ModPipe 2.3.0 – Calculate Protein Structure Model

ModPipe 2.3.0

:: DESCRIPTION

ModPipe is a completely automated software pipeline that can calculate protein structure models for a large number of sequences with almost no manual intervention. In the simplest case, it takes as input a sequence identifier and a configuration file and produces one or more comparative models for that sequence.

::DEVELOPER

Andrej Sali Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ModPipe

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Jan;39(Database issue):D465-74. Epub 2010 Nov 19.
ModBase, a database of annotated comparative protein structure models, and associated resources.
Pieper U, Webb BM, Barkan DT, Schneidman-Duhovny D, Schlessinger A, Braberg H, Yang Z, Meng EC, Pettersen EF, Huang CC, Datta RS, Sampathkumar P, Madhusudhan MS, Sj?lander K, Ferrin TE, Burley SK, Sali A.

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.

QUARK – De Novo Protein Structure Prediction

QUARK

:: DESCRIPTION

QUARK is a computer algorithm for ab initio protein folding and protein structure prediction, which aims to construct the correct protein 3D model from amino acid sequence only.

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Proteins. 2013 Feb;81(2):229-39. doi: 10.1002/prot.24179. Epub 2012 Oct 16.
Toward optimal fragment generations for ab initio protein structure assembly.
Xu D1, Zhang Y.

PSpacE Beta – Protein Structure Space Explorer

PSpacE

:: DESCRIPTION

The PSpacE is an open-source, platform-independent web application for direct exploration of protein structure space in 3D.

::DEVELOPER

Biocomputing and Media Research Lab

:: SCREENSHOTS

PSpacE

:: REQUIREMENTS

  • WEb Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013;14 Suppl 14:S10. doi: 10.1186/1471-2105-14-S14-S10. Epub 2013 Oct 9.
Towards human-computer synergetic analysis of large-scale biological data.
Singh R, Yang H, Dalziel B, Asarnow D, Murad W, Foote D, Gormley M, Stillman J, Fisher S.

Seder 2.0 – A Global Protein Structure Scoring Function

Seder 2.0

:: DESCRIPTION

Seder is a protein scoring function. The package was designed using the GEneral Neural Network program.

::DEVELOPER

Research and Information Systems

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • SAS
  • Perl
  • C/C++ Compiler
  • FORTRAN (77/90/etc.)

:: DOWNLOAD

 Seder

:: MORE INFORMATION

Citation

A global machine learning based scoring function for protein structure prediction.
Faraggi E, Kloczkowski A.
Proteins. 2014 May;82(5):752-9. doi: 10.1002/prot.24454. Epub 2013 Nov 22.

EdaFoldAA / EdaFold 0.1 – Protein Structure Prediction

EdaFoldAA / EdaFold 0.1

:: DESCRIPTION

EdaFoldAA is a fragment assembly based de novo protein structure prediction method that uses an Estimation of Distribution Algorithm for high efficiency conformational sampling.

EdaFold is a C++/MPI software prototype for fragment-based protein structure prediction based on an Estimation of Distribution Algorithm.

::DEVELOPER

Structural Bioinformatics Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 EdaFoldAA / EdaFold

:: MORE INFORMATION

Citation

PLoS One. 2013 Jul 25;8(7):e68954. doi: 10.1371/journal.pone.0068954. Print 2013.
Efficient sampling in fragment-based protein structure prediction using an estimation of distribution algorithm.
Simoncini D1, Zhang KY.

PLoS One. 2012;7(7):e38799. doi: 10.1371/journal.pone.0038799. Epub 2012 Jul 19.
A probabilistic fragment-based protein structure prediction algorithm.
Simoncini D1, Berenger F, Shrestha R, Zhang KY.

Protein Peeling 3D – Splitting Protein Structure into Proteins Units and Domains

Protein Peeling 3D

:: DESCRIPTION

Protein Peeling 3D web server dedicated to the analysis of protein structure architecture through the identification of protein units produced by an iterative splitting algorithm.

::DEVELOPER

Protein Peeling 3D team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Protein Peeling 3D: new tools for analyzing protein structures.
Gelly JC, de Brevern AG.
Bioinformatics. 2011 Jan 1;27(1):132-3. doi: 10.1093/bioinformatics/btq610.

GeNMR – Webserver for Protein Structure generation from NOE Distant Restraints and Chemical Shifts

GeNMR

:: DESCRIPTION

GeNMR (GEnerate NMR structure) is a web server for generating 3D protein structures using NOE-derived distance restraints and NMR chemical shifts.

::DEVELOPER

GeNMR team

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W670-7. doi: 10.1093/nar/gkp280. Epub 2009 Apr 30.
GeNMR: a web server for rapid NMR-based protein structure determination.
Berjanskii M1, Tang P, Liang J, Cruz JA, Zhou J, Zhou Y, Bassett E, MacDonell C, Lu P, Lin G, Wishart DS.

ASSAM / SPRITE – Side Chain 3D-motif Searching in Protein Structures

ASSAM / SPRITE

:: DESCRIPTION

The ASSAM( Amino acid Pattern Search for Substructures And Motifs) program searches for 3D patterns of amino acid side chains in PDB formatted query structures.

The SPRITE (3D Search for protein sites) server searches for protein sites and motifs in a query protein structure. The output is a list of potential functional sites.

::DEVELOPER

The Molecular Function Regulation Lab (M. Firdaus Raih research group)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nadzirin et al.:
SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures.
Nucleic Acids Research. 2012 Jul;40(Web Server issue):W380-6.

MaDCaT – Protein Structure Search tool

MaDCaT

:: DESCRIPTION

MaDCaT (Mapping of Distances for the Categorization of Topology) is a protein structure search tool

::DEVELOPER

Grigoryan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • C++ Compiler

:: DOWNLOAD

   MaDCaT

:: MORE INFORMATION

Citation:

Zhang J., Grigoryan G.,
Mining Tertiary Structural Motifs for Assessment of Designability“,
Methods Enzymol. 2013;523:21-40. doi: 10.1016/B978-0-12-394292-0.00002-3.