Tag: Molecular Modeling

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. Thompson , Planaria 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.

ZMM 2020 – Molecular Modeling program for Theoretical studies of systems of any complexity

ZMM 2020

:: DESCRIPTION

ZMM is a molecular modeling program for theoretical studies of systems of any complexity: small molecules, peptides, proteins, nucleic acids, and ligand-receptor complexes.

::DEVELOPER

 

:: SCREENSHOTS

ZMM

:: REQUIREMENTS

  • Windows / Linux / Mac

:: DOWNLOAD

 ZMM

:: MORE INFORMATION

Citation

J Comput Aided Mol Des. 2010 Feb;24(2):91-105. doi: 10.1007/s10822-009-9317-9. Epub 2010 Jan 30.
Docking flexible ligands in proteins with a solvent exposure- and distance-dependent dielectric function.
Garden DP, Zhorov BS.

Gorgon 2.2.0 – Molecular Modeling system

Gorgon 2.2.0

:: DESCRIPTION

Gorgon is an interactive molecular modeling system specifically geared towards cryo-EM and other low resolution structures of macromolecular complexes. The long term goal of the gorgon project is to be able to address to every part of the molecular modeling pipeline starting from the initial volumetric reconstruction of the complex all the way to the final placement of each individual atom.

::DEVELOPER

The National Center for Macromolecular Imaging (NCMI)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows  / Linux / MacOsX

:: DOWNLOAD

 Gorgon

:: MORE INFORMATION

Citation

J Struct Biol. 2011 May;174(2):360-73. Epub 2011 Feb 4.
Modeling protein structure at near atomic resolutions with Gorgon.
Baker ML, Abeysinghe SS, Schuh S, Coleman RA, Abrams A, Marsh MP, Hryc CF, Ruths T, Chiu W, Ju T.

VEGA ZZ 3.2.1.33 – Molecular Modeling Toolkit

VEGA ZZ 3.2.1.33

:: DESCRIPTION

VEGA ZZ is the evolution of the well known VEGA OpenGL package and includes several new features and enhancements making your research jobs very easy. VEGA was originally developed to create a bridge between most of the molecular software packages only, but in the years, enhancing its features, it’s evolved to a complete molecular modelling suite. This software is FREE for non-profit academic uses.

::DEVELOPER

Drug Design Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 VEGA ZZ

:: MORE INFORMATION

Citation

Pedretti A., Villa L., Vistoli G.,
“VEGA – An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script” programming“,
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, Vol. 18, 167-173 (2004).

Mc-Sym 3.3.2 – Molecular Modeling using Constraint Satisfaction

Mc-Sym 3.3.2

:: DESCRIPTION

Mc-Sym (Macromolecular Conformations by SYMbolic programming) is a software that builds RNA 3-D structures using coordinates and relations between residues extracted from X-ray crystallography and NMR found in the RCSB Protein Data Bank and the Rutgers Nucleic Acid Database and from theoretical models. Constraints can be applied to the building procedure to ensure that the generated models are valid. The RNA structures properties and constraints are entered in a script or interactively within the mcsym interpreter.

::DEVELOPER

Laboratoire de Biologie Informatique et Théorique

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/IRIX/SunOS

:: DOWNLOAD

 Mc-Sym

:: MORE INFORMATION

Citation:

Robert Pinard, Dominic Lambert, Nils G. Walter, Joyce E. Heckman, François Major, and John M. Burke,
Structural Basis for the Guanosine Requirement of the Hairpin Ribozyme,
Biochemistry; 1999; 38(49); 16035-16039.

SketchBio 0.0.10 – 3D Interface for Molecular Modeling and Animation

SketchBio 0.0.10

:: DESCRIPTION

SketchBio is  a tool that incorporates state-of-the-art bimanual interaction and drop shadowsto enable rapid construction of molecular structures and animations

::DEVELOPER

CISMM (Computer Integrated Systems for Microscopy and Manipulation)

:: SCREENSHOTS

SketchBio

:: REQUIREMENTS

  • Windows
  • UCSF Chimera
  • Blender

:: DOWNLOAD

 SketchBio

 :: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Oct 30;15(1):334.
SketchBio: a scientist’s 3D interface for molecular modeling and animation.
Waldon SM, Thompson PM, Hahn PJ, Taylor RM 2nd.

BetaMol v0.92d – Molecular Modeling, Analysis, and Processing software

BetaMol v0.92d

:: DESCRIPTION

BetaMol is a molecular modeling, analysis, and processing software completely based on the theory of the Voronoi diagram, the quasi-triangulation, and the Beta-complex.

::DEVELOPER

Voronoi Diagram Research Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 BetaMol

:: MORE INFORMATION

Citation

Youngsong Cho, Jae-Kwan Kim, Joonghyun Ryu, Chung-In Won, Chong-Min Kim, Donguk Kim, and Deok-Soo Kim,
BetaMol: a molecular modeling, analysis and visualization software based on the beta-complex and the quasi-triangulation,
Journal of Advanced Mechanical Design, Systems, and Manufacturing, Vol.6, Issue 3, pp. 389-403, 2012

Facio 23.1.3 – 3D-Graphics program for Molecular Modeling and Visualization

Facio 23.1.3

:: DESCRIPTION

Facio is an OpenGL-based 3D-graphics program for molecular modeling and visualization of quantum chemical calculations (GAMESS and Gaussian)

Since Facio internally uses PDB (Protein Data Bank) format, it can also display a 3D-structure of biological macromolecules, such as proteins and nucleic acid with emphasizing their secondary or quaternary structures.

::DEVELOPER

 Masahiko Suenaga @ Kyushu University

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 Facio

:: MORE INFORMATION

Citation

M. Suenaga,
Facio: New Computational Chemistry Environment for PC GAMESS
Journal of Computer Chemistry, Japan, Vol. 4, No. 1 pp. 25-32 (2005).

OpenMM 7.4 / PyOpenMM 4.0 – Library for Molecular Modeling Simulation

OpenMM 7.4 / PyOpenMM 4.0

:: DESCRIPTION

OpenMM is a library which provides tools for modern molecular modeling simulation. As a library it can be hooked into any code, allowing that code to do molecular modeling with minimal extra coding.

PyOpenMM is a python API that wraps the OpenMM library.

::DEVELOPER

OpenMM Team , PyOpenMM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX/  Linux
  • Python

:: DOWNLOAD

OpenMM , PyOpenMM

:: 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)

BALLView / BALL 1.5.0 – Molecular Modeling & Visualization

BALLView / BALL 1.5.0

:: DESCRIPTION

BALLView is a standalone molecular modeling and visualization application.BALL has been designed as a tool for rapid software prototyping in molecular modeling and drug design.

BALL (Biochemical ALgorithms Library) is an application framework implemented in C++ that has been specifically designed for Computational Molecular Biology and Molecular Modeling.

::DEVELOPER

BALL Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  MacOsX / Window

:: DOWNLOAD

BALL

:: MORE INFORMATION

Citation:

Andreas Hildebrandt, Anna Katharina Dehof, Alexander Rurainski, Andreas Bertsch, Marcel Schumann, Nora C Toussaint, Andreas Moll, Daniel Stockel, Stefan Nickels, Sabine C Mueller, Hans-Peter Lenhof, Oliver Kohlbacher:
“BALL – Biochemical Algorithms Library 1.3”
2010, BMC Bioinformatics, 11:531