WHAT IF 8.3 – Protein Structure Analysis program

WHAT IF 8.3

:: DESCRIPTION

WHAT IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc.

::DEVELOPER

Gert Vriend

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 WHAT IF

:: MORE INFORMATION

Citation

G.Vriend,
WHAT IF: A molecular modeling and drug design program.
J Mol Graph. 1990 Mar;8(1):52-6, 29.

ANOLEA 2.4.2-2 – Assess the Quality of a 3D Protein Structure

ANOLEA 2.4.2-2

:: DESCRIPTION

ANOLEA (Atomic Non-Local Environment Assessment) is a server to assess the quality of a three – dimensional protein structure. It uses a statistical potential at the atomic level and gives an energy profile as ouput. Also, the user can choose to have a molecular graphical output representation of the energy profile.

::DEVELOPER

Francisco Melo Ledermann

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ANOLEA

:: MORE INFORMATION

Citation

Proc Int Conf Intell Syst Mol Biol. 1997;5:187-90.
ANOLEA: a www server to assess protein structures.
Melo F, Devos D, Depiereux E, Feytmans E.

PACSY / PACSY Maker b032814 / PACSY Analyzer – Database Management system for Protein Structure and Chemical Shift analysis

PACSY / PACSY Maker b032814 / PACSY Analyzer

:: DESCRIPTION

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Database Bank (PDB), the Biological Magnetic Resonance Data Bank (BMRB), and the Structural Classification of Proteins (SCOP) database.

PACSY Maker is used for building the PACSY database.

PACSY Analyzer is designed to provide an easy graphical user interface (GUI) for using PACSY database.

::DEVELOPER

The National Magnetic Resonance Facility at Madison (NMRFAM)

:: SCREENSHOTS

PACSYMaker

PACSYAnalyzer

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

PACSYPACSY Maker  , PACSY Analyzer

:: MORE INFORMATION

Citation

J Biomol NMR. 2012 Oct;54(2):169-79. Epub 2012 Aug 19.
PACSY, a relational database management system for protein structure and chemical shift analysis.
Lee W1, Yu W, Kim S, Chang I, Lee W, Markley JL.

CABS-fold – Server for de novo and Consensus-based prediction of Protein Structure

CABS-fold

:: DESCRIPTION

CABS-fold is a server that provides tools for protein structure prediction from sequence only (de novo modeling) and also using alternative templates (consensus modeling).

::DEVELOPER

Laboratory of Theory of Biopolymers,  University of Warsaw

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W406-11. doi: 10.1093/nar/gkt462. Epub 2013 Jun 8.
CABS-fold: Server for the de novo and consensus-based prediction of protein structure.
Blaszczyk M1, Jamroz M, Kmiecik S, Kolinski A.

RDC-PANDA 1.0 – NMR NOE Assignment & Protein Structure Determination

RDC-PANDA 1.0

:: DESCRIPTION

RDC-PANDA (RDC-based SSE PAcking with NOEs for Structure Determination and NOE Assignment) is a suite of programs for nuclear Overhauser effect (NOE) assignment and high-resolution structure determination starting with a global fold calculated from exact solutions to the residual dipolar coupling (RDC) equations. RDC-PANDA is specifically designed for automated NMR NOE assignment and protein structure determination.

::DEVELOPER

Donald Lab at Duke University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

RDC-PANDA

:: MORE INFORMATION

Citation

Jianyang Zeng, Jeffrey Boyles, Chittaranjan Tripathy, Lincong Wang, Anthony Yan, Pei Zhou, and Bruce Randall Donald.
High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations.
Journal of Biomolecular NMR, 45(3):265-281, 2009

HEA-PSP – Ab-initio Protein Structure Prediction

HEA-PSP

:: DESCRIPTION

HEA-PSP is a hybrid evolutionary search framework with various crossover implementations for Ab-initio protein structre prediction

::DEVELOPER

Computational Biology lab, George Mason University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  HEA-PSP

:: MORE INFORMATION

Citation

Brian Olson, Kenneth A. De Jong, and Amarda Shehu.
Off-Lattice Protein Structure Prediction with Homologous Crossover.
GECCO 2013, pages 287-294, Amsterdam,

HotMAPS v1.1.4 – Hotspot Missense mutation Areas in Protein Structures

HotMAPS v1.1.4

:: DESCRIPTION

HotMAPS detects somatic mutation hotspot regions in 3D protein structures.

::DEVELOPER

Karchin Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

HotMAPS

:: MORE INFORMATION

Citation

Tokheim C, Bhattacharya R, Niknafs N, Gygax DM, Kim R, Ryan M, Masica DL, Karchin R.
Exome-Scale Discovery of Hotspot Mutation Regions in Human Cancer Using 3D Protein Structure.
Cancer Res. 2016 Jul 1;76(13):3719-31. doi: 10.1158/0008-5472.CAN-15-3190. Epub 2016 Apr 28. PMID: 27197156; PMCID: PMC4930736.

POLYVIEW-2D / POLYVIEW-3D / POLYVIEW-MM – Protein Structure Annotation using Sequence Profiles / Structures / Motions

POLYVIEW-2D / POLYVIEW-3D / POLYVIEW-MM

:: DESCRIPTION

The POLYVIEW-2D protein structure visualization server can be used to generate amino acid sequence annotations, such as secondary structure, relative solvent accessibility, evolutionary conservation, and physico-chemical property profiles. It can also be used to identify residues involved in protein-protein interactions and highlight other important sites and motifs.

POLYVIEW-3D is a web-based tool for macromolecular structure visualization and analysis. In particular, it provides a wide array of options for automated structural and functional analysis of proteins and their complexes. This tutorial aims to describe and illustrate the available rendering options and annotation capabilities of POLYVIEW-3D.

POLYVIEW-MM (Molecular Motion) enables animation of trajectories generated by Molecular Dynamics and related simulation techniques, as well as visualization of alternative conformers, e.g., obtained as a result of protein structure prediction methods or small molecule docking, using an intuitive web-based interface.

:: SCREENSHOTS

N/A

::DEVELOPER

Meller Lab

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

POLYVIEW: a flexible visualization tool for structural and functional annotations of proteins.
Porollo AA, Adamczak R, Meller J.
Bioinformatics. 2004 Oct 12;20(15):2460-2. Epub 2004 Apr 8.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W662-6. doi: 10.1093/nar/gkq445. Epub 2010 May 26.
POLYVIEW-MM: web-based platform for animation and analysis of molecular simulations.
Porollo A, Meller J.

MAPSCI 1.0 – Multiple Alignment of Protein Structures and Consensus Identification

MAPSCI 1.0

:: DESCRIPTION

MAPSCI is an algorithm to compute a multiple structure alignment for a set of proteins and to generate a consensus structure.

::DEVELOPER

MAPSCI team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • C++ Compiler

:: DOWNLOAD

 MAPSCI

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Feb 2;11:71. doi: 10.1186/1471-2105-11-71.
Multiple structure alignment and consensus identification for proteins.
Ilinkin I1, Ye J, Janardan R.

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.