RW 1.0 – Protein Structure Modeling and Structure Decoy Recognition

RW 1.0

:: DESCRIPTION

RW (Random-Walk) is distance-dependent atomic potential for protein structure modeling and structure decoy recognition. It was derived from 1,383 high-resolution PDB structures using an ideal random-walk chain as the reference state. The RW potential has been extensively optimized and tested on a variety of protein structure decoy sets and demonstrates a significant power in protein structure recognition and a strong correlation with the RMSD of decoys to the native structures

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 calRW

:: MORE INFORMATION

Citation

Zhang J, Zhang Y (2010)
A Novel Side-Chain Orientation Dependent Potential Derived from Random-Walk Reference State for Protein Fold Selection and Structure Prediction.
PLoS ONE 5(10): e15386.

BDTree 1.01 – Modeling of Gene Expression Regulation

BDTree 1.01

:: DESCRIPTION

BDTree is a Bi-dimensional Regression Tree approach for modeling transcriptional regulation

::DEVELOPER

Jianhua Ruan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  •  Java

:: DOWNLOAD

  BDTree

:: MORE INFORMATION

Citation

Bioinformatics. 2006 Feb 1;22(3):332-40. Epub 2005 Nov 22.
A bi-dimensional regression tree approach to the modeling of gene expression regulation.
Ruan J, Zhang W.

GOMoDo beta – GPCR Online MOdeling and DOcking server

GOMoDo beta

:: DESCRIPTION

GOMoDo (GPCR Online Modeling and Docking) is a web server to seamlessly model GPCR (G-protein coupled receptors ) structures and dock ligands to the models in a single consistent pipeline.

::DEVELOPER

Department of Biotechnology, University of Verona | Institute of Computational Biomedicine (INM-9/IAS-5), Forschungszentrum Jülich.

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Sandal M, Duy TP, Cona M, Zung H, Carloni P, et al. (2013)
GOMoDo: A GPCRs Online Modeling and Docking Webserver.
PLoS ONE 8(9): e74092. doi:10.1371/journal.pone.0074092

BRAGI 20091106 – A Protein Visualization and Modeling Program

BRAGI 20091106

:: DESCRIPTION

BRAGI is a well-established package for viewing and modeling of three-dimensional (3D) structures of biological macromolecules.BRAGI enables you to view and explore the three-dimensional (3D) structure of any macromolecule. You can explore proteins, DNA, RNA, carbohydrates, and complexes, such as between transcriptional regulatory proteins and DNA, or enzymes and drugs.

::DEVELOPER

BRAGI Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 BRAGI

:: MORE INFORMATION

Citation

BRAGI: linking and visualization of database information in a 3D viewer and modeling tool.
Reichelt J, Dieterich G, Kvesic M, Schomburg D, Heinz DW.
Bioinformatics. 2005 Apr 1;21(7):1291-3. Epub 2004 Nov 16.

BiPad – Web Server for Modeling Bipartite Sequence Elements

BiPad

:: DESCRIPTION

The Bipad Server is a web interface to predict sequence elements embedded within unaligned sequences. Either a bipartite model, consisting of a pair of one-block position weight matrices (PWM’s) with a gap distribution, or a single PWM matrix for contiguous single block motifs may be produced. The Bipad program performs multiple local alignment by entropy minimization and cyclic refinement using a stochastic greedy search strategy. The best models are refined by maximizing incremental information contents among a set of potential models with varying half site and gap lengths.

::DEVELOPER

Dr. Chengpeng Bi (send comments to: cbi at cmh dot edu)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • GNU C++ w
  • C++ STL library

:: DOWNLOAD

  Contact: Dr. Stephen ONeil (send request to: soneil at cmh dot edu)

:: MORE INFORMATION

Citation

BMC Bioinformatics 2006, 7:76
BIPAD: A web server for modeling bipartite sequence elements
Chengpeng Bi and Peter K Rogan

mseq 1.2 – Modeling non-uniformity in Short-read Rates in RNA-Seq data

mseq 1.2

:: DESCRIPTION

mseq is an R package for modeling non-uniformity in short-read rates in RNA-Seq data.

