PEPstrMOD – Peptide Tertiary Structure Prediction with Natural, Non-natural Modified Residues

PEPstrMOD

:: DESCRIPTION

The PEPstrMOD server predicts the tertiary structure of small peptides with sequence length varying between 7 to 25 residues. It also handles peptides having various modifications like non-natural residues, terminal modifications (Acetylation/Amidation), Cyclization (N-C, disulfide bridges), conversion of L- to D- amino acids, post translational modifications, etc. The prediction strategy is based on the realization that β-turn is an important and consistent feature of small peptides in addition to regular structures. Thus, the method uses both the regular secondary structure information predicted from PSIPRED and β-turns information predicted from BetaTurns. The structure is further refined with energy minimization and molecular dynamic simulations.

::DEVELOPER

PEPstrMOD Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Kaur, H., Garg, A. and Raghava, G. P. S. (2007)
PEPstr: A de novo method for tertiary structure prediction of small bioactive peptides.
Protein Pept Lett. 14:626-30.

PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues.
Singh S, Singh H, Tuknait A, Chaudhary K, Singh B, Kumaran S, Raghava GP.
Biol Direct. 2015 Dec 21;10:73. doi: 10.1186/s13062-015-0103-4.

MULTICOM / MULTICOM Toolbox – Protein Tertiary Structure Prediction

MULTICOM / MULTICOM Toolbox

:: DESCRIPTION

MULTICOM is a protein tertiary structure predictor using multi-template combination

::DEVELOPER

Dr. Jianlin Cheng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MULTICOM Toolbox

:: MORE INFORMATION

Citation

Z. Wang, J. Eickholt, and J. Cheng.
MULTICOM: A Multi-Level Combination Approach to Protein Structure Prediction and its Assessment in CASP8.
Bioinformatics. 26(7):882-888, 2010.

Large-scale model quality assessment for improving protein tertiary structure prediction.
Cao R, Bhattacharya D, Adhikari B, Li J, Cheng J.
Bioinformatics. 2015 Jun 15;31(12):i116-i123. doi: 10.1093/bioinformatics/btv235.

ProTSAV 1.0 – Protein Tertiary Structure Analysis and Validation server

ProTSAV 1.0

:: DESCRIPTION

ProTSAV is a meta-server, which has a collection of model quality assessment programs that evaluate the quality of a protein and correctness of the structural model.

::DEVELOPER

Supercomputing Facility for Bioinformatics & Computational Biology, IIT Delhi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ProTSAV

:: MORE INFORMATION

Citation:

ProTSAV: A protein tertiary structure analysis and validation server.
Singh A, Kaushik R, Mishra A, Shanker A, Jayaram B.
Biochim Biophys Acta. 2015 Oct 15. pii: S1570-9639(15)00260-5. doi: 10.1016/j.bbapap.2015.10.004.

InterPreTS – Interaction Prediction through Tertiary Structure

InterPreTS

:: DESCRIPTION

Given a set of protein sequences (in fasta format), InterPreTS will use BLAST to find homologues of known structure for all pairs (i.e. templates that can model each pair of sequences based on homology) and then evaluate the suitability of those templates for modelling the interaction

::DEVELOPER

the Cell Networks Protein Evolution group based at the University of Heidelberg.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 InterPreTS

:: MORE INFORMATION

Citation

Aloy P, Russell RB.
InterPreTS: protein interaction prediction through tertiary structure.
Bioinformatics. 2003 Jan;19(1):161-2.

ARTS – Alignment of RNA Tertiary Structures

ARTS

:: DESCRIPTION

ARTS (Alignment of RNA Tertiary Structures) is a method for aligning two nucleic acid structures (RNAs or DNAs) and detecting a-priori unknown common substructures.The identified common substructures can be either large global folds containing hundreds and even thousands of nucleotides or small local tertiary motifs with at least two successive base pairs.

::DEVELOPER

Oranit Dror (oranit@post.tau.ac.il) , BioInfo3D group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ARTS

:: MORE INFORMATION

Citation

O. Dror, R. Nussinov, and H. J. Wolfson (2006).
The ARTS web server for aligning RNA tertiary structures,
Nucleic Acids Research, 34, W412-W415