ALMOST 2.1.0 – Molecular Simulation toolkit for Protein Structure Determination

ALMOST 2.1.0

:: DESCRIPTION

ALMOST (all atom molecular simulation toolkit) is a fast and flexible molecular modeling environment that provides powerful and efficient algorithms for molecular simulation, homology modeling, de novo design and ab-initio calculations.

::DEVELOPER

The Vendruscolo Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ALMOST

:: MORE INFORMATION

Citation

J Comput Chem. 2014 May 30;35(14):1101-5. doi: 10.1002/jcc.23588. Epub 2014 Mar 27.
ALMOST: an all atom molecular simulation toolkit for protein structure determination.
Fu B1, Sahakyan AB, Camilloni C, Tartaglia GG, Paci E, Caflisch A, Vendruscolo M, Cavalli A.

OpenMM Zephyr 2.0.3 – Molecular Simulation Application

OpenMM Zephyr 2.0.3

:: DESCRIPTION

OpenMM Zephyr is a molecular simulation application for studying molecular dynamics of proteins, RNA, and other molecules. Zephyr guides the user through a work flow for setting up and running a specialized version of the molecular dynamics application gromacs. This version of gromacs uses the OpenMM API for GPU-accelerated molecular simulations.

::DEVELOPER

OpenMM Zephyr Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX/  Linux

:: DOWNLOAD

OpenMM Zephyr

:: MORE INFORMATION

Citation

M. S. Friedrichs, P. Eastman, V. Vaidyanathan, M. Houston, S. LeGrand, A. L. Beberg, D. L. Ensign, C. M. Bruns, V. S. Pande.
Accelerating Molecular Dynamic Simulation on Graphics Processing Units.
J. Comp. Chem., 30(6):864-872 (2009)

 

PROTEAN – Torsion Space Molecular Simulations

PROTEAN

:: DESCRIPTION

PROTEAN is a set of Fortran subroutines for calculating the equations ofmotion in torsion space for polypeptides. Torsion space is the space of all rotatable bonds. Bond lengths and bond angles remain fixed at their ideal values in a torsion space simulation. Simulations in torsion space are at least ten times more efficient than simulations in Cartesian space.

::DEVELOPER

Chris Bystroff

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

PROTEAN

:: MORE INFORMATION

Citaiton

Bystroff, C. (2001)
An alternative derivation of the equations of motion in torsion space for a branched linear chain.
Protein Engineering 14, 825-828.

YUP 1.080827 / Yammp 2 – Molecular Simulation

YUP 1.080827 / Yammp 2

:: DESCRIPTION

YUP (Yammp Under Python), also known as Yammp 2, is a molecular modeling program. Although a general purpose tool, development is currently concentrated on molecular simulations (mechanics) and on reduced representation and multiscale modeling. YUP is based on an earlier program Yammp.

::DEVELOPER

The Harvey Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

YUP

:: MORE INFORMATION

Citation:

Tan, R. K. Z., Petrov, A. S., Harvey, S. C. YUP: A Molecular Simulation Program for Coarse-Grained and Multiscaled Models. J. Chem. Theory Comput., 2006, 2(3), 529-540