Statistical potential for assessment and prediction of protein structures
Article first published online: 1 JAN 2009
Copyright © 2006 The Protein Society
Volume 15, Issue 11, pages 2507–2524, November 2006
How to Cite
Shen, M.-y. and Sali, A. (2006), Statistical potential for assessment and prediction of protein structures. Protein Science, 15: 2507–2524. doi: 10.1110/ps.062416606
- Issue published online: 1 JAN 2009
- Article first published online: 1 JAN 2009
- Manuscript Revised: 18 AUG 2006
- Manuscript Accepted: 18 AUG 2006
- Manuscript Received: 28 JUN 2006
- 1964. Triplet correlations in hard spheres. Phys. Rev. Lett. 12: 317–319.
- 1972. The formation and stabilization of protein structure. Biochem. J. 128: 737–749.
- 1973. Principles that govern the folding of protein chains. Science 181: 223–230.
- 2000. A statistical mechanical method to optimize energy functions for protein folding. Proc. Natl. Acad. Sci. 97: 3977–3981. , , and
- 1994. An improved pair potential to recognize native protein folds. Proteins 18: 254–261. and
- 1997. Statistical potentials extracted from protein structures: Are these meaningful potentials? J. Chem. Phys. 107: 3698–3706.
- 2004. Local propensities and statistical potentials of backbone dihedral angles in proteins. J. Mol. Biol. 342: 635–649. and
- 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. and
- 1991. A method to identify protein sequences that fold into a known three-dimensional structure. Science 253: 164–170. , , and
- 1988. Proteins: A theoretical perspective of dynamics, structure, and thermodynamics. pp. xiii–259. Wiley, New York. , , and
- 1993. An empirical energy function for threading protein sequence through the folding motif. Proteins 16: 92–112. and
- 1995. Funnels, pathways, and the energy landscape of protein folding: A synthesis. Proteins 21: 167–195. , , , and
- 2004a. Development of novel statistical potentials for protein fold recognition. Curr. Opin. Struct. Biol. 14: 225–232. , , and
- 2004b. Orientational potentials extracted from protein structures improve native fold recognition. Protein Sci. 13: 862–874. , , and
- 1992. Structure-derived hydrophobic potential—Hydrophobic potential derived from X-ray structures of globular-proteins is able to identify native folds. J. Mol. Biol. 224: 725–732. and
- 2005. Lessons from the design of a novel atomic potential for protein folding. Protein Sci. 14: 1741–1752. and
- 2000. How to generate improved potentials for protein tertiary structure prediction: A lattice model study. Proteins 41: 157–163. and
- 1993. Verification of protein structures: Patterns of non-bonded atomic interactions. Protein Sci. 2: 1511–1519. and
- 2006. Minimalist representations and the importance of nearest neighbor effects in protein folding simulations. J. Mol. Biol. doi:10.1016/j.jmb.2006.08.035. , , , , , , and
- 1996. Evaluation of atomic level mean force potentials via inverse folding and inverse refinement of protein structures: Atomic burial position and pairwise non-bonded interactions. Protein Eng. 9: 637–655. and
- 2006. A new generation of statistical potentials for proteins. Biophys. J. 90: 4010–4017. , , and
- 1919. Sur la théorie des probabilités géométriques. Ann. Fac. Sci. Univ. Toulouse 11: 1–65.
- 1977. Distance distributions and trip behaviour in defined regions. Geogr. Anal. 9: 332–345.
- 1985. Theory for the folding and stability of globular proteins. Biochemistry 24: 1501–1509.
- 1997. Additivity principles in biochemistry. J. Biol. Chem. 272: 701–704.
- 1998. Protein folding: A perspective from theory and experiment. Angew. Chem. Int. Ed. 37: 868–893. , , and
- 2006. A composite score for predicting errors in protein structure models. Protein Sci. 15: 1653–1666. , , , , , and
- 2005. A consistent set of statistical potentials for quantifying local side-chain and backbone interactions. Proteins 60: 90–96. and
- 1995. Why do protein architectures have Boltzmann-like statistics? Proteins 23: 142–150. , , and
- 2000. Modeling of loops in protein structures. Protein Sci. 9: 1753–1773. , , and
- 1998. Influence of protein structure databases on the predictive power of statistical pair potentials. Proteins 31: 139–149. and
- 2005. Distribution of distance in the spheroid. J. Phys. A Math. Gen. 38: 3475–3482.
