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

DOI10.1016/J.CPC.2007.11.004MaRDI QIDQ710293zbMATH OpenOpenAlexWikidataFDO

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

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)

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

Cites work

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

Cited in

(10)

• Browndye: A software package for Brownian dynamics
• An enhanced version of SMMP-open-source software package for simulation of proteins
• [SMMP] A modern package for simulation of proteins
• Golden ratio simulated annealing for protein folding problem
• Python for unified research in econometrics and statistics
• 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
• freud: a software suite for high throughput analysis of particle simulation data

Describes a project that uses

Uses Software

• Python
• PyMOL
• MPI
• SciPy

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