NameLinkDescription
3Drefinehttp://sysbio.rnet.missouri.edu/3Drefine/Program for protein structure refinement
AWSEM-Suitehttps://awsem.rice.edu/Program for protein structure prediction. Accepts polypeptide structures as  queries
BETASCANhttp://groups.csail.mit.edu/cb/betascan/Program predicting beta structure and amyloid formation propensities of proteins. Accepts peptide sequences as  queries
CCFoldhttps://pharm.kuleuven.be/apps/biocryst/ccfold.phpProgram for coiled coil prediction in proteins. Accepts sequences of peptides containing at least 30 amino acid residues.
Clickhttp://mspc.bii.a-star.edu.sg/minhn/intro.htmlProgram for comparison of secondary and tertiary structures of proteins and polypeptides
conSSerthttp://ares.tamu.edu/conSSert/Program for secondary structure prediction
DISSPredhttp://comp.chem.nottingham.ac.uk/disspred/Program for secondary structure prediction
EVAhttp://cubic.bioc.columbia.edu/evaMetaserver enabling access to programs predicting secondary structures of proteins and peptides. Programs SABLE and PORTER are sufficient for oligopeptide secondary structure prediction
FATCAThttps://fatcat.godziklab.org/Program aligning structures of proteins and polypeptides
FoldUnfoldhttp://skuld.protres.ru/~mlobanov/ogu/ogu.cgiProgram for prediction the presence of disordered regions in proteins. Accepts peptide sequences as queries
GOR Vhttp://gor.bb.iastate.edu/Server for protein and peptide secondary structure prediction
HELIQUESThttp://heliquest.ipmc.cnrs.frProgram highlighting physicochemical properties of α-helical proteins and peptides and screening protein databases (e.g. SwissProt) for protein fragments with desired properties
IBIVUhttp://www.ibi.vu.nl/Server providing access to programs predicting secondary structures
IntFOLDhttp://www.reading.ac.uk/bioinf/IntFOLD/Program for protein structure prediction. Accepts polypeptide sequences as query.
I-TASSER-MRhttps://zhanglab.ccmb.med.umich.edu/I-TASSER-MR/Program for protein structure prediction.
IUPred2Ahttps://iupred2a.elte.hu/Program for disorder prediction in protein structures. Accepts peptide sequences as a query.
Jpred 4http://www.compbio.dundee.ac.uk/jpred4/index.htmlProgram for protein structure prediction. Accepts polypeptide sequences as query.
LabWorm Protein alignment & structurehttps://labworm.com/category/protein-peptide/protein-alignment-structureWebsite providing access to programs for prtotein structure prediction
LOMETShttps://zhanglab.ccmb.med.umich.edu/LOMETS/Program for protein structure prediction. Accepts also polypeptide sequences.
metaPrDOShttp://prdos.hgc.jp/meta/Program predicting presence of disordered regions in protein and peptide sequences.
ModFOLDhttp://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
Molmilhttp://gjbekker.github.io/molmil/Program for visualization of protein and peptide structures. Accepts pdb files.
MPI Bioinformatics Toolkithttps://toolkit.tuebingen.mpg.de/Website providing access to programs for protein and peptide structure prediction
NAPShttp://bioinf.iiit.ac.in/NAPS/Program for analysis of residue-residue interactions in proteins
OnD-CRFhttp://babel.ucmp.umu.se/ond-crf/Program predicting presence of disordered regions in protein and peptide sequences
PEP-FOLDhttp://bioserv.rpbs.univ-paris-diderot.fr/PEP-FOLD/Program  for peptide structure prediction
PEPstrMODhttp://osddlinux.osdd.net/raghava/pepstrmod/Program designed for prediction of secondary and tertiary structure of small peptides (7-25 amino acid residues)
pmxhttp://pmx.mpibpc.mpg.de/Program for prediction of influence of mutations on protein and polypeptide structure
POODLEhttp://mbs.cbrc.jp/poodle/index.htmlProgram  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_T08http://www.soe.ucsc.edu/compbio/SAM_T08/T08-query.htmlProgram designed for peptide and protein structure prediction
PreDisorderhttp://casp.rnet.missouri.edu/predisorder.htmlProgram predicting presence of disordered regions in proteins and peptides
PreSSAProhttp://bioinformatica.isa.cnr.it/PRESSAPRO/Server for protein and peptide secondary structure prediction
(PS)2-v2http://ps2v2.life.nctu.edu.tw/Program for protein structure prediction. Accepts peptide sequences as a query
(PS)2-v3http://ps2v3.life.nctu.edu.tw/Program for protein structure prediction. Accepts peptide sequences (exceeding 30 amino acid residues) as a query
PSSWebhttp://pssweb.org/Program for statistical analysis of protein structures
Ramachandran Plot on the Web 2.0http://dicsoft1.physics.iisc.ernet.in/rp/index.htmlProgram displaying protein and peptide structure
RaptorX-Propertyhttp://raptorx2.uchicago.edu/StructurePropertyPred/predict/  Program for protein secondary structure and solvent accessibility prediction. Accepts peptide sequences, exceeding 26 amino acid residues
RBO Alephhttp://compbio.robotics.tu-berlin.de/rbo_aleph/Program for protein structure prediction. Accepts polypeptide sequences (exceeding 40 amino acids residues) as query.
REFoldhttp://www.reading.ac.uk/bioinf/ReFOLD/Program for accuracy estimation and refinement of protein structure models.
SCRATCHhttp://www.igb.uci.edu/servers/psss.htmlWebsite containing numerous programs predicting structure of peptides.
Sphinxhttp://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/Sphinx.phpProgram for loop prediction in protein structures.
Spider3https://sparks-lab.org/server/spider3/Program for protein structure prediction and validation. Accepts peptide sequences as a query
StructureMapperhttp://structuremapper.uta.fi/Program for mapping of protein primary amino acid sequence locations to existing three-dimensional protein structures. Accepts peptide sequences as a query
TopSuitehttps://cpclab.uni-duesseldorf.de/topsuite/Metaserver for protein structure prediction and validation.
UniAlignhttp://sacan.biomed.drexel.edu/unialign/Program aligning structures of proteins and polypeptides.
Web3DMolhttp://web3dmol.duapp.com/Program for protein structure visualization.
XSuLThttp://mordred.bioc.cam.ac.uk/xsult/Program aligning sequences and structures of proteins and polypeptides.