A distance-dependent atomic knowledge-based potential for improved protein structure selection

Proteins: Structure, Function and Genetics

Volumn 44, Issue 3, 2001, Pages 223-232

  Lu, Hui ^a   Skolnick, Jeffrey ^a  

^a DONALD DANFORTH PLANT SCIENCE CENTER   (United States)

Author keywords

Decoy set; Gapless threading z scores; Potentials

Indexed keywords

ALGORITHM; ARTICLE; ATOM; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STRUCTURE; SOLVATION; STRUCTURE ANALYSIS;

COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, FACTUAL; PROTEIN CONFORMATION; PROTEINS; SOFTWARE;

EID: 0035882533     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.1087     Document Type: Article

References (40)

1. Comparison of database potentials and molecular mechanics force fields
2. Empirical potentials and functions for protein folding and binding
3. How to derive a protein folding potential? A new approach to an old problem
4. Designing potential energy functions for protein folding
5. An empirical energy potential with a reference state for protein fold and sequence recognition
6. Effective energy functions for protein structure prediction
7. CHARMm: A program for macromolecular energy, minimization, and dynamics calculations
8. A second generation force field for the simulation of proteins, nucleic acids and organic molecules
9. Structure-derived potentials and protein simulations
10. Self-consistently optimized statitical mechanical energy functions for sequence structure alignment
11. Statistical potentials extracted from protein structure: How accurate are they?
12. Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes
13. Derivation of protein-specific pair potentials based on weak sequence fragment similarity
14. Distance-dependent, pair potential for protein folding: Results from linear optimization
15. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
16. A new approach to protein fold recognition
17. Method to identify protein sequences that fold into known three-dimensional structures
18. A topology fingerprint approach to the inverse folding problem
19. An empirical energy function for threading protein sequence through folding motif
20. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
21. MONSSTER: A method for folding globular proteins with a small number of distance restraints
22. Folding protein α-carbon chains into compact forms by Monte Carlo methods
23. Reduced representation model of protein structure prediction: Statistical potential and generic algorithms
24. An efficient Monte Carlo model of protein chains. Modeling the short-range correlations between side groups centers of mass
25. Evaluation of atomic level mean force potentials via inverse folding and inverse refinement of protein structures: Atomic burial position and pairwise non-bonded interactions
26. Helmholtz free energies of atom pair interactions in proteins
27. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
28. Novel knowledge-based mean force potential at atomic level
29. Computer modeling of protein folding: Conformational and energetic analysis of reduced and detailed protein models
30. Accurate reconstruction of all-atom protein representation from side-chain based low resolution model
31. Energy functions that discriminate X-ray and near-native foldes from well-constructed decoys
32. Generalized Comparative Modeling (GENECOMP): A combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement
33. Assessing the performance of fold recognition methods by means of a comprehensive benchmark
34. Selection of a representative set of structures from Brookhaven Protein Databank
35. A method for the improvement of threading-based protein models
36. Defrosting the frozen approximation, PROSPECTOR: A new approach to threading
37. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins
38. 3D protein folds: Homologs against errors - An estimate based on the random energy model
39. Averaging interaction energies over homologs improves fold recognition in gapless threading
40. Correlation between knowledge-based and detailed atomic potentials