Potential energy function for continuous state models of globular proteins

Journal of Computational Biology

Volumn 7, Issue 3-4, 2000, Pages 363-379

  Ohkubo, Y Z ^a   Crippen, G M ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Boltzmann statistics; Global minimum; Potential energy function; Protein folding; Threading

Indexed keywords

GLOBULAR PROTEIN;

CONFERENCE PAPER; ENERGY; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; MODELS, CHEMICAL; MODELS, STATISTICAL; PROTEIN CONFORMATION; PROTEINS; THERMODYNAMICS;

EID: 0033693249     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/106652700750050835     Document Type: Conference Paper

References (42)

1. Linear programming based approach to the derivation of a contact potential for protein threading
2. The protein data bank
3. The protein data bank: A computer-based archival file for macromolecular structures
4. A method to identify protein sequences that fold into a known three-dimensional structure
5. An empirical energy function for threading protein sequence through the folding motif
6. Folding Lennard-Jones proteins by a contact potential
7. A fast, stochastic threading algorithm for proteins
8. Easily searched protein folding potentials
9. Statistical mechanics of protein folding by exhaustive enumeration
10. New algorithm for protein design
11. Protein structure and energy landscape dependence on sequence using a continuous energy function
12. Theoretical studies of protein folding
13. Are proteins ideal mixtures of amino-acids? Analysis of energy parameter sets
14. Optimizing potential functions for protein folding
15. Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force
16. Enlarged representative set of protein structures
17. Recognizing native folds by the arrangement of hydrophobic and polar residues
18. Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular dynamics simulations
19. A discussion of the solution for the best rotation to relate two sets of vectors
20. Cooperativity in protein folding: From lattice models with sidechains to real proteins
21. Global optimum protein threading with gapped alignment and empirical pair score functions
22. Contact potential that recognizes the correct folding of globular proteins
23. Size independent comparison of protein three-dimensional structures
24. How to derive a protein folding potential? A new approach to an old problem
25. Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
26. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
27. The mean geometry of the peptide unit from crystal structure data
28. Development of pseudoenergy potentials for assessing protein 3-D-1-D compatibility and detecting weak homologies
29. The complexity and accuracy of discrete state models of protein structure
30. Energy functions that discriminate X-ray and near-native folds from well-constructed decoys
31. Factors affecting the ability of energy functions to discriminate correct from incorrect folds
32. Clustering of low-energy conformations near the native structures of small protein
33. Statistical potentials extracted from protein structures: How accurate are they?
34. An iterative method for extracting energy-like quantities from protein structures
35. Perspectives in protein-fold recognition
36. Perspectives in protein-fold recognition
37. Pairwise contact potentials are unsuitable for protein folding
38. Discriminating compact nonnative structures from the native structure of globular proteins
39. Forces of tertiary structural organization in globular proteins