SDA 7.1.2 / webSDA 1.0 – Simulation of Diffusional Association

SDA 7.1.2 / webSDA 1.0

:: DESCRIPTION

SDA simulates the diffusional association of two proteins/molecules or a protein/molecule to a solid state surface. If the atomic structure of the bound complex is known, SDA can be used to calculate bimolecular association rates. It can also be used to record Brownian dynamics trajectories or encounter complexes and calculate bimolecular electron transfer rate constants. SDA may also be used for rigid-body docking to predict the structure of protein-protein encounter complexes or the orientation in which a protein binds to a surface.

webSDA is a web server to simulate macromolecular diffusional association.

::DEVELOPER

Molecular and Cellular Modeling ,HITS gGmbH

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SDA

:: MORE INFORMATION

Citation

webSDA: a web server to simulate macromolecular diffusional association.
Yu X, Martinez M, Gable AL, Fuller JC, Bruce NJ, Richter S, Wade RC.
Nucleic Acids Res. 2015 Jul 1;43(W1):W220-4. doi: 10.1093/nar/gkv335.

Gabdoulline RR and Wade RC.
Simulation of the Diffusional Association of Barnase and Barstar.
Biophys. J. (1997) 72, 1917-1929.

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.

PASMet – Prediction, Analysis and Simulation of Metabolic Reaction Networks

PASMet

:: DESCRIPTION

PASMet is a web-based platform for predicting, modelling and analysing metabolic systems. It is a non-commercial and user-friendly tool for assisting non-experts in mathematical modelling, computing or programming to work on computational biology.

::DEVELOPER

Metabolic Systems Research Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

PASMet: a web-based platform for prediction, modelling and analyses of metabolic systems.
Sriyudthsak K, Mejia RF, Arita M, Hirai MY.
Nucleic Acids Res. 2016 May 12. pii: gkw415.

Princeton_TIGRESS – proTeIn Geometry REfinement using Simulations and Support vector machines

Princeton_TIGRESS

:: DESCRIPTION

Princeton_TIGRESS is an automated refinement method that intends to refine an input protein structure by addressing both sampling and selection.

::DEVELOPER

the Multi-scale Systems Engineering Laboratory (MSEL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Proteins. 2014 May;82(5):794-814. doi: 10.1002/prot.24459. Epub 2013 Nov 22.
Princeton_TIGRESS: protein geometry refinement using simulations and support vector machines.
Khoury GA1, Tamamis P, Pinnaduwage N, Smadbeck J, Kieslich CA, Floudas CA.

CisEvolver – Molecular Evolution Simulation Program

CisEvolver 0.4

:: DESCRIPTION

CisEvolver is a molecular evolution simulation program

::DEVELOPER

Eisen Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 CisEvolver

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2006 Oct;2(10):e130. Epub 2006 Aug 21.
Large-scale turnover of functional transcription factor binding sites in Drosophila.
Moses AM1, Pollard DA, Nix DA, Iyer VN, Li XY, Biggin MD, Eisen MB.

BioNetCAD 1.1 – Design, Simulation and Experimental Validation of Synthetic Biochemical Networks

BioNetCAD 1.1

:: DESCRIPTION

BioNetCAD ,a CellDesigner plug-in, is a computer assisted design tool for synthetic biology.

::DEVELOPER

BioNetCAD team

:: SCREENSHOTS

BioNetCAD

:: REQUIREMENTS

:: DOWNLOAD

 BioNetCAD

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Sep 15;26(18):2298-304. doi: 10.1093/bioinformatics/btq409
BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks.
Rialle S1, Felicori L, Dias-Lopes C, Pérès S, El Atia S, Thierry AR, Amar P, Molina F.

OpenMM 6.3 / PyOpenMM 3.0.0 – Library for Molecular Modeling Simulation

OpenMM 6.3 / PyOpenMM 3.0.0

:: 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)

GROMACS 5.1.1 – Molecular Simulation

GROMACS 5.1.1

:: DESCRIPTION

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

::DEVELOPER

GROMACS Team 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 GROMACS

:: MORE INFORMATION

Citation

Hess, et al. (2008)
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
J. Chem. Theory Comput. 4: 435-447.

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.
Pronk S, Páll S, Schulz R, Larsson P, Bjelkmar P, Apostolov R, Shirts MR, Smith JC, Kasson PM, van der Spoel D, Hess B, Lindahl E.
Bioinformatics (2013) 29 (7): 845-854.

YASARA 15.11.18 – Molecular Graphics, Modeling & Simulation program

YASARA 15.11.18

:: 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.

DL_POLY 4.07 – Molecular Dynamics Simulations

DL_POLY 4.07

:: DESCRIPTION

DL_POLY is a general purpose classical molecular dynamics (MD) simulation software.

::DEVELOPER

Ilian Todorov (ilian.todorov@stfc.ac.uk) and W. Smith. @ Daresbury Laboratory

:: SCREENSHOTS

DL_POLY

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 DL_POLY

:: MORE INFORMATION

Citation

Philos Trans A Math Phys Eng Sci. 2004 Sep 15;362(1822):1835-52.
DL_POLY_3: the CCP5 national UK code for molecular-dynamics simulations.
Todorov IT1, Smith W.