JabberDock – Protein Docking using a density-based descriptor for Atoms Charge and Dynamics

JabberDock

:: DESCRIPTION

JabberDock tackles the problem of protein-protein docking while accommodating for rearrangements upon binding including side chain reorientations and backbone flexibility.

::DEVELOPER

Degiacomi Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

JabberDock

:: MORE INFORMATION

Citation:

Rudden LSP, Degiacomi MT.
Transmembrane Protein Docking with JabberDock.
J Chem Inf Model. 2021 Mar 22;61(3):1493-1499. doi: 10.1021/acs.jcim.0c01315. Epub 2021 Feb 26. PMID: 33635637; PMCID: PMC8041277.

ADAM 1.1 – Analyze the Dynamics of Discrete Biological Systems

ADAM 1.1

:: DESCRIPTION

ADAM (Analysis of Dynamic Algebraic Models) uses a combination of simulation and mathematical algorithms to analyze the dynamics of discrete biological systems.

::DEVELOPER

PlantSimLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 ADAM

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Jul 20;12:295. doi: 10.1186/1471-2105-12-295.
ADAM: analysis of discrete models of biological systems using computer algebra.
Hinkelmann F, Brandon M, Guang B, McNeill R, Blekherman G, Veliz-Cuba A, Laubenbacher R.

SimBoolNet 1.0 – Simulate the Dynamics of Signaling Transduction using Boolean networks

SimBoolNet 1.0

:: DESCRIPTION

SimBoolNet is an open source Cytoscape plugin that simulates the dynamics of signaling transduction using Boolean networks. Given a user-specified level of stimulation to signal receptors, SimBoolNet simulates the response of downstream molecules and visualizes with animation and records the dynamic changes of the network.

::DEVELOPER

Teresa Przytycka Research Group

:: SCREENSHOTS

SimBoolNet

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 SimBoolNet

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jan 1;26(1):141-2. doi: 10.1093/bioinformatics/btp617. Epub 2009 Nov 3.
SimBoolNet–a Cytoscape plugin for dynamic simulation of signaling networks.
Zheng J1, Zhang D, Przytycki PF, Zielinski R, Capala J, Przytycka TM.

MOLARIS-XG 9.15 – Tool for the study of Energetics and Dynamics of Protein

MOLARIS-XG 9.15

:: DESCRIPTION

MOLARIS-XG includes powerful programs POLARIS and ENZYMIX in a unique package with an extremely improved interface and maximum robustness. MOLARIS incorporates the methodologies of the old packages ENZYMIX and POLARIS and also the more recent advances developed in our group:

ENZYMIX is a macromolecular simulation program designed to study the functions of proteins ranging from ligand binding to free energy profiles of enzymatic reactions using the Empirical Valence Bond (EVB) approach and the Free Energy Perturbation (FEP) method.

POLARIS is a fast converging computational software based on the Protein Dipoles-Langevin Dipoles (PDLD) approach, it is used for the calculation of free energies and electrostactic properties of molecules and macromolecules in solution through the evaluation of the permanent dipoles, induce dipoles, charges, dispersion contributions and hydrophobicity.

::DEVELOPER

Warshel Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MOLARIS-XG

:: MORE INFORMATION

Citation

Y.Y. Sham, Z.T. Chu, H. Tao and A. Warshel,
Examining Methods for Calculations of Binding Free Energies: LRA, LIE, PDLD-LRA and PDLD/S-LRA Calculations of Ligands Binding to an HIV Protease,
PROTEINS: Structure, Function, Genetics, 2000, 39, 393-407.

MERMAID – Prepare and Run Coarse-Grained Membrane Protein Dynamics

MERMAID

:: DESCRIPTION

MERMAID (Martini coarsE gRained MembrAne proteIn Dynamics) is a publicly available web interface that allows the user to prepare and run coarse-grained molecular dynamics (CGMD) simulations and to analyse the trajectories

::DEVELOPER

MERMAID team, University of Verona

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res, 47 (W1), W456-W461 2019 Jul 2
MERMAID: Dedicated Web Server to Prepare and Run Coarse-Grained Membrane Protein Dynamics
Mangesh Damre , Alessandro Marchetto , Alejandro Giorgetti

TESD 1.0 – Transposable Element Simulator Dynamics

TESD 1.0

:: DESCRIPTION

TESD simulates the number of genomic TE copies in different populations across generations (according to the Island Model), using classical models of TE dynamics. The parameters of the models (transposition and excision rates, selection intensity, recombination rate, migration rate, population sizes and number of populations) are defined by the users.

::DEVELOPER

TESD team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  Mac OsX / Windows
  • Java

:: DOWNLOAD

  TESD

:: MORE INFORMATION

Citation:

Grégory Deceliere, Yann Letrillard, Sandrine Charles and Christian Biémont
TESD: a transposable element dynamics simulation environment
Bioinformatics November 1, 2006 22:2702-2703

BetaWB – Study Dynamics of Biological Systems

BetaWB

:: DESCRIPTION

BetaWB (Beta Workbench) builds molecular and scalable models as well as manages complexity and the combinatorial explosions of models

::DEVELOPER

The Microsoft Research – University of Trento Centre for Computational and Systems Biology

:: SCREENSHOTS

BetaWB

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 BetaWB

:: MORE INFORMATION

Citation

The Beta Workbench: a computational tool to study the dynamics of biological systems.
Dematté L, Priami C, Romanel A.
Brief Bioinform. 2008 Sep;9(5):437-49. doi: 10.1093/bib/bbn023. Epub 2008 May 7.

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.

Treekin 0.4 – Computation of RNA Folding Dynamics

Treekin 0.4

:: DESCRIPTION

The program  treekin  computes folding dynamics on coarse grained version of an energy landscape, where all conformations belonging to the same local minimum have been contracted into a single macro-state.

::DEVELOPER

Theoretical Biochemistry Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Treekin

:: MORE INFORMATION

Citation

Michael T Wolfinger, W Andreas Svrcek-Seiler, Christoph Flamm, Ivo L Hofacker and Peter F Stadler
Efficient computation of RNA folding dynamics
J. Phys. A: Math. Gen. 37 4731,