Increasing the precision of comparative models with YASARA NOVA - A self-parameterizing force field

Proteins: Structure, Function and Genetics

Volumn 47, Issue 3, 2002, Pages 393-402

  Krieger, Elmar ^a   Koraimann, Gúnther ^b   Vriend, Gert ^a  

^a RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^b UNIVERSITY OF GRAZ   (Austria)

Author keywords

Force field parameter optimization; Protein modeling; Structure refinement; WHAT IF

Indexed keywords

ARTICLE; FORCE; MOLECULAR DYNAMICS; MOLECULAR MODEL; MONTE CARLO METHOD; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STRUCTURE; VALIDATION PROCESS;

ALGORITHMS; MODELS, MOLECULAR; MONTE CARLO METHOD; NUCLEOTIDES; PROTEIN CONFORMATION; PROTEINS; REPRODUCIBILITY OF RESULTS;

EID: 0037093644     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10104     Document Type: Article

References (24)

1. The structure of proteins: Two hydrogen-bonded helical conformations of the polypeptide chain
2. A second generation force field for the simulation of proteins, nucleic acids and organic molecules
3. All-atom empirical potential for molecular modeling and dynamics studies of proteins
4. Implicit solvent models
5. Dynamical theory of activated processes in globular proteins
6. Molecular simulation study of cooperativity in hydrophobic association
7. Influence of rotational energy barriers to the conformational search of protein loops in molecular dynamics and ranking the conformations
8. Ab initio structure prediction of CASP III targets using ROSETTA
9. PRODRG. A program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules
10. Energy refinement of hen egg-white lysozyme
11. SMILES. A chemical language and information system
12. Verification of protein structures: Side-chain planarity
13. Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures
14. Zur gittertheorie der lonenkristalle
15. Improved simulation of liquid water by molecular dynamics
16. Protein structure comparison by alignment of distance matrices
17. WHAT IF - A molecular modeling and drug design program
18. The PDBFINDER database: A summary of PDB, DSSP and HSSP information with added value
19. The 1.2 A crystal structure of hirustasin reveals the intrinsic flexibility of a family of highly disulphide-bridged inhibitors
20. Quality control of protein models: Directional atomic contact analysis
21. Directory of protein secondary structure: Pattern recognition of hydrogen bonded and geometrical features