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https://www.arca.fiocruz.br/handle/icict/57694
ROTATIONAL PROFILER: A FAST, AUTOMATED, AND INTERACTIVE SERVER TO DERIVE TORSIONAL DIHEDRAL POTENTIALS FOR CLASSICAL MOLECULAR SIMULATIONS
Author
Affilliation
Fundação Oswaldo Cruz, Instituto Aggeu Magalhães, Recife, Pernambuco, Brasil.
Swiss National Supercomputing Centre, Lugano, Ticino, Switzerland.
Universidade Federal de Pernambuco, Depatamento de Quimica Fundamental, Recife, PE, Brasil.
Universidade Federal de Viçosa, Depatamento de Biologia Geral, Viçosa, Minas Gerais , Brasil.
4
Laboratório Nacional de Computação Científica do Brasil, Petrópolis, Rio de Janeiro Brasil.
5
Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia, Rio Grande do Sul, Brasil.
Abstract
Rotational Profiler provides an analytical algorithm to compute sets of classical torsional dihedral parameters by fitting an empirical energy profile to a reference one that can be obtained experimentally or by quantum-mechanical methods. The resulting profiles are compatible with the functional forms in the most widely used biomolecular force fields (e.g., GROMOS, AMBER, OPLS, and CHARMM). The linear least-squares regression method is used to generate sets of parameters that best satisfy the fitting. Rotational Profiler is free to use, analytical, and force field/package independent. The formalism is herein described, and its usage, in an interactive and automated manner, is made available as a Web server at http://rotprof.lncc.br.
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