::DEVELOPER

Jun Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX/  Linux / WIndows
  • R Package

:: DOWNLOAD

 mseq

:: MORE INFORMATION

Citation

Jun Li, Hui Jiang, and Wing H Wong (2010)
Modeling non-uniformity in short-read rates in RNA-Seq data.
Genome Biology 11(5): R50.

PottersWheel 4.0 – MatLab Toolbox of Mathematical Modeling of Dynamical Systems

PottersWheel 4.0

:: DESCRIPTION

PottersWheel is a MATLAB toolbox for mechanistic mathematical modeling. It allows reaction network or ordinary differential equation (ODE) based modeling.

PottersWheel has been developed to provide an intuitive and yet powerful framework for data-based modeling of dynamical systems like biochemical reaction networks. Its key functionality is multi-experiment fitting, where several experimental data sets from different laboratory conditions are fitted simultaneously in order to improve the estimation of unknown model parameters, to check the validity of a given model, and to discriminate competing model hypotheses. New experiments can be designed interactively. Models are either created text based or using a visual model designer. Dynamically generated and compiled C files provide fast simulation and fitting procedures. Each function can either be accessed using a graphical user interface or via command line, allowing for batch processing within custom Matlab scripts.

::DEVELOPER

TIKANIS GmbH

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • MATLAB

:: DOWNLOAD

PottersWheel

:: MORE INFORMATION

Citation

Mathematical modeling of biochemical systems with PottersWheel.
Maiwald T, Eberhardt O, Blumberg J.
Methods Mol Biol. 2012;880:119-38. doi: 10.1007/978-1-61779-833-7_8.

DLCoal 1.0 – Modeling Gene Duplications, Losses, and Coalescence

DLCoal 1.0

:: DESCRIPTION

DLCoal is a software package containing the DLCoalRecon program as well as several other useful utilities for working with gene trees.

DLCoalRecon  is a reconciliation method for inferring gene duplications, losses, and coalescence (incomplete lineage sorting).

::DEVELOPER

Matt Rasmussen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler
  • Python
  • GSL

:: DOWNLOAD

  DLCoal

:: MORE INFORMATION

Citation

Unified modeling of gene duplication, loss, and coalescence using a locus tree
Matthew D. Rasmussen and Manolis Kellis.
Genome Res. 2012 Apr;22(4):755-65.

ABM-TKI 0.11 – Multi-scale Agent-Based Brain Tumor Modeling

ABM-TKI 0.11

:: DESCRIPTION

ABM-TKI is a tool, employing agent-based model (ABM), to simulate brain tumor growth that includes an EGFR signaling pathway together with a related cell-cycle pathway, angiogenesis and tyrosine kinase inhibitors (TKIs) treatment. The users can apply this tool to predict the responses of brain cancer to TKIs, and to reveal the dual role of angiogenesis during TKI treatment.

::DEVELOPER

ABM-TKI team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Matlab

:: DOWNLOAD

  ABM-TKI

:: MORE INFORMATION

Citation

Multi-scale agent-based brain cancer modeling and prediction of TKI treatment response: incorporating EGFR signaling pathway and angiogenesis.
Sun X, Zhang L, Tan H, Bao J, Strouthos C, Zhou X.
BMC Bioinformatics. 2012 Aug 30;13:218. doi: 10.1186/1471-2105-13-218.

Bayes – Modeling Incomplete Alignments in Phylogenetic Inference

Bayes

:: DESCRIPTION

Bayes is a statistical method for inferring phylogenetic trees from EST-based incomplete MSA data.

::DEVELOPER

Mayetri Gupta

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package

:: DOWNLOAD

 Bayes

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Mar 1;25(5):592-8. doi: 10.1093/bioinformatics/btp015.
A hierarchical model for incomplete alignments in phylogenetic inference.
Cheng F, Hartmann S, Gupta M, Ibrahim JG, Vision TJ.