[SMMP] A modern package for simulation of proteins

DOI10.1016/S0010-4655(01)00197-7zbMath0980.92011WikidataQ58429998 ScholiaQ58429998MaRDI QIDQ5944557

Chin-Kun Hu, Frank Eisenmenger, Ulrich H. E. Hansmann, Shura Hayryan

Publication date: 7 March 2002

Published in: Computer Physics Communications (Search for Journal in Brave)

zbMATH Keywords

energy minimization; conformation; Fortran package; protein simulation

Mathematics Subject Classification ID

65C20: Probabilistic models, generic numerical methods in probability and statistics

65C05: Monte Carlo methods

92C40: Biochemistry, molecular biology

92-08: Computational methods for problems pertaining to biology

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A COMBINATION OF REPLICA EXCHANGE MONTE CARLO AND ENERGY LANDSCAPE PAVING ALGORITHMS TO INCREASE THE EFFECTIVENESS OF CONFORMATIONAL SAMPLING, NUMERICAL COMPARISON OF WANG–LANDAU SAMPLING AND PARALLEL TEMPERING FOR MET-ENKEPHALIN, CAVE: A package for detection and quantitative analysis of internal cavities in a system of overlapping balls: Application to proteins, Application of Wang-Landau sampling to a protein model using SMMP, Generalized ensemble techniques and protein folding simulations, ARVO: A Fortran package for computing the solvent accessible surface area and the excluded volume of overlapping spheres via analytic equations, An enhanced version of SMMP-open-source software package for simulation of proteins, SMMP v. 3.0-simulating proteins and protein interactions in Python and Fortran, Application of biased Metropolis algorithms: from protons to proteins, New algorithms and the physics of proteins

Uses Software

• SMMP

Cites Work

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• Equation of State Calculations by Fast Computing Machines