Table 1. Key methods in contact prediction or its application available as servers or downloads.

Name of method	Description	Availability	URL	Citation
HHblits	Sequence-alignment generation by database search	Web server and local installation	https://toolkit.tuebingen.mpg.de/hhblits	Remmert et al. (2011 ▸)
Jackhmmer	Sequence alignment generation by database search	Web server and local installation	https://www.ebi.ac.uk/Tools/hmmer/search/jackhmmer	Johnson et al. (2010 ▸)
CCMpred	Contact-prediction application	Local installation	https://github.com/soedinglab/CCMpred	Seemayer et al. (2014 ▸)
MetaPSICOV	Intramolecular contact-prediction server	Web server and local installation	http://bioinf.cs.ucl.ac.uk/MetaPSICOV	Jones et al. (2015 ▸)
GREMLIN	Intramolecular and intermolecular contact-prediction server	Web server and local installation	http://gremlin.bakerlab.org	Ovchinnikov, Kinch et al. (2015 ▸)
RaptorX-Contact	Applies an ultradeep learning model to predict contacts: one of the best methods in CASP12	Web server and local installation	http://raptorx.uchicago.edu/ContactMap/	Wang et al. (2017 ▸)
EVfold	Intramolecular and intermolecular contact-prediction server with optional ab initio structure prediction	Web server	http://evfold.org/evfold-web/evfold.do	Marks et al. (2011 ▸)
CONFOLD	Ab initio structure-prediction server that takes input contacts	Web server	http://protein.rnet.missouri.edu/confold/	Adhikari et al. (2015 ▸)
ConKit	Python interface to contact prediction, visualization and evaluation with command-line scripts available	Local installation	http://www.conkit.org	Simkovic et al. (2017 ▸)
ConEVA	Contact-prediction evaluation server	Web server	http://cactus.rnet.missouri.edu/coneva/	Adhikari et al. (2016 ▸)
MSAVOLVE	MATLAB toolbox that includes numerous contact-prediction and related algorithms	Local installation	http://146.9.23.191/~gatti/coevolution/msavolve---simulation-and.html	Gatti (2015 ▸)
Domainpred	Perl scripts using kernel density estimation to parse domains from a list of predicted contacts	Local installation	Not currently available, but similar functionality is available in ConKit	Sadowski (2013 ▸)
i-COMS	Interprotein COrrelated Mutations Server: a webserver to calculate correlated mutations between proteins	Web server	http://i-coms.leloir.org.ar/index.php	Iserte et al. (2015 ▸)
InterEvDock	Protein–protein binding mode prediction server that uses contact predictions to help score poses	Web server	http://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::InterEvDock	Yu et al. (2016 ▸)