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,

MMB 2.19 – Model the Structure and Dynamics of Macromolecules

MMB 2.19

:: DESCRIPTION

MMB (a contraction of MacroMolecule Builder) was previously known as RNABuilder. The latter is available up to revision 2.2. We renamed the software since even some longtime users were unaware that the package now handles protein as well as RNA. Aside from the renaming, MMB 2.3 differs from RNABuilder 2.2 in two important ways. Release 2.3 has fully overhauled guts. It uses the BiopolymerClassContainer, a much cleaner programming construct which will make future upgrades and extensions more efficient. As of release 2.3.4, we link against new Molmodel binaries which have more efficient tracking of atoms in rigid regions. This yields a two-fold speed improvement and four-fold lower memory requirement for many problems. Also in this release, some rarely used features have been removed, but these were never in the tutorial literature so their absence should go largely unnoticed. The default input file name is now commands.dat rather than contacts.dat. A couple of somewhat obscure bugs were fixed. The error messages are more informative, and more aggressively prevent the user from risky or incorrect construction of the input file.

::DEVELOPER

MMB Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • VMD

:: DOWNLOAD

 MMB

:: MORE INFORMATION

Citation:

Samuel Coulbourn Flores, Russ B. Altman.
Structural insights into Pre-Translocation Ribosome Motions.
In Proceedings of Pacific Symposium on Biocomputing’2011. pp.205~216 (2011)

Samuel Flores and Russ Altman,
Turning limited experimental information into 3D models of RNA,
RNA 16(9):1769-78 (2010).

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.

ProDy 1.7 – Python package for Analysis and Modeling of Protein Structural Dynamics

ProDy 1.7

:: 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

Ahmet Bakan in Bahar lab at the University of Pittsburgh.

:: 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.

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.

Pint 20151019 – Formal analysis of Dynamics for Large-scale Biological Networks

Pint 20151019

:: DESCRIPTION

Pint allows the qualitative modelling of large biological networks using the Process Hitting framework.

::DEVELOPER

Loïc Paulevé

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX

:: DOWNLOAD

 Pint

:: MORE INFORMATION

LCGserver – Exploring Conservation and Dynamics of Gene Orders

LCGserver

:: DESCRIPTION

LCGserver is a webserver for exploring evolutionary dynamics of gene orders over diverse lineages.

::DEVELOPER

CAS Key Lab of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

OMICS. 2015 Aug 10.
LCGserver: A Webserver for Exploring Evolutionary Trajectory of Gene Orders in a Large Number of Genomes.
Wang D, Yu J

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.

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

Laubenbacher Research Group

:: 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.

HDXanalyzer 1.0 – Statistical Analysis of Protein Structure Dynamics

HDXanalyzer 1.0

:: DESCRIPTION

HDXanalyzer is software package to enable the statistical analysis of HDX mass spectrometry data. The software will help the protein structure dynamics study tremendously.

::DEVELOPER

Joshua Yuan lab

:: SCREENSHOTS

HDXanalyzer

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Python

:: DOWNLOAD

 HDXanalyzer

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S43. doi: 10.1186/1471-2105-12-S1-S43.
HDX-analyzer: a novel package for statistical analysis of protein structure dynamics.
Liu S, Liu L, Uzuner U, Zhou X, Gu M, Shi W, Zhang Y, Dai SY, Yuan JS.