Journal ArticleDOI
Monte Carlo backbone sampling for polypeptides with variable bond angles and dihedral angles using concerted rotations and a Gaussian bias
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In this paper, an efficient concerted rotation algorithm for use in Monte Carlo statistical mechanics simulations of polypeptides was reported that includes flexible bond and dihedral angles, and Jacobian weighting is required in the Metropolis test to correct for imbalances in resultant transition probabilities.Abstract:
An efficient concerted rotation algorithm for use in Monte Carlo statistical mechanics simulations of polypeptides is reported that includes flexible bond and dihedral angles. A Gaussian bias is applied with driver bond and dihedral angles to optimize the sampling efficiency. Jacobian weighting is required in the Metropolis test to correct for imbalances in resultant transition probabilities. Testing of the methodology includes Monte Carlo simulations for polyalanines with 8–14 residues and a 36-residue protein as well as a search to find the lowest-energy conformer of the pentapeptide Met-enkephalin. The results demonstrate the formal correctness and efficiency of the method.read more
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Molecular dynamics: survey of methods for simulating the activity of proteins.
TL;DR: This review offers an outline of the origin of molecular dynamics simulation for protein systems and how it has developed into a robust and trusted tool, and covers more recent advances in theory and an illustrative selection of practical studies in which it played a central role.
Journal ArticleDOI
Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins
TL;DR: In this paper, the free energy of 15 amino acid side chain analogs derived from recent versions of the OPLS-AA, CHARMM, and AMBER parameter sets in TIP3P water using thermodynamic integration was obtained.
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Molecular modeling of organic and biomolecular systems using BOSS and MCPRO.
TL;DR: An overview is provided of the capabilities for the current versions of the BOSS and MCPRO programs for molecular modeling of organic and biomolecular systems, particularly for QM/MM studies of organicand enzymatic reactions and for protein‐ligand binding.
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Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction.
TL;DR: This work implements a backrub-inspired sampling method in the Rosetta structure prediction and design program and suggests that backrub sampling captures a sizable fraction of localized conformational changes that occur in natural proteins.
Journal ArticleDOI
LowModeMD—Implicit Low-Mode Velocity Filtering Applied to Conformational Search of Macrocycles and Protein Loops
TL;DR: The results of several computational experiments suggest that the method is capable of efficiently sampling low-strain energy conformations of complex systems with nontrivial nonbonded interaction networks.
References
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Journal ArticleDOI
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
TL;DR: In this article, the parametrization and testing of the OPLS all-atom force field for organic molecules and peptides are described, and the parameters for both torsional and non-bonded energy properties have been derived, while the bond stretching and angle bending parameters have been adopted mostly from the AMBER force field.
Journal ArticleDOI
The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii
TL;DR: In this article, a simple analytical formula for calculating Born radii rapidly and with useful accuracy is presented. But it is based on an atomic pairwise rij-4 treatment and contains several empirically determined parameters that were established by optimization against a data set of >10,000 accurate Born radi computed numerically using the Poisson equation on a diverse group of organic molecules, molecular complexes, oligopeptides, and a small protein.
Journal ArticleDOI
Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions.
TL;DR: Helix‐capping interactions were found to contribute to helix stability, even when the substitution site was not at the end of the peptide, and the implication for protein folding is that formation of peptide H‐bonds can largely offset the unfavorable entropy change caused by fixing the peptides backbone.
Journal ArticleDOI
Ring Closure and Local Conformational Deformations of Chain Molecules
Nobuhiro Go,Harold A. Scheraga +1 more
Journal ArticleDOI
NMR structure of the 35-residue villin headpiece subdomain.
TL;DR: The NMR structure of an autonomously folding subdomain from villin headpiece that forms a novel three helix structure with the actin-binding residues arrayed on the C-terminal helix is reported.
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