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.

metaRNAmodules 1.0.2 – Automated RNA 3D Module Extraction and Modeling

metaRNAmodules 1.0.2

:: DESCRIPTION

metaRNAmodules is a pipeline which completely automates extracting putative FR3D modules and mapping of such modules to Rfam alignments to obtain comparative evidence.

::DEVELOPER

Center for non-coding RNA in Technology and Health (RTH)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

  metaRNAmodules

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2013 Dec;41(22):9999-10009. doi: 10.1093/nar/gkt795.
Automated identification of RNA 3D modules with discriminative power in RNA structural alignments.
Theis C, Höner Zu Siederdissen C, Hofacker IL, Gorodkin J.

MolIDE 1.7 – Protein 3D Homology Modeling

MolIDE 1.7

:: DESCRIPTION

MolIDE is an open-source cross-platform graphical environment for homology modeling. It implements the most frequently used steps involved in modeling: sequence search, secondary structure prediction, multiple-round psiblast alignments, assisted alignment editing (integrating a template viewer and secondary structure prediction), side chain replacement and loop building. MolIDE takes an input target sequence and uses PSIBLAST to identify and align templates for comparative modeling of the target. The sequence alignment to any template can be manually modified within a graphical window of the target–template alignment and visualization of the alignment on the template structure. MolIDE builds the model of the target structure on the basis of the template backbone, predicted side.

::DEVELOPER

Dunbrack Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX /  Linux
  • SCWRL

:: DOWNLOAD

MolIDE

:: MORE INFORMATION

Citation

Qiang Wang, Adrian A Canutescu & Roland L Dunbrack Jr
SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling
Nature Protocols 3:1832-1847 (2008)

ProDy 1.10.10 – Python package for Analysis and Modeling of Protein Structural Dynamics

ProDy 1.10.10

:: DESCRIPTION

ProDy is a free and open-source Python package for analysis and modeling of protein structural dynamics. It allows for efficient analysis of large datasets and is suitable for development or prototyping of structure-based analysis and modeling software.

::DEVELOPER

Bahar lab

:: SCREENSHOTS

N/A

: REQUIREMENTS

:: DOWNLOAD

 ProDy

:: MORE INFORMATION

Citation:

Bakan A, Meireles LM, Bahar I
ProDy: Protein Dynamics Inferred from Theory and Experiments
Bioinformatics 2011 27(11):1575-1577.

GPCRautomodel – Automatic Modeling of Mammalian Olfactory Receptors and Docking of Odorants

GPCRautomodel

:: DESCRIPTION

GPCRautomodel allows the user to upload a GPCR sequence, choose a ligand in a library and obtain the 3D structure of the free receptor and ligand-receptor complex

::DEVELOPER

GPCRautomodel team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Automatic modeling of mammalian olfactory receptors and docking of odorants.
Launay G, Téletchéa S, Wade F, Pajot-Augy E, Gibrat JF, Sanz G.
Protein Eng Des Sel. 2012 Aug;25(8):377-86. doi: 10.1093/protein/gzs037.

InteractiveROSETTA 2.3.0 – GUI for PyRosetta Protein Modeling Suite

InteractiveROSETTA 2.3.0

:: DESCRIPTION

InteractiveROSETTA is a wxPython graphical interface for the PyRosetta and Rosetta protein modeling suites

::DEVELOPER

Chris Bystroff

:: SCREENSHOTS

InteractiveROSETTA

:: REQUIREMENTS

:: DOWNLOAD

 InteractiveROSETTA

:: MORE INFORMATION

Citation

InteractiveROSETTA: a graphical user interface for the PyRosetta protein modeling suite.
Schenkelberg CD, Bystroff C.
Bioinformatics. 2015 Aug 26. pii: btv492

YASARA 19.12.14 – Molecular Graphics, Modeling & Simulation program

YASARA 19.12.14

:: DESCRIPTION

YASARA (Yet Another Scientific Artificial Reality Application)is a molecular-graphics, -modeling and -simulation program.With an intuitive user interface, photorealistic graphics and support for affordable shutter glasses, autostereoscopic displays and input devices, YASARA creates a new level of interaction with the ‘artificial reality’, that allows you to focus on your goal and forget about the details of the program.

YASARA View is available for free and contains the basic functions you need to explore a macromolecular structure interactively, comparable to other molecule viewers.

YASARA Model contains YASARA View and adds all the functions you need to explore, analyze and model small and macromolecules in a production environment. This includes many features you often miss: unlimited undo/redo, macro recorder, quad-buffered stereo with shutter glasses or the DTI virtual window .

YASARA Dynamics contains YASARA Model and adds support for molecular simulations.

YASARA Structure contains YASARA Dynamics and adds all the functions needed to predict and validate macromolecular structures, including ligand docking and highly accurate force fields with knowledge-based potentials, and an optional module for NMR structure determination.

::DEVELOPER

YASARA Biosciences

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

YASARA

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jul 4. pii: btu426.
YASARA View – molecular graphics for all devices – from smartphones to workstations.
Krieger E1, Vriend G

Bioinformatics. 2002 Feb;18(2):315-8.
Models@Home: distributed computing in bioinformatics using a screensaver based approach.
Krieger E, Vriend G.

3DIANA – A Toolbox for Quaternary Structure Modeling

3DIANA

:: DESCRIPTION

3DIANA (3D Domain Interaction Analysis) is a web based environment designed to integrate bioinformatics-like information for the analysis of protein interactions and quaternary structure modellling

::DEVELOPER

Biocomputing Unit – CNB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • UCSF Chimera

:: DOWNLOAD

  3DIANA Chimera Plug-in

:: MORE INFORMATION

Citation:

3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling.
Segura J, Sanchez-Garcia R, Tabas-Madrid D, Cuenca-Alba J, Sorzano CO, Carazo JM.
Biophys J. 2016 Feb 23;110(4):766-75. doi: 10.1016/j.bpj.2015.11.3519

3DBIONOTES – Interactive View of Macromolecular Information

3DBIONOTES

:: DESCRIPTION

3DBIONOTES is a web based application designed to integrate protein structure, protein sequence and protein annotations in a unique graphical environment.

::DEVELOPER

Biocomputing Unit – CNB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

3DBIONOTES: A unified, enriched and interactive view of macromolecular information.
Tabas-Madrid D, Segura J, Sanchez-Garcia R, Cuenca-Alba J, Sorzano CO, Carazo JM.
J Struct Biol. 2016 May;194(2):231-4. doi: 10.1016/j.jsb.2016.02.007.

PRISM 2.0 – Prediction of Protein-protein Interactions and Modeling their 3D Complexes

PRISM 2.0

:: DESCRIPTION

The PRISM web server enables fast and accurate prediction of protein-protein interactions (PPIs).

::DEVELOPER

the COSBI (Computational Systems Biology) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

PRISM PROTOCOL

:: MORE INFORMATION

Citation

Baspinar A, Cukuroglu E, Nussinov R, Keskin O, Gursoy A.
PRISM: A web server and repository for prediction of protein-protein interactions and modeling their 3D complexes.
Nucl. Acids Res. (2014) doi: 10.1093/nar/gku397