Linear Epitope Prediction Tools Linear Epitope Prediction Tools Linear Epitope Prediction Tools Linear Epitope Prediction Tools Linear Epitope Prediction Tools
Tool Method Access Reference Reference
Hopp and Wood (1981)
Propensity scale
Unavailable in February 2023
DOI:10.1073/PNAS.78.6.3824 DOI: 10.1016/0161-5890(83)90029-9 DOI:10.1073/PNAS.78.6.3824 DOI: 10.1016/0161-5890(83)90029-9
PREDITOP (1993) Propensity scale Unavailable in February 2023 DOI: 10.1016/0263-7855(93)80074-2 DOI: 10.1016/0263-7855(93)80074-2
PEOPLE (1999) Propensity scale Unavailable in February 2023 DOI: 10.1016/S0264-410X(99)00329-1 DOI: 10.1016/S0264-410X(99)00329-1
BEPITOPE (2003) Combinations of physical and chemical parameters bepitope.ibs.fr DOI: 10.1002/jmr.602 DOI: 10.1002/jmr.602
BcePred (2004) Combinations of physical and chemical parameters webs.iiitd.edu.in/raghava/bcepred DOI: 10.1007/978-3-540-30220-9_16 DOI: 10.1007/978-3-540-30220-9_16
ABCpred server (2006) Machine learning webs.iiitd.edu.in/raghava/abcpred DOI: 10.1002/prot.21078 DOI: 10.1002/prot.21078
SVMtrip (2012) Machine learning sysbio.unl.edu/SVMTriP DOI: 10.1371/journal.pone.0045152 DOI: 10.1371/journal.pone.0045152
LBtope (2013) Machine learning webs.iiitd.edu.in/raghava/lbtope DOI: 10.1371/journal.pone.0062216 DOI: 10.1371/journal.pone.0062216
BepiPred (2017) Machine learning services.healthtech.dtu.dk/services/BepiPred-3.0 DOI: 10.1093/nar/gkx352 DOI: 10.1093/nar/gkx352
Continuous Epitope Prediction Tools Continuous Epitope Prediction Tools Continuous Epitope Prediction Tools Continuous Epitope Prediction Tools Continuous Epitope Prediction Tools
Tool Method Access Reference Reference
CEP (2005) Use X-ray crystal structures of Ag-Ab complexes to predicts conformational epitopes www.hsls.pitt.edu/obrc/index.php?page=URL1127484564 DOI: 10.1093/nar/gki460 DOI: 10.1093/nar/gki460
DiscoTope (2006) Combines the propensity scale matrices, spatial proximity and surface exposure tools.iedb.org/discotope DOI: 10.1110/ps.062405906 DOI: 10.1110/ps.062405906
ElliPro (2008) Modified version of Thornton’s approach tools.iedb.org/ellipro DOI: 10.1186/1471-2105-9-514 DOI: 10.1186/1471-2105-9-514
PEPITO (2008)
Combine single physicochemical properties of amino acids with geometrical structural properties
PEPITO is available as part of the SCRATCH suite of protein structure predictors: scratch.proteomics.ics.uci.edu
DOI: 10.1093/bioinformatics/btn199
DOI: 10.1093/bioinformatics/btn199
SEPPA 3.0 (2009) Combine single physicochemical properties of amino acids with geometrical structural properties www.badd-cao.net/seppa3/index.html DOI: 10.1093/nar/gkp417 DOI: 10.1093/nar/gkp417
EPITOPIA server (2009) Machine learning epitopia.tau.ac.il DOI: 10.1186/1471-2105-10-287 DOI: 10.1186/1471-2105-10-287
COBEpro (2009) Machine learning scratch.proteomics.ics.uci.edu DOI: 10.1093/protein/gzn075 DOI: 10.1093/protein/gzn075
CBTOPE (2010)
Machine learning
crdd.osdd.net/raghava/cbtope (unavailable in February 2023)
DOI: 10.1186/1745-7580-6-6
DOI: 10.1186/1745-7580-6-6
Mimotope Prediction Tools Mimotope Prediction Tools Mimotope Prediction Tools Mimotope Prediction Tools Mimotope Prediction Tools
Examples: tools.iedb.org/main/analysis-tools/mapping-mimotopes tools.iedb.org/main/analysis-tools/mapping-mimotopes tools.iedb.org/main/analysis-tools/mapping-mimotopes tools.iedb.org/main/analysis-tools/mapping-mimotopes
