ArgusLab 4.0.1 – Molecular Modeling, Graphics & Drug Design Program

ArgusLab 4.0.1

:: DESCRIPTION

ArgusLab is a molecular modeling, graphics, and drug design program.The ArgusDock docking engine, implemented in ArgusLab4.0, approximates an exhaustive search method, with similarities to DOCK and Glide. Flexible ligand docking is possible with ArgusLab, where the ligand is described as a torsion tree and grids are constructed that overlay the binding site. Ligand’s root node (group of bonded atoms that do not have rotatable bonds) is placed on a search point in the binding site and a set of diverse and energetically favorable rotations is created. For each rotation, torsions in breadth-first order are constructed and those poses that survive the torsion search are scored. The N-lowest energy poses are retained and the final set of poses undergoes coarse minimization, re-clustering and ranking.

::DEVELOPER

Mark A. ThompsonPlanaria Software LLC, Seattle, WA

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

ArgusLab

:: MORE INFORMATION

Citation

Thompson, M. A. (2004).
Molecular docking using ArgusLab, an efficient shape-based search algorithm and the AScore scoring function.
ACS meeting, Philadelphia, 172, CINF 42, PA.

Gromita 4.6 – GUI for GROMACS

Gromita 4.6

:: DESCRIPTION

Gromita is a Graphical User Interface (GUI) for GROMACS (v.3 and 4). It is writen in perl making extensive use of perl/tk achieving portability in a wide variety of operating systems and architectures. Gromita provides friendly to use buttons in a windows-based environment while maintaining a terminal mode for the experienced user.

::DEVELOPER

Gromita Team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 Gromita

:: MORE INFORMATION

Citation

Sellis D, Vlachakis D, Vlassi M. (2009)
Gromita: A Fully Integrated Graphical User Interface to Gromacs 4.
Bioinform Biol Insights 2009:3 99-102

Desmond 2023.2 – High-speed Molecular Dynamics Simulation

Desmond 2023.2

:: DESCRIPTION

Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters. The code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms containing a large number of processors, but may also be executed on a single computer.

::DEVELOPER

D. E. Shaw Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Window / Linux / Mac OsX
  • Python

:: DOWNLOAD

Desmond

:: MORE INFORMATION

Citation

Kevin J. Bowers, Edmond Chow, Huafeng Xu, Ron O. Dror, Michael P. Eastwood, Brent A. Gregersen, John L. Klepeis, István Kolossváry, Mark A. Moraes, Federico D. Sacerdoti, John K. Salmon, Yibing Shan, and David E. Shaw,
Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters,”
Proceedings of the ACM/IEEE Conference on Supercomputing (SC06), Tampa, Florida, November 11–17, 2006

FoldX 3.0 – Force Field for Energy Calculations and Protein Design

FoldX 3.0

:: DESCRIPTION

FoldX conduct rapid evaluation of the effect of mutations on the stability, folding and dynamics of proteins and nucleic acids.

The FoldX/Yasara ( FoldX plugin for YASARA) is a software package to access and run FoldX commands in YASARA.

::DEVELOPER

Serrano’s laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FoldX

:: MORE INFORMATION

Citation

The FoldX web server: an online force field.
Schymkowitz J, Borg J, Stricher F, Nys R, Rousseau F, Serrano L.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W382-8.

p3d 0.4.3 – Python module for Structural Bioinformatics

p3d 0.4.3

:: DESCRIPTION

p3d is an object oriented Python module that adds a simple yet powerful interface to the Python interpreter to process and analyse three dimensional protein structure files (PDB files).

::DEVELOPER

CELLULAR AND MOLECULAR FUNCTIONS OF REACTIVE OXYGEN SPECIES

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Python

:: DOWNLOAD

  p3d

:: MORE INFORMATION

Citation

Christian Fufezan and Michael Specht
p3d – Python module for structural bioinformatics
BMC Bioinformatics 2009, 10:258 doi:10.1186/1471-2105-10-258

Tuftsviewer / Molli 0.99 – Cross Platform Open Source PDB Viewer

Tuftsviewer / Molli 0.99

:: DESCRIPTION

TuftsViewer is an open source program that allows the visualization, rotation and coordinated viewing of multiple 3D protein molecules on the 2D screen.

TuftsViewer has been renamed to Molli. Molli is an open source cross-platform protein structure viewer based on the OpenGL and wxWidgets libraries.

::DEVELOPER

Cowen Group

:: SCREENSHOTS

tuftsviewer

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 Molli

:: MORE INFORMATION

Citation:

Matt Menke, Sara Su, Connor Gramazio, Caitlin Crumm, Daniela Extrum-Fernandez and Lenore Cowen,
TuftsViewer: An Intuitive Interface for viewing 3D Protein Structures,
Proceedings of ISMB 3DSIG, p. 24.

pdb-tools 0.2.1 – Editing and Performing Calculations on wwPDB Files

pdb-tools 0.2.1

:: DESCRIPTION

pdbTools is a set of command line python scripts that manipulate wwPDB protein and nucleic acid structure files. There are many programs, both open source and proprietary, that perform similar tasks; however, most of these tools are buried within programs of larger functionality.

::DEVELOPER

Harms Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Python

:: DOWNLOAD

  pdb-tools

:: MORE INFORMATION

Reconstruct 1.0 – Reconstructing 3D Structures from Contact Maps

Reconstruct 1.0

:: DESCRIPTION

RECONSTRUCT is a command line program for reconstruction of protein contact maps that uses the distgeom program of the TINKER package.

::DEVELOPER

Reconstruct team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java
  • Tinker

:: DOWNLOAD

 Reconstruct

:: MORE INFORMATION

Citation

Optimal contact definition for reconstruction of Contact Maps.
Jose M Duarte, Rajagopal Sathyapriya, Henning Stehr, Ioannis Filippis and Michael Lappe.
BMC Bioinformatics 2010, 11:283.

CMView 1.1.1 – Protein Contact Map Visualization and Analysis

CMView 1.1.1

:: DESCRIPTION

CMView is an intervative contact map visualization and analysis tool. The tool provides functions for contact map calculation from structure, basic editing, visualization in contact map and 3D space and structural comparison with different built-in alignment methods.

::DEVELOPER

CMView team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 CMView

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jun 1;27(11):1573-4. Epub 2011 Apr 5.
CMView: interactive contact map visualization and analysis.
Vehlow C, Stehr H, Winkelmann M, Duarte JM, Petzold L, Dinse J, Lappe M.