SUBWAI 1.0 – Protein Structure Prediction program

SUBWAI 1.0

:: DESCRIPTION

SUBWAI (SUBoptimal Weighted AlIgnment) is the protein structure prediction program based on threading strategy with SPAD.

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SUBWAI

:: MORE INFORMATION

Citation

Proteins. 2008 May 15;71(3):1255-74.
Estimating quality of template-based protein models by alignment stability.
Chen H1, Kihara D.

PSVS 1.5 – Protein Structure Validation Software Suite

PSVS 1.5

:: DESCRIPTION

PSVS systematically evaluates the quality of protein structures. PSVS integrates analyses from several widely-used structure quality evaluation tools, including RPF , PROCHECK, MolProbity , Verify3D  Prosa II , the PDB validation software, and various structure-validation tools.PSVS provides standard constraint analyses, statistics on the PDB validation goodness-of-fit between structures and experimental data, and knowledge-based structure quality scores in standardized format suitable for database integration. Global quality measures are reported as Z scores, based on calibration with a set of high-resolution X-ray crystal structures.

::DEVELOPER

CABM Structural Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web BRowser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Proteins. 2007 Mar 1;66(4):778-95.
Evaluating protein structures determined by structural genomics consortia.
Bhattacharya A, Tejero R, Montelione GT.

Concavity 0.1 – Ligand Binding Site Prediction from Protein Sequence and Structure

Concavity 0.1

:: DESCRIPTION

Concavity predicts ligand-binding sites from structure.

::DEVELOPER

John A. Capra , Thomas Funkhouser , Mona Singh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX

:: DOWNLOAD

 Concavity

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2009 Dec;5(12):e1000585. doi: 10.1371/journal.pcbi.1000585. Epub 2009 Dec 4.
Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.
Capra JA1, Laskowski RA, Thornton JM, Singh M, Funkhouser TA.

SAINT2 – Cotranslational Protein Structure prediction

SAINT2

:: DESCRIPTION

SAINT2 is a fragment-based de novo protein structure prediction software. It is based on the notion that some proteins fold as they are being synthesised, which is known as the cotranslational protein folding hypothesis.

::DEVELOPER

the Oxford Protein Informatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOs/ Linux

:: DOWNLOAD

SAINT2

:: MORE INFORMATION

Citation

Bioinformatics. 2018 Apr 1;34(7):1132-1140. doi: 10.1093/bioinformatics/btx722.
Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction.
de Oliveira SHP, Law EC, Shi J, Deane CM.

RFQAmodel – Identify Predicted Protein Structure in the Correct Fold

RFQAmodel.

:: DESCRIPTION

RFQAmodel (Random Forest Quality Assessment) assesses whether models produced by a protein structure prediction pipeline have the correct fold.

::DEVELOPER

the Oxford Protein Informatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux
  • R

:: DOWNLOAD

RFQAmodel

:: MORE INFORMATION

Citation

PLoS One. 2019 Oct 21;14(10):e0218149. doi: 10.1371/journal.pone.0218149. eCollection 2019.
RFQAmodel: Random Forest Quality Assessment to identify a predicted protein structure in the correct fold.
West CE, de Oliveira SHP, Deane CM.

 

MaxCluster – Protein Structure Comparison and Clustering

MaxCluster

:: DESCRIPTION

MaxCluster (MaxSub and Clustering) is a command-line tool for the comparison of protein structures. It provides a simple interface for a large number of common structure comparison tasks. A key feature of the program is the ability to process thousands of structures, either against a single reference protein or in an all-verses-all comparison.
::DEVELOPER

Alex Herbert , Structural Bioinformatics Group, Imperial College

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • GCC

:: DOWNLOAD

 MaxCluster

:: MORE INFORMATION

SuperMimic – Fit Peptide Mimetics into Protein Structures

SuperMimic

:: DESCRIPTION

SuperMimic is a tool for conformer based fitting of peptide mimetics into protein structures.Many protein recognition mechanisms, mostly involving other proteins or peptides, are known, and more and more of them are being deciphered. To intervent these interactions is the main goal of drug design. As peptides are often poor drug candidates, the need for bioequivalent compounds with better pharmacological properties arises. Starting from a known spatial structure, the goal is to find compounds that mimic the function of a peptide while obtaining improved cellular transport properties, stable structures and resistance against proteases.

The approach used in the program SuperMimic is to identify peptide mimetics starting from a known protein structure and conformations of a mimic, which are spatially superposed with the protein backbone. A compound library with peptidomimetic compounds collected from the literature as well as several protein structure libraries are provided, which can be scanned exhaustively.

::DEVELOPER

Structural Bioinformatics Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

SuperMimic

:: MORE INFORMATION

Citation:

SuperMimic – Fitting peptide mimetics into protein structures
Reviewed by Andrean Goede, Elke Michalsky, Ulrike Schmidt, and Robert Preissner
BMC Bioinformatics. 2006; 7: 11.

MEPI – Predict Catalytic Residues from Protein Structures

MEPI

:: DESCRIPTION

The MEPI is a web server to predict catalytic residues from protein structures, which integrates the Micro-Environment(ME) and Position Information of each residue.

::DEVELOPER

Ziding Zhang’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

PLoS One. 2012;7(7):e41370. doi: 10.1371/journal.pone.0041370. Epub 2012 Jul 19.
Identification of catalytic residues using a novel feature that integrates the microenvironment and geometrical location properties of residues.
Han L1, Zhang YJ, Song J, Liu MS, Zhang Z.

Pro-origami – Protein Structure Cartoons

Pro-origami

:: DESCRIPTION

Pro-origami is a system for automatically generating protein structure cartoons. The cartoons are intended to make protein structure easy to interpret by laying out the secondary and super-secondary structure in two dimensions in a manner that makes the structure clear.

::DEVELOPER

IALab: Immersive Analytics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Python
  • BioPython
  • Dunnart

:: DOWNLOAD

Pro-origami

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Dec 1;27(23):3315-6. doi: 10.1093/bioinformatics/btr575.
Automatic generation of protein structure cartoons with Pro-origami.
Stivala A1, Wybrow M, Wirth A, Whisstock JC, Stuckey PJ.

PDBpaint 20111209 – Tag Protein Structures with Sequence Annotations

PDBpaint 20111209

:: DESCRIPTION

PDBpaint is a simple tool that displays protein sequence features gathered from bioinformatics resources on top of protein structures, which are displayed in an interactive window (using the Jmol Java viewer). PDBpaint can be used either with existing protein structures or with novel structures provided by the user.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 PDBpaint

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Sep 15;27(18):2605-6. Epub 2011 Jul 14.
PDBpaint, a visualization webservice to tag protein structures with sequence annotations.
Fournier D, Andrade-Navarro MA.