SMMP v. 3.0-simulating proteins and protein interactions in Python and Fortran

DOI10.1016/J.CPC.2007.11.004zbMATH Open1196.82058OpenAlexW2058823465WikidataQ123129457 ScholiaQ123129457MaRDI QIDQ710293FDOQ710293

Frank Eisenmenger, Sandipan Mohanty, Ulrich H. E. Hansmann, Jan H. Meinke

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.2007.11.004

zbMATH Keywords

Monte Carlominimizationprotein 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)

Cites Work

• Annealing Markov Chain Monte Carlo with Applications to Ancestral Inference
• [SMMP] A modern package for simulation of proteins
• An enhanced version of SMMP-open-source software package for simulation of proteins

Cited In (4)

• [SMMP] A modern package for simulation of proteins
• SMMP
• Golden Ratio Simulated Annealing for Protein Folding Problem
• Python for Unified Research in Econometrics and Statistics

Uses Software

• SciPy
• MPI
• PyMOL
• Python

   Recommendations

• An enhanced version of SMMP-open-source software package for simulation of proteins 👍 👎
• [SMMP A modern package for simulation of proteins] 👍 👎
• Parallel molecular dynamics simulation of a protein 👍 👎
• 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 👍 👎
• DL_POLY_3: the CCP5 national UK code for molecular–dynamics simulations 👍 👎

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