The Power of Hard-Sphere Models: Explaining Side-Chain Dihedral Angle Distributions of Thr and Val
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TLDR
It is shown that the observed side-chain dihedral angle distributions for both Val and Thr can be explained using only local steric interactions in a dipeptide mimetic, emphasizing the power of simple physical approaches and their importance for future advances in protein engineering and design.About:
This article is published in Biophysical Journal.The article was published on 2012-05-16 and is currently open access. It has received 29 citations till now. The article focuses on the topics: Dihedral angle.read more
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Diversity of Secondary Structure in Catalytic Peptides with β-Turn-Biased Sequences
Anthony J. Metrano,Nadia C. Abascal,Brandon Q. Mercado,Eric K. Paulson,Anna E. Hurtley,Scott J. Miller +5 more
TL;DR: X-ray crystallography has been applied to the structural analysis of a series of tetrapeptides that were previously assessed for catalytic activity in an atroposelective bromination reaction, suggesting that the conformational space available to simple peptide-based catalysts is more diverse than precedent might suggest.
Journal ArticleDOI
Protein Design: Past, Present, and Future
Lynne Regan,Diego Caballero,Michael R. Hinrichsen,Alejandro Virrueta,Danielle M. Williams,Corey S. O'Hern +5 more
TL;DR: Past milestones in protein design are surveyed, in addition to highlighting recent progress and future aspirations.
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Predicting the side-chain dihedral angle distributions of nonpolar, aromatic, and polar amino acids using hard sphere models.
TL;DR: It is found that a hard‐sphere model for a dipeptide mimetic that includes only steric interactions plus stereochemical constraints is able to recapitulate the key features of the back‐bone dependent observed amino acid side‐chain dihedral angle distributions.
Journal ArticleDOI
Interactions between Proteins and the Membrane Surface in Multiscale Modeling of Organic Fouling.
TL;DR: An improved multiscale modeling aimed at describing membrane fouling in the UltraFiltration (UF) process was proposed, and a good agreement between simulated and experimental permeate flux decays was observed.
Journal ArticleDOI
Enzyme Immobilization on Polymer Membranes: A Quantum and Molecular Mechanics Study
TL;DR: The proposed methodology made use of fundamental quantities, calculated without resorting to adjustable or empirical parameters, providing basic outputs useful for ascertaining enzymatic catalysis rate.
References
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PROCHECK: a program to check the stereochemical quality of protein structures
TL;DR: The PROCHECK suite of programs as mentioned in this paper provides a detailed check on the stereochemistry of a protein structure and provides an assessment of the overall quality of the structure as compared with well refined structures of the same resolution.
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CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Bernard R. Brooks,Robert E. Bruccoleri,Barry D. Olafson,David J. States,S. Swaminathan,Martin Karplus +5 more
TL;DR: The CHARMM (Chemistry at Harvard Macromolecular Mechanics) as discussed by the authors is a computer program that uses empirical energy functions to model macromolescular systems, and it can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations.
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GROMACS: Fast, flexible, and free
David van der Spoel,Erik Lindahl,Berk Hess,Gerrit Groenhof,Alan E. Mark,Herman J. C. Berendsen +5 more
TL;DR: The software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s is described, which is a very fast program for molecular dynamics simulation.