 8344-8349
    • Karlin, S.1    Zhu, Z.Y.2
  • 15
    • 0027542118 scopus 로고
    • Quality control of protein models: Directional atomic contact analysis
    • G. Vriend, and C. Sander Quality control of protein models: directional atomic contact analysis J. Appl. Crystallog. 26 1993 47 60
    • (1993) J. Appl. Crystallog. , vol.26 , pp. 47-60
    • Vriend, G.1    Sander, C.2
  • 16
    • 0027180507 scopus 로고
    • Verification of protein structures: Patterns of nonbonded atomic interactions
    • C. Colovos, and T.O. Yeates Verification of protein structures: patterns of nonbonded atomic interactions Protein Sci. 2 1993 1511 1519
    • (1993) Protein Sci. , vol.2 , pp. 1511-1519
    • Colovos, C.1    Yeates, T.O.2
  • 17
    • 0028063257 scopus 로고
    • Polar and non-polar atomic environment in the protein core: Implications for folding and binding
    • P. Koehl, and M. Delaurue Polar and non-polar atomic environment in the protein core: implications for folding and binding Proteins: Struct. Funct. Genet. 20 1994 264 278
    • (1994) Proteins: Struct. Funct. Genet. , vol.20 , pp. 264-278
    • Koehl, P.1    Delaurue, M.2
  • 18
    • 0029044472 scopus 로고
    • Atomic environment energies in proteins defined from statistics of accessible and contact surface areas
    • M. Delarue, and P. Koehl Atomic environment energies in proteins defined from statistics of accessible and contact surface areas J. Mol. Biol. 249 1995 675 690
    • (1995) J. Mol. Biol. , vol.249 , pp. 675-690
    • Delarue, M.1    Koehl, P.2
  • 19
    • 0028950817 scopus 로고
    • Characterizing the microenvironment surrounding protein sites
    • S.C. Bagley, and R.B. Altman Characterizing the microenvironment surrounding protein sites Protein Sci. 4 1995 622 635
    • (1995) Protein Sci. , vol.4 , pp. 622-635
    • Bagley, S.C.1    Altman, R.B.2
  • 20
    • 0031306229 scopus 로고    scopus 로고
    • Using the radial distributions of physical features to compare amino acid environments and align amino acid sequences
    • L. Wei, R.B. Altman, and J.T. Chang Using the radial distributions of physical features to compare amino acid environments and align amino acid sequences Pacific Symp. Biocomput. 2 1997 465 476
    • (1997) Pacific Symp. Biocomput. , vol.2 , pp. 465-476
    • Wei, L.1    Altman, R.B.2    Chang, J.T.3
  • 22
    • 0029987862 scopus 로고    scopus 로고
    • Energy functions that discriminate X-ray and near native folds from well-constructed decoys
    • B. Park, and M. Levitt Energy functions that discriminate X-ray and near native folds from well-constructed decoys J. Mol. Biol. 258 1996 367 392
    • (1996) J. Mol. Biol. , vol.258 , pp. 367-392
    • Park, B.1    Levitt, M.2
  • 23
    • 0033853177 scopus 로고    scopus 로고
    • Decoys 'R' Us: A database of incorrect protein conformations for evaluating scoring functions
    • R. Samudrala, and M. Levitt Decoys 'R' Us: a database of incorrect protein conformations for evaluating scoring functions Protein Sci. 9 2000 1399 1401
    • (2000) Protein Sci. , vol.9 , pp. 1399-1401
    • Samudrala, R.1    Levitt, M.2
  • 26
    • 0029633167 scopus 로고
    • Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution
    • M. Levitt, M. Hirschberg, R. Sharon, and V. Daggett Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution Comp. Phys. Commun. 91 1995 215 231
