The SMMP (Simple Molecular Mechanics for Proteins) package is designed for molecular simulation of linear proteins using torsion angles as internal degrees of freedom. The package contains various modern Monte Carlo algorithms and energy minimization routines. The energy of the protein can be calculated by exploiting different force fields. Subroutines for approximating protein-solvent interaction by means of calculating the solvent accessible area of atomic groups are included.

References in zbMATH (referenced in 12 articles , 1 standard article )

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  1. Bazavov, Alexei; Berg, Bernd A.; Zhou, Huan-Xiang: Application of biased Metropolis algorithms: from protons to proteins (2010)
  2. Buša, Ján; Hayryan, Shura; Hu, Chin-Kun; Skřivánek, Jaroslav; Wu, Ming-Chya: CAVE: A package for detection and quantitative analysis of internal cavities in a system of overlapping balls: Application to proteins (2010)
  3. Hu, Chin-Kun; Ma, Wen-Jong: Molecular dynamics approach to relaxation and aggregation of polymer chains (2010)
  4. Yang, Jae-Suk; Kwak, Wooseop: Application of Wang-Landau sampling to a protein model using SMMP (2010)
  5. Meinke, Jan H.; Mohanty, Sandipan; Eisenmenger, Frank; Hansmann, Ulrich H.E.: SMMP v. 3.0-simulating proteins and protein interactions in Python and Fortran (2008)
  6. Eisenmenger, Frank; Hansmann, Ulrich H.E.; Hayryan, Shura; Hu, Chin-Kun: An enhanced version of SMMP-open-source software package for simulation of proteins (2006)
  7. Buša, Ján; Džurina, Jozef; Hayryan, Edik; Hayryan, Shura; Hu, Chin-Kun; Plavka, Ján; Pokorný, Imrich; Skřivánek, Jaroslav; Wu, Ming-Chya: ARVO: A Fortran package for computing the solvent accessible surface area and the excluded volume of overlapping spheres via analytic equations (2005)
  8. Arkin, Handan: A combination of replica exchange Monte Carlo and energy landscape paving algorithms to increase the effectiveness of conformational sampling (2004)
  9. Hansmann, Ulrich H.E.: New algorithms and the physics of proteins (2003)
  10. Hansmann, Ulrich H.E.: Generalized ensemble techniques and protein folding simulations (2002)
  11. Eisenmenger, Frank; Hansmann, Ulrich H.E.; Hayryan, Shura; Hu, Chin-Kun: [SMMP] A modern package for simulation of proteins (2001)
  12. Gao, Qingshi: A unified $O(\log N)$ and optimal sorting vector algorithm (1995)