Database Availability Availability Availability Reference
MIMOX (2006) web.archive.org/web/20191025115806/http://immunet.cn/mimox web.archive.org/web/20191025115806/http://immunet.cn/mimox web.archive.org/web/20191025115806/http://immunet.cn/mimox DOI: 10.1186/1471-2105-7-451
PEPITOPE (2007) pepitope.tau.ac.il pepitope.tau.ac.il pepitope.tau.ac.il DOI: 10.1093/bioinformatics/btm493
EpiSearch (2009) curie.utmb.edu/episearch.html curie.utmb.edu/episearch.html curie.utmb.edu/episearch.html DOI: 10.4137/bbi.s2745
MIMOPRO (2011)
informatics.nenu.edu.cn/MimoPro (unavailable in February 2023) informatics.nenu.edu.cn/MimoPro (unavailable in February 2023) informatics.nenu.edu.cn/MimoPro (unavailable in February 2023)
DOI: 10.1186/1471-2105-12-199
Pep-3D-Search (2008)
kyc.nenu.edu.cn/Pep3DSearch (unavailable in February 2023) kyc.nenu.edu.cn/Pep3DSearch (unavailable in February 2023) kyc.nenu.edu.cn/Pep3DSearch (unavailable in February 2023)
DOI: 10.1186/1471-2105-9-538
MEPS (2007)
www.caspur.it/meps (unavailable in February 2023) www.caspur.it/meps (unavailable in February 2023) www.caspur.it/meps (unavailable in February 2023)
DOI: 10.1186/1471-2105-8-S1-S6
MIMOP (2006) upon request upon request upon request DOI: 10.1093/bioinformatics/btl012
3D-Epitope-Explorer (3DEX) (2005)
www.schreiber-abc.com/3dex (unavailable in February 2023) www.schreiber-abc.com/3dex (unavailable in February 2023) www.schreiber-abc.com/3dex (unavailable in February 2023)
DOI: 10.1002/jcc.20229
PEPMAPPER (2012)
informatics.nenu.edu.cn/PepMapper (unavailable in February 2023) informatics.nenu.edu.cn/PepMapper (unavailable in February 2023) informatics.nenu.edu.cn/PepMapper (unavailable in February 2023)
DOI: 10.1371/journal.pone.0037869
Antibodies Databases Antibodies Databases Antibodies Databases Antibodies Databases Antibodies Databases
Database Availability Availability Availability Reference
SAbDab opig.stats.ox.ac.uk/webapps/sabdab opig.stats.ox.ac.uk/webapps/sabdab opig.stats.ox.ac.uk/webapps/sabdab DOI: 10.1093/nar/gkz827
IMGT/mAb-DB imgt.org imgt.org imgt.org DOI: 10.3390/antib11040065
Docking Tools Docking Tools Docking Tools Docking Tools Docking Tools
Tool Method Access Reference Reference
ZDOCK Rigid protein docking program using Fast Fourier Transform (FFT) techniques zdock.umassmed.edu DOI: 10.1002/prot.10389 DOI: 10.1002/prot.10389
PatchDock (2005) Geometry-based molecular docking algorithm bioinfo3d.cs.tau.ac.il/PatchDock DOI: 10.1093/nar/gki481 DOI: 10.1093/nar/gki481
SnugDock (2010) Docking and the relative orientation of the antibody and antigen bodies can be optimized rosie.rosettacommons.org/snug_dock DOI: 10.1371/journal.pcbi.1000644 DOI: 10.1371/journal.pcbi.1000644
FRODOCK (2016) Uses FFT correlation algorithms, with differences in spherical harmonic (SH) based rotational search chaconlab.org/modeling/frodock DOI: 10.1093/bioinformatics/btw141 DOI: 10.1093/bioinformatics/btw141
HADDOCK (2015) Combines a global rigid body search with ambiguous restraints wenmr.science.uu.nl/haddock2.4 DOI: 10.1016/j.jmb.2015.09.014 DOI: 10.1016/j.jmb.2015.09.014
ClusPro 2.0 (2017) Algorithm based on the FFT cluspro.bu.edu DOI: 10.1038/nprot.2016.169 DOI: 10.1038/nprot.2016.169