Journal ArticleDOI
Estimation of absolute and relative entropies of macromolecules using the covariance matrix
TLDR
In this paper, a new method for estimating absolute and relative entropies of conformers of a macromolecule was proposed based on the evaluation of the covariance matrix of Cartesian positional coordinates obtainable by computer simulation.About:
This article is published in Chemical Physics Letters.The article was published on 1993-12-17. It has received 586 citations till now. The article focuses on the topics: Covariance matrix.read more
Citations
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g_mmpbsa--a GROMACS tool for high-throughput MM-PBSA calculations.
TL;DR: A new tool, g_mmpbsa, which implements the MM-PBSA approach using subroutines written in-house or sourced from the GROMACS and APBS packages is described, and the calculated interaction energy of 37 structurally diverse HIV-1 protease inhibitor complexes is compared.
Journal ArticleDOI
End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design
TL;DR: In this review, methods to adjust the polar solvation energy and to improve the performance of MM/PBSA and MM/GBSA calculations are reviewed and discussed and guidance is provided for practically applying these methods in drug design and related research fields.
Journal ArticleDOI
Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms.
TL;DR: There is no one perfect "one size fits all" algorithm for clustering MD trajectories and that the results strongly depend on the choice of atoms for the pairwise comparison, so the best performance was observed with the average-linkage, means, and SOM algorithms.
Journal ArticleDOI
Parmbsc1: a refined force field for DNA simulations
Ivan Ivani,Pablo D. Dans,Agnes Noy,Alberto Perez,Ignacio Faustino,Jürgen Walther,Pau Andrio,Ramon Goni,Alexandra Balaceanu,Guillem Portella,Federica Battistini,Josep Lluís Gelpí,Carlos González,Michele Vendruscolo,Charles A. Laughton,Sarah A. Harris,David A. Case,Modesto Orozco +17 more
TL;DR: Parmbsc1, a force field for DNA atomistic simulation, which has been parameterized from high-level quantum mechanical data and tested for nearly 100 systems and provides high-quality results in diverse systems is presented.
Journal ArticleDOI
Water: A Tale of Two Liquids
Paola Gallo,Katrin Amann-Winkel,Charles Angell,Mikhail A. Anisimov,Frédéric Caupin,Charusita Chakravarty,Erik Lascaris,Thomas Loerting,Athanassios Z. Panagiotopoulos,John Russo,Jonas A. Sellberg,Harry Eugene Stanley,Hajime Tanaka,Carlos Vega,Limei Xu,Lars G. M. Pettersson +15 more
TL;DR: The behavior of water in the regime from ambient conditions to the deeply supercooled region is described and some of the possible experimental lines of research that are essential to complete a global picture that still needs to be completed.
References
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Journal ArticleDOI
Method for estimating the configurational entropy of macromolecules
Martin Karplus,Joseph N. Kushick +1 more
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Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme.
TL;DR: A new method for modelling protein dynamics using normal-mode analysis in internal co-ordinates, particularly well suited for modelling collective motion, makes possible direct visualization of biologically interesting modes, and is complementary to the more time-consuming simulation of molecular dynamics trajectories.
Journal ArticleDOI
Multiple Conformational States of Proteins: A Molecular Dynamics Analysis of Myoglobin
Ron Elber,Martin Karplus +1 more
TL;DR: A molecular dynamics simulation of myoglobin provides the first direct demonstration that the potential energy surface of a protein is characterized by a large number of thermally accessible minima in the neighborhood of the native structure.
Journal ArticleDOI
Free energy simulations.
Mihaly Mezei,David L. Beveridge +1 more
TL;DR: This paper focuses on the intermolecular case, where the particles of the system undergo diffusional motion and a harmonic or quasiharmonic treatment breaks down, and considers on free energy in molecular simulations take a distinctly different form for intramolecular and intermolescular degrees of freedom.
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Configurational entropy of native proteins
TL;DR: Simulations of the residual configurational entropy of a protein in the native state suggest that it is nearly an order of magnitude larger than the entropy of denaturation.