YASARA 19.9.16 – Molecular Graphics, Modeling & Simulation program

YASARA 19.9.16

:: 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.

VCell 7.1 – Environment for Modeling & Simulation of Cell Biology

VCell 7.1

:: DESCRIPTION

VCell (Virtual Cell) is a unique computational environment for modeling and simulation of cell biology . It has been specifically designed to be a tool for a wide range of scientists, from experimental cell biologists to theoretical biophysicists. The creation of biological or mathematical models can range from the simple, to evaluate hypotheses or to interpret experimental data, to complex multi-layered models used to probe the predicted behavior of complex, highly non-linear systems. Such models can be based on both experimental data and purely theoretical assumptions.

::DEVELOPER

VCell Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • JAVA

:: DOWNLOAD

VCell

:: MORE INFORMATION

Citation

Moraru, II, J.C. Schaff, B.M. Slepchenko, and L.M. Loew. 2002.
The virtual cell: an integrated modeling environment for experimental and computational cell biology.
Ann N Y Acad Sci. 971:595-6. PMID 12438191

GPCR-ModSim – Computational Modeling and Simulation of G-Protein Coupled Receptors

GPCR-ModSim

:: DESCRIPTION

GPCR-ModSim is a centralized and easy to use service dedicated to the structural modeling of G-protein Coupled Receptors (GPCRs).

::DEVELOPER

GPCR-ModSim team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

GPCR-ModSim: A comprehensive web based solution for modeling G-protein coupled receptors.
Esguerra M, Siretskiy A, Bello X, Sallander J, Gutiérrez-de-Terán H.
Nucleic Acids Res. 2016 May 10. pii: gkw403.

InfMod3DGen – Inferential Modeling of 3D Chromatin Structure

InfMod3DGen

:: DESCRIPTION

InfMod3DGen is a new Bayesian framework to derive the 3D architecture of a chromosome from 3C-based data.

::DEVELOPER

InfMod3DGen team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • MatLab

:: DOWNLOAD

 InfMod3DGen

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2015 Apr 30;43(8):e54. doi: 10.1093/nar/gkv100.
Inferential modeling of 3D chromatin structure.
Wang S, Xu J, Zeng J.

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

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

GrammR 1.1.0 – Graphical Representation and Modeling of Metagenomic reads

GrammR 1.1.0

:: DESCRIPTION

GrammR represents metagenomic samples on the Euclidean space to examine similarity amongst samples by studying clusters in the model. Given the matrix of metagenomic counts for samples, this package (1) quantifies dissimilarity between samples using Kendall’s tau-distance, (2) constructs multidimensional models of different dimension, and (3) plots the models for visualization and comparison.

::DEVELOPER

Statistical Genetics and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOs
  • R

:: DOWNLOAD

 GrammR

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Jan 20. pii: btv032. [Epub ahead of print]
GrammR: Graphical Representation and Modeling of Count Data with Application in Metagenomics.
Ayyala DN, Lin S

BayesFlow 0.1 – Latent Modeling of Flow Cytometry Cell Populations

BayesFlow 0.1

:: DESCRIPTION

BayesFlow is a Bayesian hierarchical model, that models the variation across indivuals for clow cytometry data.

::DEVELOPER

Jonas Wallin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Python

:: DOWNLOAD

 BayesFlow

:: MORE INFORMATION

Citation

Erratum to: BayesFlow: latent modeling of flow cytometry cell populations.
Johnsson K, Wallin J, Fontes M.
BMC Bioinformatics. 2016 Mar 31;17(1):149.

InteractiveROSETTA 2.1 – GUI for PyRosetta Protein Modeling Suite

InteractiveROSETTA 2.1

:: 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

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.