- 2000. Discrimination of near-native protein structures from misfolded models by empirical free energy functions. Proteins 41: 518–534. , , and
- 1996. Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials. J. Mol. Biol. 257: 1112–1126. and
- 1997. Predicting protein stability changes upon mutation using database-derived potentials: Solvent accessibility determines the importance of local versus non-local interactions along the sequence. J. Mol. Biol. 272: 276–290. and
- 1950. The distribution of distance in a hypersphere. Ann. Math. Stat. 21: 447–452.
- 1990. 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. 216: 167–180. , , , , , , , and
- 1956. Statistical mechanics: Principles and selected applications. p. 432. McGraw-Hill, New York.
- 1995. Recognizing native folds by the arrangements of hydrophobic and polar residues. J. Mol. Biol. 252: 709–720. , , and
- 1996. Structure-derived potentials and protein simulations. Curr. Opin. Struct. Biol. 6: 195–209. and
- 2003. Comparative protein structure modeling by iterative alignment, model building and model assessment. Nucleic Acids Res. 31: 3982–3992. and
- 1999a. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292: 195–202.
- 1999b. GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol. 287: 797–815.
- 1996. Potential energy functions for threading. Curr. Opin. Struct. Biol. 6: 210–216. and
- 2003. A novel approach to decoy set generation: Designing a physical energy function having local minima with native structure characteristics. J. Mol. Biol. 329: 159–174. and
- 1935. Statistical mechanics of fluid mixtures. J. Chem. Phys. 3: 300–313.
- 1994. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J. Mol. Biol. 235: 1598–1613. , , and
- 1999. A method for the improvement of threading-based protein models. Proteins 37: 592–610. , , , and
- 2006. The RCSB PDB information portal for structural genomics. Nucleic Acids Res. 34: D302–D305. , , , , , , and
- 2000. Effective energy functions for protein structure prediction. Curr. Opin. Struct. Biol. 10: 139–145. and
- 1954. The distribution of distance in a hypersphere. Ann. Math. Stat. 25: 794–798.
- 2001. A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins 44: 223–232. and
- 1992. Contact potential that recognizes the correct folding of globular proteins. J. Mol. Biol. 227: 876–688. and
- 1975. Statistical mechanics. pp. xiv–641. Harper & Row, New York.
- 1997. Novel knowledge-based mean force potential at atomic level. J. Mol. Biol. 267: 207–222. and
- 2002. Statistical potentials for fold assessment. Protein Sci. 11: 430–448. , , and
- 2006. Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proc. Natl. Acad. Sci. 103: 5361–5366. , , , , and
- 1985. Estimation of effective interresidue contact energies from protein crystal-structures—Quasi-chemical approximation. Macromolecules 18: 534–552. and
- 1996. Residue–residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J. Mol. Biol. 256: 623–644. and
- 1999. An empirical energy potential with a reference state for protein fold and sequence recognition. Proteins 36: 357–369. and
- 2000. Identifying sequence–structure pairs undetected by sequence alignments. Protein Eng. 13: 459–475. and
- 1997. Comparison of database potentials and molecular mechanics force fields. Curr. Opin. Struct. Biol. 7: 194–199.
- 1997. Tertiary structure prediction using mean-force potentials and internal energy functions: Successful prediction for coiled-coil geometries. Fold. Des. 2: S47–S52. and
- 1933. Theories of concentrated electrolytes. Chem. Rev. 13: 73–89.
- 1993. Prediction of protein structure by evaluation of sequence–structure fitness: Aligning sequences to contact profiles derived from three-dimensional structures. J. Mol. Biol. 232: 805–825. , , , and
- 2000. Combination of threading potentials and sequence profiles improves fold recognition. J. Mol. Biol. 296: 1319–1331. , , and
- 1998. Analysis and application of potential energy smoothing and search methods for global optimization. J. Phys. Chem. B 102: 9725–9742. , , and
- 1996. Energy functions that discriminate X-ray and near native folds from well-constructed decoys. J. Mol. Biol. 258: 367–392. and
- 1997. Factors affecting the ability of energy functions to discriminate correct from incorrect folds. J. Mol. Biol. 266: 831–846. , , and
- 2006. MODBASE: A database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 34: D291–D295. , , , , , , , , , and , et al.
