An enhanced version of SMMP-open-source software package for simulation of proteins

DOI10.1016/J.CPC.2005.10.013MaRDI QIDQ709898zbMATH OpenOpenAlexWikidataFDO

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

Publication date 18 October 2010

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

Full work available at URL https://doi.org/10.1016/j.cpc.2005.10.013

zbMATH Keywords

Monte Carlominimizationstructure predictionprotein foldingFORTRAN packagegeneralized-ensemble simulations

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Statistical mechanics of polymers (82D60) Molecular structure (graph-theoretic methods, methods of differential topology, etc.) (92E10)

Recommendations

• SMMP v. 3.0-simulating proteins and protein interactions in Python and Fortran
• [SMMP] A modern package for simulation of proteins
• AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
• Browndye: A software package for Brownian dynamics
• Parallel molecular dynamics simulation of a protein

Cites work

• scientific article; zbMATH DE number 274399 (Why is no real title available?)
• ARVO: A Fortran package for computing the solvent accessible surface area and the excluded volume of overlapping spheres via analytic equations
• [SMMP] A modern package for simulation of proteins

Cited in

(9)

• CAVE: A package for detection and quantitative analysis of internal cavities in a system of overlapping balls: Application to proteins
• Browndye: A software package for Brownian dynamics
• [SMMP] A modern package for simulation of proteins
• Application of Wang-Landau sampling to a protein model using SMMP
• Ribosome Builder: a software project to simulate the ribosome
• REACH: A program for coarse-grained biomolecular simulation
• Data extraction module. A supplementary tool for the Ammos\_Protlig software package
• SMMP v. 3.0-simulating proteins and protein interactions in Python and Fortran
• sDMD: an open source program for discontinuous molecular dynamics simulation of protein folding and aggregation

Describes a project that uses

Uses Software

• NSOL
• SMMP

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