    • (1995) Comp. Phys. Commun. , vol.91 , pp. 215-231
    • Levitt, M.1    Hirschberg, M.2    Sharon, R.3    Daggett, V.4
  • 27
    • 0025341310 scopus 로고
    • Calculation of conformational ensembles from potentials of mean force
    • M.J. Sippl Calculation of conformational ensembles from potentials of mean force J. Mol. Biol. 213 1990 859 883
    • (1990) J. Mol. Biol. , vol.213 , pp. 859-883
    • Sippl, M.J.1
  • 28
    • 0031582083 scopus 로고    scopus 로고
    • Novel knowledge-based mean force potential at atomic level
    • F. Melo, and E. Feytmans Novel knowledge-based mean force potential at atomic level J. Mol. Biol. 267 1997 207 222
    • (1997) J. Mol. Biol. , vol.267 , pp. 207-222
    • Melo, F.1    Feytmans, E.2
  • 29
    • 0032488962 scopus 로고    scopus 로고
    • An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
    • R. Samudrala, and J. Moult An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction J. Mol. Biol. 275 1998 895 916
    • (1998) J. Mol. Biol. , vol.275 , pp. 895-916
    • Samudrala, R.1    Moult, J.2
  • 30
    • 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
    • H. Zhou, and Y. Zhou Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction Protein Sci. 11 2002 2714 2726
    • (2002) Protein Sci. , vol.11 , pp. 2714-2726
    • Zhou, H.1    Zhou, Y.2
  • 31
    • 0031585984 scopus 로고    scopus 로고
    • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
    • K.T. Simons, C. Kooperberg, E. Huang, and D. Baker Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions J. Mol. Biol. 268 1997 209 225
    • (1997) J. Mol. Biol. , vol.268 , pp. 209-225
    • Simons, K.T.1    Kooperberg, C.2    Huang, E.3    Baker, D.4
  • 32
    • 0032577270 scopus 로고    scopus 로고
    • A graph-theoretic algorithm for comparative modeling of protein structure
    • R. Samudrala, and J. Moult A graph-theoretic algorithm for comparative modeling of protein structure J. Mol. Biol. 279 1998 287 302
    • (1998) J. Mol. Biol. , vol.279 , pp. 287-302
    • Samudrala, R.1    Moult, J.2
  • 33
    • 4544355522 scopus 로고    scopus 로고
    • Improved protein structure selection using decoy-dependent discriminatory functions
    • K. Wang, B. Fain, M. Levitt, and R. Samudrala Improved protein structure selection using decoy-dependent discriminatory functions BMC Struct. Biol. 8 2004
    • (2004) BMC Struct. Biol. , vol.8
    • Wang, K.1    Fain, B.2    Levitt, M.3    Samudrala, R.4
  • 34
    • 0030806961 scopus 로고    scopus 로고
    • Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment
    • P.J. Munson, and R.K. Singh Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment Protein Sci. 6 1997 1467 1481
    • (1997) Protein Sci. , vol.6 , pp. 1467-1481
    • Munson, P.J.1    Singh, R.K.2
  • 35
    • 0033578690 scopus 로고    scopus 로고
    • Identification of side-chain clusters in protein structures by a graph spectral method
    • N. Kannan, and S. Vishveshwara Identification of side-chain clusters in protein structures by a graph spectral method J. Mol. Biol. 292 1999 441 464
    • (1999) J. Mol. Biol. , vol.292 , pp. 441-464
    • Kannan, N.1    Vishveshwara, S.2
  • 36
    • 0029976427 scopus 로고    scopus 로고
    • Statistical potentials extracted from protein structures: How accurate are they?
