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 |