IntFOLD 5.0 – Integrated Protein Structure and Function Prediction Server

IntFOLD 5.0

:: DESCRIPTION

The IntFOLD server is a novel independent server that integrates several cutting edge methods for the prediction of structure and function from sequence.

::DEVELOPER

McGuffin Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences.
McGuffin LJ, Atkins JD, Salehe BR, Shuid AN, Roche DB.
Nucleic Acids Res. 2015 Mar 27. pii: gkv236.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W171-6. doi: 10.1093/nar/gkr184. Epub 2011 Mar 31.
The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.
Roche DB1, Buenavista MT, Tetchner SJ, McGuffin LJ.

Buenavista, M. T., Roche, D. B., & McGuffin, L. J. (2012)
Improvement of 3D protein models using multiple templates guided by single-template model quality assessment.
Bioinformatics, 28, 1851-1857

PROCLASS – Protein Structure Classification Server

PROCLASS

:: DESCRIPTION

 PROCLASS allows to predict the class of protein from its amino acid sequence. It predict weather protein belong to class Alpha or Beta or Alpha+Beta or Alpha/Beta.

::DEVELOPER

Dr. G P S Raghava,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Raghava, G P S (1999)
Proclass: A computer program for predicting the protein structural classes.
J. Biosciences 24, 176.

PDBFlex – Exploring Flexibility in Protein Structures

PDBFlex

:: DESCRIPTION

The PDBFlex database explores the intrinsic flexibility of protein structures by analyzing structural variations between different depositions and chains in asymmetric units of the same protein in PDB. It allows to easily identify regions and types of structural flexibility present in a protein of interest.

::DEVELOPER

Godzik Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2016 Jan 4;44(D1):D423-8. doi: 10.1093/nar/gkv1316. Epub 2015 Nov 28.
PDBFlex: exploring flexibility in protein structures.
Hrabe T, Li Z, Sedova M, Rotkiewicz P, Jaroszewski L, Godzik A.

PROSTA-inter 20141229 – PROtein STructure Alignment tools

PROSTA-inter 20141229

:: DESCRIPTION

PROSTA-inter is a sequence-order independent alignment tool that automatically determines and aligns interaction interfaces
between two arbitrary types of complex structures (protein-protein, protein-DNA, and/or protein-RNA).

::DEVELOPER

Structural and Functional Bioinformatics Group, King Abdullah University of Science and Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

PROSTA-inter

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Jun 15;31(12):i133-i141. doi: 10.1093/bioinformatics/btv242.
Finding optimal interaction interface alignments between biological complexes.
Cui X1, Naveed H1, Gao X

VLDP – Analysing Protein Structures in their Environment

VLDP

:: DESCRIPTION

VLDP ( Voronoi Laguerre Delaunay Protein) webserver is designed to determine protein contacts, accessibility and residue volume using Laguerre diagram.

::DEVELOPER

the DSIMB bioinformatic group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

VLDP web server: a powerful geometric tool for analysing protein structures in their environment.
Esque J, Léonard S, de Brevern AG, Oguey C.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W373-8. doi: 10.1093/nar/gkt509.

I-TASSER 5.1 – Protein Structure & Function Predictions

I-TASSER 5.1

:: DESCRIPTION

I-TASSER was ranked best in tertiary structure prediction (as ‘Zhang-Server’) in the community-wide blind benchmarks CASP7 and CASP8. It uses mainly profile-profile comparison to identify templates and alignments for deriving distance constraints. Its power lies in how it combines the distance constraints from up to the 50 best-ranked templates. It performs some knowledge-based free modelling in regions without any template-based information.

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 I-TASSER

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2015 Apr 16. pii: gkv342.
I-TASSER server: new development for protein structure and function predictions.
Yang J, Zhang Y

Ambrish Roy, Alper Kucukural, Yang Zhang.
I-TASSER: a unified platform for automated protein structure and function prediction.
Nature Protocols, vol 5, 725-738 (2010)

BHAGEERATH-H / Bhageerath 1.0 – Energy Based Protein Structure Prediction

Bhageerath 1.0 / BHAGEERATH-H

:: DESCRIPTION

Bhageerath is an energy based computer software suite for narrowing down the search space of tertiary structures of small globular proteins. The protocol comprises eight different computational modules that form an automated pipeline. It combines physics based potentials with biophysical filters to arrive at 10 plausible candidate structures starting from sequence and secondary structure information. The methodology has been validated here on 50 small globular proteins consisting of 2-3 helices and strands with known tertiary structures. For each of these proteins, a structure within 3-6 A RMSD (root mean square deviation) of the native has been obtained in the 10 lowest energy structures.

BHAGEERATH-H is a homology ab-intio hybrid eeb server for protein tertiary structure prediction

::DEVELOPER

Supercomputing Facility for Bioinformatics & Computational Biology, IIT Delhi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Solaris

:: DOWNLOAD

  Bhageerath

:: MORE INFORMATION

Citation:

B Jayaram, Priyanka Dhingra, Avinash Mishra, Rahul Kaushik, Goutam Mukherjee, Ankita Singh and Shashank Shekhar,
Bhageerath-H: A homology ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins“,
BMC Bioinformatics, 2014, 15(Suppl 16):S7

Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins.
Jayaram B, Bhushan K, Shenoy SR, Narang P, Bose S, Agrawal P, Sahu D, Pandey V.
Nucleic Acids Res. 2006;34(21):6195-204

Prelude & Fugue – Predicting local Protein Structure, early Folding Regions and Structural Weaknesses

Prelude & Fugue

:: DESCRIPTION

Prelude & Fugue predict the local structure of a protein in terms of backbone dihedral angle domains, identify sequence regions that form early during folding, and locate structural weaknesses, defined as regions whose sequence is not optimal with respect to the tertiary fold.

::DEVELOPER

Service de Biomodélisation, Bioinformatique et Bioprocédés (3BIO)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Prelude and Fugue, predicting local protein structure, early folding regions and structural weaknesses.
Kwasigroch JM, Rooman M.
Bioinformatics. 2006 Jul 15;22(14):1800-2.

BiopLib 3.10 / BiopTools 1.9 – C Programming Library and Toolset for Manipulating Protein Structure.

BiopLib 3.10 / BiopTools 1.9

:: DESCRIPTION

BiopLib is a library of C routines for general programming and handling protein structure

BiopTools is a set of command line tools written in C and making use of the BiopLib library for manipulation of protein structure and sequence

::DEVELOPER

Andrew C.R. Martin’s Bioinformatics Group at UCL

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • C Compiler

:: DOWNLOAD

 BiopLib , BiopTools

:: MORE INFORMATION

Citation

BiopLib and BiopTools – a C programming library and toolset for manipulating protein structure.
Porter CT, Martin AC.
Bioinformatics. 2015 Aug 30. pii: btv482.

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.