Evolution and physics in comparative protein structure modeling

Accounts of Chemical Research

Volumn 35, Issue 6, 2002, Pages 413-421

  Fiser, Andras ^a   Feig, Michael ^b   Brooks III, Charles L ^b   Sali, Andrej ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; SOLVENT;

ARTICLE; MOLECULAR EVOLUTION; PROTEIN FOLDING; PROTEIN STRUCTURE; SOLVATION; X RAY CRYSTALLOGRAPHY; BIOPHYSICS; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; PROTEIN CONFORMATION; REVIEW;

BIOPHYSICS; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS;

EID: 0036283048     PISSN: 00014842     EISSN: None     Source Type: Journal    
DOI: 10.1021/ar010061h     Document Type: Article

References (66)

1. The relation between the divergence of sequence and structure in proteins
2. Protein structure prediction and structural genomics
3. Ab initio protein structure prediction: Progress and prospects
4. Knowledge-based prediction of protein structures and the design of novel molecules
5. Comparative protein structure modeling of genes and genomes
6. Comparative protein modeling as an optimization problem
7. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
8. Perspectives in protein-fold recognition
9. The protein data bank
10. A possible three-dimensional structure of bovine lactalburnin based onthat of hen's egg-white lysosyme
11. Comparative model-building of the mammalian serine proteases
12. Accurate modeling of protein conformation by automatic segment matching
13. Using known substructures in protein model building and crystallography
14. A new method for building protein conformations from sequence alignments with homologues of known structure
15. Comparative protein modelling by satisfaction of spatial restraints
16. Generalized comparative modeling (GENECOMP): A combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement
17. Modeling of loops in protein structures
18. Predicting the conformational class of short and medium size loops connecting regular secondary structures: Application to comparative modelling
19. PDB-based protein loop prediction: Parameters for selection and methods for optimization
20. Backbone-dependent rotamer library for proteins. Application to side-chain prediction
21. Extending the accuracy limits of prediction for side-chain conformations
22. Large-scale protein structure modeling of the saccharomyces cerevisiae genome
23. LiveBench 1: Continuous benchmarking of protein structure prediction servers
24. EVA: Continuous automatic evaluation of protein structure prediction servers
25. Assessment of protein models with three-dimensional profiles
26. Recognition of errors in three-dimensional structures of proteins
27. Statistical potentials for fold assessment
28. ModBase, a database of annotated comparative protein structure models
29. MODBASE, a database of annotated comparative protein structure models
30. Mapping the protein universe
31. Completeness in structural genomics
32. Derivation of rules for comparative protein modeling from a database of protein structure alignments
33. Model of protein folding: Inclusion of short-, medium-, and long-range interactions
34. Why do protein architectures have boltzmann-like statistics?
35. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
36. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins
37. All-atom empirical potential for molecular modleing and dynamics studies of proteins
38. Multiple conformational states of proteins: A molecular dynamics analysis of myoglobin
39. Energy parameters in peptides A. Improved geometrical parameters and non-bonded intercations for use in the ECEPP/3 algorithm, with application to proline-containing peptides
40. A second generation force field for the simulation of proteins and nucleic acids
41. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
42. Brighter future for protein structure prediction
43. Correlation between knowledge-based and detailed atomic potentials: Application to the unfolding of the GCN4 leucine zipper
44. Effective energy function for proteins in solution
45. Generalized born models of macromolecular solvation effects
46. A universal organic solvation model
47. Biomolecular simulations: Recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions
48. The GB/SA continuum model for solvation. A fast analytical method for Th ecalculation of approximate born Radii
49. Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models
50. Electrostatic contributions to molecular free energies in solution
51. Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis
52. Large-scale ab initio quantum chemical calculations on biological systems
53. Discrimination of the native from misfolded protein models with an energy function including implicit solvation
54. Discrimination of near-native protein structures from misfolded models by empirical free energy functions
55. Prediction of loop geometries using a generalized born model of solvation effects
56. Anti-insulin antibody structure and conformation. II. Molecular dynamics with explicit solvent
57. An algorithm for determining the conformation of polypeptide segments in proteins by systematic search
58. Evaluation of the conformational free energies of loops in proteins
59. Conformational sampling using high-temperature molecular dynamics
60. Structural families in loops of homologous proteins: Automatic classification, modelling and application to antibodies
61. Comparison of systematic search and database methods for constructing segments of protein structure
62. Development of a generalized born model parameterization for proteins and nucleic acids
63. Identifying native-like protein structures using physics-based potentials
64. Iron superoxide dismutase from the archaeon sulfolobus solfataricus: Analysis of structure and thermostability