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

BRAGI

:: 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.

OSCAR – Protein Side Chain Modeling

OSCAR

:: DESCRIPTION

OSCAR (Optimized Side Chain Atomic eneRgy) is a software of new force fields for protein side chain modeling

::DEVELOPER

Systems Immunology Laboratory , Osaka University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 OSCAR

:: MORE INFORMATION

Citation

J Comput Chem. 2011 Jun;32(8):1680-6. doi: 10.1002/jcc.21747.
Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions.
Liang S, Zhou Y, Grishin N, Standley DM.

LigandScout 3.12 – Pharmacophore 3D Modeling

LigandScout 3.12

:: DESCRIPTION

LigandScout is a fully integrated platform for accurate virtual screening based on 3D chemical feature pharmacophore models. It offers seamless workflows, starting both from ligand- and structure based pharmacophore modeling, and includes novel high performance alignment algorithms for excellent prediction quality with unprecedented screening speed. Additionally, we have included user-friendly screening analysis tools, including the automated generation of ROC curves for performance assessments. All functions are accessible through a well elaborated graphic user interface that reflects our years of experience in creation of the most user-friendly pharmacophore modeling tools. The algorithms are scientifically validated and based on our well-established knowledge in pharmacophore research, while the application corresponds to state-of-the-art information technology.

::DEVELOPER

Inte:Ligand

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux

:: DOWNLOAD

LigandScout

:: MORE INFORMATION

Citation

Wolber, G.; Langer, T.;
LigandScout: 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters.
J. Chem. Inf. Model; 2005; 45(1); 160-169.

PHYLDOG 2.0beta – Organism and Gene PHYlogenies Modeling Gene Duplications and Losses

PHYLDOG 2.0beta

:: DESCRIPTION

Phyldog is a program made to simultaneously build gene and species trees when gene families have undergone duplications and losses.

::DEVELOPER

Bastien Boussau

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Boost libraries
  • Bio++

:: DOWNLOAD

 PHYLDOG

:: MORE INFORMATION

Citation:

Genome Res. 2013 Feb;23(2):323-30. doi: 10.1101/gr.141978.112.
Genome-scale coestimation of species and gene trees.
Boussau B, Szöllosi GJ, Duret L, Gouy M, Tannier E, Daubin V.