    • P.D. Thomas, and K.A. Dill Statistical potentials extracted from protein structures: how accurate are they? J. Mol. Biol. 257 1996 457 469
    • (1996) J. Mol. Biol. , vol.257 , pp. 457-469
    • Thomas, P.D.1    Dill, K.A.2
  • 37
    • 0008863560 scopus 로고
    • Some factors in the interpretation of protein denaturation
    • W. Kauzmann Some factors in the interpretation of protein denaturation Advan. Protein Chem. 14 1959 1 64
    • (1959) Advan. Protein Chem. , vol.14 , pp. 1-64
    • Kauzmann, W.1
  • 38
    • 0026539511 scopus 로고
    • Structure-derived hydrophobic potential
    • M.J. Sippl, and G. Casari Structure-derived hydrophobic potential J. Mol. Biol. 224 1992 725 732
    • (1992) J. Mol. Biol. , vol.224 , pp. 725-732
    • Sippl, M.J.1    Casari, G.2
  • 39
    • 0022596727 scopus 로고
    • Solvation energy in protein folding and binding
    • D. Eisenberg, and A.D. McLachlan Solvation energy in protein folding and binding Nature 319 1986 199 203
    • (1986) Nature , vol.319 , pp. 199-203
    • Eisenberg, D.1    McLachlan, A.D.2
  • 40
    • 0029871791 scopus 로고    scopus 로고
    • Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular dynamics simulations
    • E.S. Huang, S. Subbiah, J. Tsai, and M. Levitt Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular dynamics simulations J. Mol. Biol. 257 1996 716 725
    • (1996) J. Mol. Biol. , vol.257 , pp. 716-725
    • Huang, E.S.1    Subbiah, S.2    Tsai, J.3    Levitt, M.4
  • 41
    • 0345827721 scopus 로고    scopus 로고
    • Quantifying the effect of burial of amino acid residues on protein stability
    • H. Zhou, and Y. Zhou Quantifying the effect of burial of amino acid residues on protein stability Protein SFG 54 2004 315 322
    • (2004) Protein SFG , vol.54 , pp. 315-322
    • Zhou, H.1    Zhou, Y.2
  • 42
    • 3042655537 scopus 로고    scopus 로고
    • Compuational design of a biologically active enzyme
    • M.A. Dwyer, L.L. Looger, and H.W. Hellinga Compuational design of a biologically active enzyme Science 304 2004 1967 1971
    • (2004) Science , vol.304 , pp. 1967-1971
    • Dwyer, M.A.1    Looger, L.L.2    Hellinga, H.W.3
  • 43
    • 0026589733 scopus 로고
    • The dead-end elimination theorem and its use in protein side-chain positioning
    • J. Desmet, M. De Maeyer, B. Hazes, and I. Lasters The dead-end elimination theorem and its use in protein side-chain positioning Nature 356 1992 539 542
    • (1992) Nature , vol.356 , pp. 539-542
    • Desmet, J.1    De Maeyer, M.2    Hazes, B.3    Lasters, I.4
  • 44
    • 0033200183 scopus 로고    scopus 로고
    • Branch-and-terminate: A combinatorial optimization algorithm for protein design
    • D.B. Gordon, and S.L. Mayo Branch-and-terminate: a combinatorial optimization algorithm for protein design Struct. Fold. Des. 7 1999 1089 1098
    • (1999) Struct. Fold. Des. , vol.7 , pp. 1089-1098
    • Gordon, D.B.1    Mayo, S.L.2
  • 45
    • 0028826985 scopus 로고
    • Enhanced dead-end elimination in the search for the global minimum energy conformation of a collection of protein side chains
    • I. Lasters, M. De Maeyer, and J. Desmet Enhanced dead-end elimination in the search for the global minimum energy conformation of a collection of protein side chains Protein Eng. 8 1995 815 822
    • (1995) Protein Eng. , vol.8 , pp. 815-822
    • Lasters, I.1    De Maeyer, M.2    Desmet, J.3
  • 46
    • 53249119262 scopus 로고    scopus 로고
    • Dead-end based modeling tools to explore the sequence space that is compatible with a given scaffold
    • I. Lasters, J. Desmet, and M. DeMaeyer Dead-end based modeling tools to explore the sequence space that is compatible with a given scaffold J. Protein Chem. 16 1997 449 452
    • (1997) J. Protein Chem. , vol.16 , pp. 449-452
    • Lasters, I.1    Desmet, J.2    Demaeyer, M.3
