Exhaustive mutagenesis in silico: Multicoordinate free energy calculations on proteins and peptides

Proteins: Structure, Function and Genetics

Volumn 41, Issue 3, 2000, Pages 385-397

  Pitera, Jed W ^a   Kollman, Peter A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

AMBER; Computer simulation; Free energy; Protein engineering; T4 lysozyme

Indexed keywords

M PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CONFORMATIONAL TRANSITION; ENERGY RECOVERY; MUTAGENESIS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STABILITY; THERMODYNAMICS;

EID: 0034669841     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/1097-0134(20001115)41:3<385::AID-PROT100>3.0.CO;2-R     Document Type: Article

References (40)

1. Designing an optimum guest for a host using multi-molecule free energy calculations: Predicting the best ligand for Rebek's 'Tennis Ball.'
2. Construction and ranking of new HIV-1 reverse transcriptase TIBO inhibitors combining computational methods at different levels of accuracy
3. Simulation of the solvation free energies of methane, ethane, and propane and corresponding amino acid dipeptides: A critical test of the 'bond-PMF' correction, a new set of hydrocarbon parameters, and the gas phase-water hydrophobicity scale
4. Modeling protein stability: A theoretical analysis of the stability of T4 lysozyme mutants
5. Probing protein stability with unnatural amino acids
6. Affinities of amino acid side-chains for solvent water
7. Dominant forces in protein folding
8. Can the stability of protein mutants be predicted by free energy calculations?
9. Equation of state calculations by fast computing machines
10. The lag between the Hamiltonian and the system configuration in free energy perturbation calculations
11. Enhanced sampling in molecular dynamics: Use of the time-dependent hartree approximation for a simulation of carbon monoxide diffusion through myoglobin
12. Use of locally enhanced sampling in free energy calculations: Testing and application to the alpha→beta anomerization of glucose
13. Overcoming barriers in macromolecular simulations: Non-Boltzmann thermodynamic integration
14. Treatment of rotational isomers in free-energy evaluations: Analysis of the evaluation of free-energy differences by molecular dynamics simulations of systems with rotational isomeric states
15. A rapidly convergent simulation method: Mixed monte carlo stochastic dynamics
16. Optimization methods for conformational sampling using a Boltzmann-weighted mean field approach
17. Computational method for the design of enzymes with altered substrate specificity
18. Conformational equilibria of valine studied by dynamics simulation
19. Precision of free energies calculated by molecular dynamics simulations of peptides in solution
20. Free energy calculations of the mutation of ile96-ala in barnase: Contributions to the difference in stability
21. De novo protein design: Fully automated sequence selection
22. Lambda-dynamics: A new approach to free energy calculations
23. Hydrophobic packing in T4 lysozyme probed by cavity-filling mutants
24. Structure of bacteriophage T4 lysozyme refined at 1.7 A resolution
25. Can one predict protein stability? An attempt to do so for residue 133 of T4 lysozyme using a combination of free energy derivatives, PROFEC, and free energy perturbation methods
26. Efficient estimation of free energy differences from Monte Carlo data
27. A comparison of alternative approaches to free energy calculations
28. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structure and energetic properties of molecules
29. Numerical Integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of N-Alkanes
30. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
31. Comparison of simple potential functions for the simulation of liquid water
32. Molecular dynamics with coupling to an external bath
33. Molecular dynamics simulations at constant pressure and/or temperature
34. Nonphysical sampling distributions in Monte Carlo free energy estimation: Umbrella sampling
35. The weighted histogram analysis method for free-energy calculations on biomolecules 1. The method
36. Stabilizing and destabilizing effects of placing beta-branched amino acids in protein alpha-helices
37. Multiple alanine replacements within alpha-helix 126-134 of T4 lysozyme have independent, additive effects on both structure and stability
38. Solvation thermodynamics of nonionic solutes
39. Biosynthetic method for introducing unnatural amino acids site-specifically into proteins
40. Estimating the relative free energy of different molecular states with respect to a single reference state