- 1992. Numerical recipes in FORTRAN: The art of scientific computing, 2nd ed., pp. xxvi–963. Cambridge University Press, Cambridge, UK.
- 2005. Atomically detailed potentials to recognize native and approximate protein structures. Proteins 61: 44–55. and
- 1964. Triplet correlations in liquids. Phys. Rev. Lett. 12: 575–577.
- 1997. Residue–residue mean-force potentials for protein structure recognition. Protein Eng. 10: 865–876. , , , and
- 1999. Knowledge-based interaction potentials for proteins. Proteins 36: 54–67. and
- 1998. Different derivations of knowledge-based potentials and analysis of their robustness and context-dependent predictive power. Eur. J. Biochem. 254: 135–143. and
- 1995. Are database-derived potentials valid for scoring both forward and inverted protein folding? Protein Eng. 8: 849–858. and
- 1993. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234: 779–815. and
- 1998. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J. Mol. Biol. 275: 895–916. and
- 2006. Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet. Chem. Rev. 106: 1559–1588.
- 2005. The optimal size of a globular protein domain: A simple sphere-packing model. Chem. Phys. Lett. 405: 224–228. , , and
- 1997. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J. Mol. Biol. 268: 209–225. , , , and
- 1999. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 34: 82–95. , , , , , and
- 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.
- 1993a. Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures. J. Comput. Aided Mol. Des. 7: 473–501.
- 1993b. Recognition of errors in three-dimensional structures of proteins. Proteins 17: 355–362.
- 1992. Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations. Proteins 13: 258–271. and
- 1997. Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? Protein Sci. 6: 676–688. , , , and
- 2000. Derivation of protein-specific pair potentials based on weak sequence fragment similarity. Proteins 38: 3–16. , , and
- 2005. An atomic environment potential for use in protein structure prediction. J. Mol. Biol. 352: 986–1001. , , and
- 1993. Reduced representation model of protein structure prediction: Statistical potential and genetic algorithms. Protein Sci. 2: 762–785.
- 1976. Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. Macromolecules 9: 945–950. and
- 1996a. An iterative method for extracting energy-like quantities from protein structures. Proc. Natl. Acad. Sci. 93: 11628–11633. and
- 1996b. Statistical potentials extracted from protein structures: How accurate are they? J. Mol. Biol. 257: 457–469. and
- 2000. Distance-dependent, pair potential for protein folding: Results from linear optimization. Proteins 41: 40–46. and
- 2000. On the design and analysis of protein folding potentials. Proteins 40: 71–85. , , , and
- 2005. Combining electron microscopy and comparative protein structure modeling. Curr. Opin. Struct. Biol. 15: 578–585. and
- 2006. Refinement of protein structures by iterative comparative modeling and CryoEM density fitting. J. Mol. Biol. 357: 1655–1668. , , , , and
- 2002. Random distance distribution for spherical objects: General theory and applications to physics. J. Phys. A Math. Gen. 35: 6557–6570. and
- 1997. Empirical potentials and functions for protein folding and binding. Curr. Opin. Struct. Biol. 7: 222–228. , , and
- 2000. Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading? Proteins 38: 134–148. , , and
- 2003. PISCES: A protein sequence culling server. Bioinformatics 19: 1589–1591. and
- 2004. Improved protein structure selection using decoy-dependent discriminatory functions. BMC Struct. Biol. 4: 8. , , , and
- 2006. Self-consistent assignment of asparagine and glutamine amide rotamers in protein crystal structures. Structure 14: 967–972. and
- 1980. Analytical approximation to the accessible surface area of proteins. Proc. Natl. Acad. Sci. 77: 1736–1740. and
- 2000. Ab initio construction of protein tertiary structures using a hierarchical approach. J. Mol. Biol. 300: 171–185. , , , and
- 2004. The dependence of all-atom statistical potentials on structural training database. Biophys. J. 86: 3349–3358. , , , and
- 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. and
- 2003. Erratum: Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci. 12: 2121. and