Influence of rotational energy barriers to the conformational search of protein loops in molecular dynamics and ranking the conformations

Proteins: Structure, Function and Genetics

Volumn 44, Issue 3, 2001, Pages 167-179

  Tappura, Kirsi ^a  

^a VTT TECHNICAL RESEARCH CENTRE OF FINLAND   (Finland)

Author keywords

Equilibrium properties; Protein loop prediction; Protein loop simulation with explicit water; Quality scores; Soft core potential

Indexed keywords

ARTICLE; CONFORMATIONAL TRANSITION; ENERGY TRANSFER; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; ROTATION;

COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; MODELS, THEORETICAL; PLANT PROTEINS; PROTEIN STRUCTURE, SECONDARY; WATER;

EID: 0035882571     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.1082     Document Type: Article

References (43)

1. Optimization by simulated annealing
2. Modelling of protein loops by simulated annealing
3. Why energy embedding works
4. A structure refinement method based on molecular dynamics in four spatial dimensions
5. Global energy minimization by rotational energy embedding
6. An approach to the multiple-minima problem by relaxation dimensionality
7. Conformational search by potential energy annealing: Algorithm and application to cyclosporin A
8. Local elevation: A method for improving the searching properties of molecular dynamics
9. The GROMOS biomoleuler simulation program package
10. The multiple-minima problem in the conformational analysis of molecules. Deformation of the potential energy hypersurface by the diffusion equation method
11. Protein folding by restrained energy minimization and molecular dynamics
12. Determination of three-dimensional structures of proteins from interproton distance data by dynamical simulated annealing from a random array of atoms. Circumvented problems associated with folding
13. Three-dimensional structure of the Apo form of the N-terminal EGF-like module of blood coagulation factor as determined by NMR spectroscopy and simulated folding
14. Structure optimization combining soft-core interaction functions, the diffusion equation method and molecular dynamics
15. A new soft-core potential function for molecular dynamics applied to the prediction of protein loop conformations
16. Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations
17. Van der Waals volumes and radii
18. Progress in protein structure prediction
19. Conformations of immunoglobulin hyper-variable regions
20. PDB-based protein loop prediction: Parameters for selection and methods for optimization
21. Reversible peptide folding in solution by molecular dynamics simulation
22. Loop closure via scaling and relaxation
23. Accuracy and reliability of the scaling-relaxation method for loop closure: An evaluation based on extensive and multiple copy conformational samplings
24. Evaluation of the conformational free energies of loops in proteins
25. Does conformational free energy distinguish loop conformations in proteins
26. A molecular dynamics study of the decane/water interface
27. Molecular dynamics simulations of peptides from BPTI: A closer look at amide-aromatic interactions
28. LINCS: A linear constraint solver for molecular simulations
29. SETTLE: An analytical version of the SHAKE and RATTLE algorithms for rigid water models
30. Interactions models for water in relation to protein hydration
31. Molecular dynamics with coupling to an external bath
32. WHAT IF: A molecular modeling and drug design program
33. Errors in protein structures
34. A fast and efficient program for modeling protein loops
35. Prediction of loop geometries using a generalized born model of solvation effects
36. Folding proteins with a simple energy function and extensive conformational searching
37. A second generation force field for the simulation of proteins and nucleic acids
38. Simulations of peptide conformational dynamics and thermodynamics