VMD 1.9.4 – Molecular Graphics Viewer

VMD 1.9.4

:: DESCRIPTION

VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.

::DEVELOPER

Theoretical and Computational Biophysics group at the University of Illinois.

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

VMD

:: MORE INFORMATION

Humphrey, W., Dalke, A. and Schulten, K., “VMD – Visual Molecular Dynamics”, J. Molec. Graphics, 1996, vol. 14, pp. 33-38.

DOCK 6.9 – Docking Molecules to each other

DOCK 6.9

:: DESCRIPTION

DOCK addresses the problem of “docking” molecules to each other. In general, “docking” is the identification of the low-energy binding modes of a small molecule, or ligand, within the active site of a macromolecule, or receptor, whose structure is known. A compound that interacts strongly with, or binds, a receptor associated with a disease may inhibit its function and thus act as a drug. Solving the docking problem computationally requires an accurate representation of the molecular energetics as well as an efficient algorithm to search the potential binding modes.

::DEVELOPER

DOCK Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

DOCK

:: MORE INFORMATION

Lang, P.T., Brozell, S.R., Mukherjee, S., Pettersen, E.T., Meng, E.C., Thomas, V., Rizzo, R.C., Case, D.A., James, T.L., Kuntz, I.D.
DOCK 6: Combining Techniques to Model RNA-Small Molecule Complexes.
RNA 15:1219-1230, 2009.

UCSF Chimera 1.14 – Molecular Modeling System

UCSF Chimera 1.14

:: DESCRIPTION

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, government, non-profit, and personal use.

::DEVELOPER

the Resource for Biocomputing, Visualization, and Informatics (RBVI) at UCSF

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  MacOsX / Window

:: DOWNLOAD

UCSF Chimera

:: MORE INFORMATION

Citation:

UCSF Chimera–a visualization system for exploratory research and analysis. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. J Comput Chem. 2004 Oct;25(13):1605-12.

Rchemcpp 2.24.0 – An R package for Computing the Similarity of Molecules

Rchemcpp 2.24.0

:: DESCRIPTION

Chemcpp is an R package that is the computation of similarities between molecules by kernel functions.

::DEVELOPER

Institute of Bioinformatics, Johannes Kepler University Linz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

Rchemcpp

:: MORE INFORMATION

Citation

Rchemcpp: a web service for structural analoging in ChEMBL, Drugbank and the Connectivity Map.
Klambauer G, Wischenbart M, Mahr M, Unterthiner T, Mayr A, Hochreiter S.
Bioinformatics. 2015 Oct 15;31(20):3392-4. doi: 10.1093/bioinformatics/btv373.

ICM-Browser 3.8-7d – Molecules & Sequence Alignments Visualization

ICM-Browser 3.8-7d

:: DESCRIPTION

ICM-Browser provides a biologist or a chemist with direct access to the treasures of structural biology and protein families.It reads a variety of file formats directly from the database web-sites including: PDB, chemical, electron density maps, sequence and alignment files. ICM-Browser provides a rich professional molecular graphics environment with powerful representations of proteins, DNA and RNA, and multiple sequence alignments.

When you purchase the license ICM-Browser will become ICM-Browser-Pro.ICM-Browser-Pro is a high quality visualizer and annotator for three dimensional molecular structures, sequences, alignments, chemical spreadsheets and biological data. It allows you to read data from multiple file formats, annotate the data, and write multi-slide documents in a single small cross-platform file. ICM Browser Pro is well suited for creating, storing and sharing structural, biological and chemical information. The files can then be opened and viewed with the free ICM Browser.

::DEVELOPER

Molsoft LLC.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/Mac OS X

:: DOWNLOAD

ICM-Browser ; Manual

:: MORE INFORMATION

Layers – An Algorithm that Peels Molecule as Layers

Layers

:: DESCRIPTION

Layers is a molecular surface peeling algorithm and its applications to analyze protein structures.

::DEVELOPER

Computational Structural Biology Lab , Indian Institute of Technology Kharagpur

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Layers: A molecular surface peeling algorithm and its applications to analyze protein structures.
Karampudi NB, Bahadur RP.
Sci Rep. 2015 Nov 10;5:16141. doi: 10.1038/srep16141.

Avogadro 2.0.8.0 – Molecule Editor & Visualizer

Avogadro 2.0.8.0

:: DESCRIPTION

Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.

::DEVELOPER

Marcus D. HanwellGeoff HutchisonTim Vandermeersch

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux

:: DOWNLOAD

Avogadro

:: MORE INFORMATION

Citation

J Cheminform. 2012 Aug 13;4(1):17. doi: 10.1186/1758-2946-4-17.
Avogadro: an advanced semantic chemical editor, visualization, and analysis platform.
Hanwell MD, Curtis DE, Lonie DC, Vandermeersch T, Zurek E, Hutchison GR.

iMolview 1.8.7 – iPhone, iPad and Android App for Browsing Protein, DNA & Drug Molecules in 3D

iMolview 1.8.7

:: DESCRIPTION

iMolview is an app for the iPhone , iPad and Android that lets you browse protein, DNA, and drug molecules in 3D. The app has a direct link to the Protein Data Bank (PDB) and DrugBank and has a fast and easy to use interface. Touching the molecules via the screen allows you to interact immediately with the 3D structures in a unique way. You can zoom in and out, rotate, spin, pan, and clip the 3D molecules with your finger tips in ways that are impossible using a traditional mouse and desktop computer.

::DEVELOPER

Molsoft LLC.

:: SCREENSHOTS

:: REQUIREMENTS

  • IPhone / IPad / Android

:: DOWNLOAD

iMolview

:: MORE INFORMATION