MODELLER 10.1 – Comparative Protein Structure Modeling

MODELLER 10.1

:: DESCRIPTION

MODELLER is used for homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints, and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc

::DEVELOPER

Andrej Sali Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

  MODELLER

:: MORE INFORMATION

Citation

Methods Mol Biol. 2014;1137:1-15. doi: 10.1007/978-1-4939-0366-5_1.
Protein structure modeling with MODELLER.
Webb B1, Sali A.

N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan, D. Eramian, M. Shen, U. Pieper, A. Sali.
Comparative Protein Structure Modeling With MODELLER.
Current Protocols in Bioinformatics, John Wiley & Sons, Inc., Supplement 15, 5.6.1-5.6.30, 2006.

iMADS 1.0.3 – integrative Modeling and Analysis of Differential Specificity

iMADS 1.0.3

:: DESCRIPTION

iMADS is a combined computational-experimental strategy to identify and study the differences in DNA-binding specificity between transcription factor (TF) family members, i.e. paralogous TFs.

::DEVELOPER

The Gordan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

iMADS

:: MORE INFORMATION

Citation:

Shen N, Zhao J, Schipper JL, Zhang Y, Bepler T, Leehr D, Bradley J, Horton J, Lapp H, Gordan R.
Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In Vivo Binding.
Cell Syst. 2018 Apr 25;6(4):470-483.e8. doi: 10.1016/j.cels.2018.02.009. Epub 2018 Mar 28. PMID: 29605182; PMCID: PMC6008103.

TASSER-Lite 1.0 – Protein Structure Modeling tool

TASSER-Lite 1.0

:: DESCRIPTION

TASSER-Lite is a protein structure comparative modeling tool. It is limited to protein target-template pairs whose pairwise sequence identity is >25% to the best threading template. It is optimized to model single domain proteins whose lengths range from 41-200 residues.

::DEVELOPER

Center for the Study of Systems Biology

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

TASSER-Lite

:: MORE INFORMATION

Citation

Pandit, S B, Zhang Y, Skolnick J. 2006.
TASSER-Lite: an automated tool for protein comparative modeling.
Biophysical journal. 91(11):4180-90.

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

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.