  • 47
    • 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
    • L.L. Looger, and H.W. Hellinga Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics J. Mol. Biol. 307 2001 429 445
    • (2001) J. Mol. Biol. , vol.307 , pp. 429-445
    • Looger, L.L.1    Hellinga, H.W.2
  • 48
    • 0030593470 scopus 로고    scopus 로고
    • Easily searched protein folding potentials
    • G.M. Crippen Easily searched protein folding potentials J. Mol. Biol. 260 1996 467 475
    • (1996) J. Mol. Biol. , vol.260 , pp. 467-475
    • Crippen, G.M.1
  • 49
    • 0026785519 scopus 로고
    • Contact potential that recognizes the correct folding of globular proteins
    • V.N. Maiorov, and G.M. Crippen Contact potential that recognizes the correct folding of globular proteins J. Mol. Biol. 227 1992 876 888
    • (1992) J. Mol. Biol. , vol.227 , pp. 876-888
    • Maiorov, V.N.1    Crippen, G.M.2
  • 50
  • 51
    • 0030596063 scopus 로고    scopus 로고
    • How to derive a protein folding potential? a new approach to an old problem
    • L.A. Mirny, and E.I. Shakhnovich How to derive a protein folding potential? A new approach to an old problem J. Mol. Biol. 264 1996 1164 1179
    • (1996) J. Mol. Biol. , vol.264 , pp. 1164-1179
    • Mirny, L.A.1    Shakhnovich, E.I.2
  • 52
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: A protein sequence culling server
    • G. Wang, and R.L. Dunbrack Jr PISCES: a protein sequence culling server Bioinformatics 19 2003 1589 1591
    • (2003) Bioinformatics , vol.19 , pp. 1589-1591
    • Wang, G.1    Dunbrack Jr., R.L.2
  • 53
    • 0032169688 scopus 로고    scopus 로고
    • PQS: A protein quaternary structure file server
    • K. Henrick, and J.M. Thornton PQS: A protein quaternary structure file server Trends Biochem. Sci. 23 1998 358 361
    • (1998) Trends Biochem. Sci. , vol.23 , pp. 358-361
    • Henrick, K.1    Thornton, J.M.2
  • 54
    • 0033614004 scopus 로고    scopus 로고
    • Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation
    • J.M. Word, S.C. Lovell, J.S. Richardson, and D.C. Richardson Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation J. Mol. Biol. 285 1999 1735 1747
    • (1999) J. Mol. Biol. , vol.285 , pp. 1735-1747
    • Word, J.M.1    Lovell, S.C.2    Richardson, J.S.3    Richardson, D.C.4
  • 55
    • 0038708222 scopus 로고    scopus 로고
    • A novel approach to decoy set generation: Designing a physical energy function having local minima with native structure characteristics
    • C. Keasar, and M. Levitt A novel approach to decoy set generation: designing a physical energy function having local minima with native structure characteristics J. Mol. Biol. 329 2003 159 174
    • (2003) J. Mol. Biol. , vol.329 , pp. 159-174
    • Keasar, C.1    Levitt, M.2
  • 56
    • 0034733381 scopus 로고    scopus 로고
    • Ab initio construction of protein tertiary structures using a hierarchical approach
    • Y. Xia, E.S. Huang, M. Levitt, and R. Samudrala Ab initio construction of protein tertiary structures using a hierarchical approach J. Mol. Biol. 300 2000 171 185
    • (2000) J. Mol. Biol. , vol.300 , pp. 171-185
    • Xia, Y.1    Huang, E.S.2    Levitt, M.3    Samudrala, R.4
  • 59
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • P.J. Kraulis MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures J. Appl. Crystallog. 24 1991 946 950
    • (1991) J. Appl. Crystallog. , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 60
    • 0030815133 scopus 로고    scopus 로고
    • Raster3D: Photorealistic molecular graphics
    • E.A. Merrit, and D.J. Bacon Raster3D: photorealistic molecular graphics Methods Enzymol. 277 1997 505 524
    • (1997) Methods Enzymol. , vol.277 , pp. 505-524
    • Merrit, E.A.1    Bacon, D.J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.