Journal Article10.1080/07391102.1989.10507740
New methodology for computer-aided modelling of biomolecular structure and dynamics. 2. Local deformations and cycles.
Ruben Abagyan,Alexey K. Mazur +1 more
66
TL;DR: A unified approach is proposed for the efficient energy minimization and simulation of dynamic behavior of multimolecular systems having any set of variable internal coordinates, local deformation regions and cycles.
read more
Abstract: A new methodology for the conformational modelling of biomolecular systems (1) is extended to local deformations of chain molecules and to flexible molecular rings. It is shown that these two cases may be reduced to considering an equivalent molecular model with a regular tree-like topology. A simple procedure is developed to analyze any flexible rings (the five- and six-membered sugar rings of carbohydrates and nucleic acids, in particular) and local deformation regions by energy minimization. Dynamic equations are also derived for such molecular systems. As a result, a unified approach is proposed for the efficient energy minimization and simulation of dynamic behavior of multimolecular systems having any set of variable internal coordinates, local deformation regions and cycles. Advantages and domains of applicability of the approach are discussed.
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Citations
Protein structure prediction by global energy optimization
Ruben Abagyan
- 01 Jan 1997
TL;DR: The theoretical prediction of biomolecular structure from first principles and without the crutches of experimental restraints remains a dream.
27
Tabu search based strategies for conformational search.
Svetlana Stepanenko,Bernd Engels +1 more
TL;DR: The refinement of ranking procedure of the original GOTS method and the exploitation of simulated annealing elements are described, and the modifications of the GOTS algorithm necessary to adopt it to conformation searches are explained.
25
Reduced variable molecular dynamics
TL;DR: Application of this methodology is anticipated to provide a 10‐ to 100‐improvement in the speed of a large molecular trajectory as compared with the time required to run a conventional atomistic unconstrained simulation.
24
First-Principles-Based Multiscale, Multiparadigm Molecular Mechanics and Dynamics Methods for Describing Complex Chemical Processes
Andres Jaramillo-Botero,Robert J. Nielsen,Ravi Abrol,Julius T. Su,Tod A. Pascal,Jonathan E. Mueller,William A. Goddard +6 more
TL;DR: Some of the significant progress towards solving problems via a general multiscale, multiparadigm strategy based on first-principles quantum mechanics is described, including understanding the solvation effects on the reactivity of organic and organometallic structures, predicting transmembrane protein structures, understanding carbon nanotube nucleation and growth.
21
Mapping Conformational Dynamics of Proteins Using Torsional Dynamics Simulations
TL;DR: The relatively short simulation times required to capture these long-timescale conformational dynamics indicate that GNEIMO is a promising molecular-dynamics technique for studying domain motion in proteins.
20
References
Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes
TL;DR: In this paper, a numerical algorithm integrating the 3N Cartesian equations of motion of a system of N points subject to holonomic constraints is formulated, and the relations of constraint remain perfectly fulfilled at each step of the trajectory despite the approximate character of numerical integration.
20.9K
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.
15.5K