Structure prediction and visualisation

Name

Link

Description

3Drefine

http://sysbio.rnet.missouri.edu/3Drefine/

Program for protein structure refinement

BETASCAN

http://groups.csail.mit.edu/cb/betascan/

Program predicting beta structure and amyloid formation propensities of proteins. Accepts peptide sequences as  queries

Click

http://mspc.bii.a-star.edu.sg/minhn/intro.html

Program for comparison of secondary and tertiary structures of proteins and polypeptides

conSSert

http://ares.tamu.edu/conSSert/

Program for secondary structure prediction

DISSPred

http://comp.chem.nottingham.ac.uk/disspred/

Program for secondary structure prediction

EVA

http://cubic.bioc.columbia.edu/eva

Metaserver enabling access to programs predicting secondary structures of proteins and peptides. Programs SABLE and PORTER are sufficient for oligopeptide secondary structure prediction

FoldUnfold

http://skuld.protres.ru/~mlobanov/ogu/ogu.cgi

Program for prediction the presence of disordered regions in proteins. Accepts peptide sequences as queries

GOR V

http://gor.bb.iastate.edu/

Server for protein and peptide secondary structure prediction

HELIQUEST

http://heliquest.ipmc.cnrs.fr

Program highlighting physicochemical properties of α-helical proteins and peptides and screening protein databases (e.g. SwissProt) for protein fragments with desired properties

IBIVU

http://www.ibi.vu.nl/

Server providing access to programs predicting secondary structures

IntFOLD

http://www.reading.ac.uk/bioinf/IntFOLD/

Program for protein structure prediction. Accepts polypeptide sequences as query.

I-TASSER-MR

https://zhanglab.ccmb.med.umich.edu/I-TASSER-MR/

Program for protein structure prediction.

Jpred 4

http://www.compbio.dundee.ac.uk/jpred4/index.html

Program for protein structure prediction. Accepts polypeptide sequences as query.

LabWorm Protein alignment & structure

https://labworm.com/category/protein-peptide/protein-alignment-structure

Website providing access to programs for prtotein structure prediction

metaPrDOS

http://prdos.hgc.jp/meta/

Program predicting presence of disordered regions in protein and peptide sequences.

ModFOLD

http://www.reading.ac.uk/bioinf/ModFOLD/

Program for quality assessment of models of protein and polypeptide structures.

ModLink+

http://sbi.imim.es/modlink/

Program predicting fold of a target protein by aligning to the ones with known sequences. Program may also assign peptide sequences to known domains in proteins

Molmil

http://gjbekker.github.io/molmil/

Program for visualization of protein and peptide structures. Accepts pdb files.

MPI Bioinformatics Toolkit

https://toolkit.tuebingen.mpg.de/

Website providing access to programs for protein and peptide structure prediction

NAPS

http://bioinf.iiit.ac.in/NAPS/

Program for analysis of residue-residue interactions in proteins

OnD-CRF

http://babel.ucmp.umu.se/ond-crf/

Program predicting presence of disordered regions in protein and peptide sequences

PEP-FOLD

http://bioserv.rpbs.univ-paris-diderot.fr/PEP-FOLD/

Program  for peptide structure prediction

PEPstrMOD

http://osddlinux.osdd.net/raghava/pepstrmod/

Program designed for prediction of secondary and tertiary structure of small peptides (7-25 amino acid residues)

pmx

http://pmx.mpibpc.mpg.de/

Program for prediction of influence of mutations on protein and polypeptide structure

POODLE

http://mbs.cbrc.jp/poodle/index.html

Program  for prediction the presence of disordered regions in proteins. Accepts  peptide sequences as queries

Pôle Bioinformatique Lyonnais/NPS@

http://pbil.univ-lyon1.fr/

Server with the access to many programs able to process peptide sequences: e.g. constructing multiple alignments between sequences, secondary structure prediction calculating amino acids composition and profiles of physico-chemical features

PREDICT-2ND/SAM_T08

http://www.soe.ucsc.edu/compbio/SAM_T08/T08-query.html

Program designed for peptide and protein structure prediction

PreDisorder

http://casp.rnet.missouri.edu/predisorder.html

Program predicting presence of disordered regions in proteins and peptides

PreSSAPro

http://bioinformatica.isa.cnr.it/PRESSAPRO/

Server for protein and peptide secondary structure prediction

(PS)2-v2

http://ps2v2.life.nctu.edu.tw/

Program for protein structure prediction. Accepts peptide sequences as a query

(PS)2-v3

http://ps2v3.life.nctu.edu.tw/

Program for protein structure prediction. Accepts peptide sequences (exceeding 30 amino acid residues) as a query

PSSWeb

http://pssweb.org/

Program for statistical analysis of protein structures

Ramachandran Plot on the Web 2.0

http://dicsoft1.physics.iisc.ernet.in/rp/index.html

Program displaying protein and peptide structure

RaptorX-Property

http://raptorx2.uchicago.edu/StructurePropertyPred/predict/

Program for protein secondary structure and solvent accessibility prediction. Accepts peptide sequences, exceeding 26 amino acid residues

RBO Aleph

http://compbio.robotics.tu-berlin.de/rbo_aleph/

Program for protein structure prediction. Accepts polypeptide sequences (exceeding 40 amino acids residues) as query.

REFold

http://www.reading.ac.uk/bioinf/ReFOLD/

Program for accuracy estimation and refinement of protein structure models.

SCRATCH

http://www.igb.uci.edu/servers/psss.html

Website containing numerous programs predicting structure of peptides.

Sphinx

http://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/Sphinx.php

Program for loop prediction in protein structures.

UniAlign

http://sacan.biomed.drexel.edu/unialign/

Program aligning structures of proteins and polypeptides.

Web3DMol

http://web3dmol.duapp.com/

Program for protein structure visualization.

XSuLT

http://mordred.bioc.cam.ac.uk/xsult/

Program aligning sequences and structures of proteins and polypeptides.