An automatic homology modeling method consisting of database searches and simulated annealing

Journal of Molecular Graphics and Modelling

Volumn 18, Issue 3, 2000, Pages

  Ogata, Koji ^a   Umeyama, Hideaki ^a  

^a KITASATO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ANNEALING; DATABASE SYSTEMS; MOLECULAR STRUCTURE; PROTEINS; ATOMS; CHEMICAL BONDS; COMPUTER SIMULATION; COMPUTER SOFTWARE; CONFORMATIONS; MONTE CARLO METHODS; SIMULATED ANNEALING; WORLD WIDE WEB;

MAIN-CHAIN ATOMS;

MOLECULAR GRAPHICS; MOLECULAR STRUCTURE;

ARTICLE; AUTOMATION; DATA BASE; MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; SIMULATION; X RAY ANALYSIS;

SUGARCANE RAMU STUNT DISEASE PHYTOPLASMA;

DATABASE SEARCHES; LOCAL SPACE HOMOLOGY; PROTEIN STRUCTURES; SOFTWARE PACKAGE FAMS; STRUCTURALLY CONSERVED REGIONS;

EID: 0034465184     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1093-3263(00)00037-1     Document Type: Article

References (33)

1. Conformations of folded proteins in restricted spaces
2. A method to identify protein sequences that fold into a known three-dimensional structure
3. Assessment of pseudoenergy potentials by the best-five test: A new use of the three-dimensional profiles of proteins
4. 55 in serine proteases
5. Knowledge-based prediction of protein structures and the design of novel molecules
6. Comparative modeling methods: Application to the family of the mammalian serine proteases
7. Database algorithm for generating protein backbone and side-chain co-ordinates from a Cα trace. Application to model building and detection of co-ordinate errors
8. Accurate modeling of protein conformation by automatic segment matching
9. A computer modeling study of the interaction between tissue factor pathway inhibitor and blood coagulation factor Xa
10. A graph-theoretic algorithm for comparative modeling of protein structure
11. Tertiary templates for proteins: Use of packing criteria in the enumeration of allowed sequence for different structural classes
12. Prediction of protein side-chain conformation by packing optimization
13. Fast and simple Monte Carlo algorithm for side-chain optimization in proteins: Application to model building by homology
14. The dead-end elimination theorem and its use in protein side-chain positioning
15. Backbone-dependent rotamer library for proteins: Application to side-chain prediction
16. Determinants of protein side-chain packing
17. Prediction of protein sidechain conformations by principal component analysis for fixed main-chain atoms
18. An all-atom force field for simulation for proteins and nucleic acids
19. Comparative protein modeling by satisfaction of spatial restraints
20. ICM: A new method for structure modeling and design: Applications to docking and structure prediction from the distorted native conformation
21. Prediction of polyelectroyte polypeptide structures using Monte Carlo conformational search methods with implicit solvation modeling
22. Homology modeling using simulated annealing of restrained molecular dynamics and conformational search calculations with CONGEN: Application in predicting the three-dimensional structure of murine homeodomain Msx-1
23. The role played by environmental residues on side-chain torsional angles within homologous families of proteins: A new method of side-chain modeling
24. The Protein Data Bank: A computer based archival file for micromolecular structures
25. Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels
26. Touring protein fold space with Dali/FSSP
27. Identification of common molecular subsequences
28. A structural basis for sequence comparisons. An evaluation of scoring methodologies
29. Derivation of rules for comparative protein modeling from a database of protein structure alignments
30. Assessment of comparative modeling in CASP2
31. Evaluation of comparative protein structure modeling by MODELLER-3
32. Model building by comparison: A combination of expert knowledge and computer automation
33. Analysis of comparative modeling predictions for CASP2 targets 1.3.9.17