Computational Antibody Tools & Databases

Below you can find a list of database and computational antibody tools. This list was created as part of our review on computational antibody tools that you can read here. If you think that we have missed some tools, please send us an email at konrad@naturalantibody.com. Please come back to this page for updates on newly released antibody tools and resources. .

Databases

Below you can see the databases with antibody-specific datasets.

Database NameLinkDescriptionReference
TABSlinkDatabase of therapeutic antibodiesn/a
Therapeutic antibodies in SAbDablinkTherapeutic antibodies found in SAbDabRaybould et al. 2019, PNAS
Andrew Martin's Antibody Resources link Resources on antibody-related analytics n/a
AAAAA link Resources on antibody-related analytics Honegger & Plueckthun, 2001, J Mol Biol
AbMiner link Database of available monoclonal antibodies Major et al. 2006 BMC Bioinformatics
IMGT link Leading antibody genetics database Lefranc et al. 2015, NAR
IgPDB link Database of inferred allelic variants for immunoglobulins Ohlin et al. 2019, Front Immun
Abysis link Sequence and structural data on antibodies Swindells et al. 2017, J Mol Biol
DIGIT link Antibody sequence database (Chailyan et al., 2012, NAR)
Ireceptor link NGS sequence data on B-cell receptors (Corrie et al., 2018, Immunog Rev)
PCLICK link Clusters of antibody-antigen interactions (Nguyen et al., 2017, Bioinformatics)
PyIgClassify (commercial license available) link Database of CDR canonical classes (Adolf-Bryfogle et al., 2015, NAR)
Structural Antibody Database link Self-updatable database of antibody/nanobody structures (James Dunbar et al., 2013, NAR)
AbDb link Database of antibody structures (Ferdous and Martin, 2018, Database)
Immune Epitope Database link Manually curated epitope data. (Vita et al., 2018, NAR)
PDBBind link Affinity data on proteins in the PDB (Wang et al., 2004, J Med Chem)
SKEMPI (non-commercial use) link Not-antibody specific interaction database (Jankauskaite, 2019, Bioinformatics)
Non-redundant Nanobody database link Non-redundant structures of nanobodies (Zavrtanik and Hadži, 2019, Data in Brief)
Single Domain Antibody Database link Sequence and structural data on nanobodies (Wilton et al., 2018, ACS Synth Biol)
Institute for analysis and collection of nanobodies link Sequences and structural data on nanobodies (Zuo et al., 2017, BMC Genomics)

Tools

Below you can see the tools with antibody-specific methods.

Database NameLinkDescriptionReference
IgBLAST link Raw data processing (Ye et al., 2013, NAR)
IMGT V-Quest link Raw data processing (Brochet et al., 2008, NAR)
MiXCR link Raw data processing (Bolotin et al., 2015, Nat Methods)
Immcantation link Raw data processing (Gupta et al., 2015, Bioinformatics), (Vander Heiden et al., 2014, Bioinformatics)
IgRec link Raw data processing (Shlemov et al., 2017, J Immunol)
ImmuneDiversity link Raw data processing (Cortina-Ceballos et al., 2015, MAbs)
IMSEQ link Raw data processing (Kuchenbecker et al., 2015, Bioinformatics)
Partis link Raw data processing (Ralph and Matsen, 2016, Plos Comp Bio)
IGoR link Raw data processing (Marcou et al., 2018, Nat Comm)
VDJTools link Raw data processing (Shugay et al., 2015)
Vidjil link Raw data processing (Giraud et al., 2014, BMC Genomics), (Duez et al., 2016, Plos One)
ImmuneDB link Raw data processing (Rosenfeld et al., 2018, Front Immun)
AbRSA link Numbering (Li et al., 2019, Protein Sci)
Abnum link Numbering (Abhinandan K R, 2008, Mol Immunol)
ANARCI link Numbering (Dunbar and Deane, 2015, Bioinformatics)
AbodyBuilder link Full FV modelling (Leem et al., 2016, MAbs)
LYRA link Full FV modelling (Klausen et al., 2015, NAR)
PIGS link Full FV modelling (Marcatili et al., 2008, Bioinformatics)
Kotai Antibody Builder link Full FV modelling (Yamashita et al., 2014, Bioinformatics)
RosettaAntibody link Full FV modelling (Sivasubramanian et al., 2009, Proteins), (Weitzner et al., 2017, Nat Prot)
BIOVIA link Full FV modelling (Kemmish et al., 2017, Plos ONE)
MoFvAb link Full Fv Modelling (Bujotzek, Fuchs, et al., 2015, MAbs)
WAM link Full Fv Modelling (Whitelegg and Rees, 2000, Protein Eng)
BioLuminate link Full Fv Modelling (Zhu et al., 2014, Proteins)
MOE link Full Fv Modelling n/a
ABGEN link Full Fv Modelling (Mandal et al., 1996, Nat Biotech)
AbPredict link Full FV modelling (Lapidoth et al., 2019, Bioinformatics)
SmrtMolAntibody link Full FV modelling (Berrondo et al., 2014, Proteins)
PEARS link Ab-specific side chain prediction (Leem et al., 2018, Proteins)
H3LoopPred link Antibody specific loop prediction (Messih et al., 2014, Bioinformatics)
SCWRL link Side Chain Prediction (Krivov et al., 2009, Proteins)
BetaSCPWeb link Side Chain Prediction (Ryu et al., 2016, NAR)
SPHINX link Antibody specific ab ignition loop prediction (Marks et al., 2017, Bioinformatics)
FREAD link Database-search loop prediction (Choi and Deane, 2010, Proteins)
PLOP link Ab initio loop prediction (Jacobson et al., 2004, Proteins)
Chothia Canonical Assignment link CDR Canonical structure prediction Based on (Martin and Thornton, 1996, J Mol Biol)
SCALOP link CDR Canonical structure prediction (Wong et al., 2018, Bioinformatics)
Roche VH/VL orientation link VH/VL orientation (Bujotzek, Dunbar, et al., 2015, Proteins)
Rosetta VH/VL orientation link VH/VL orientation (Marze et al., 2016, Protein Eng Des Sel)
AbAngle link VH/VL orientation (J Dunbar et al., 2013, Protein Eng Des Sel)
Antibody i-Patch link Paratope Prediction (Krawczyk et al., 2013, Protein Eng Des Sel)
ProABC link Paratope Prediction (Olimpieri et al., 2013, Bioinformatics)
Parapred link Paratope Prediction (Liberis et al., 2018, Bioinformatics)
AntibodyInterfacePrediction link Paratope Prediction (Daberdaku and Ferrari, 2018, Bioinformatics)
AG-FAST-Parapred link Paratope Prediction (Deac et al., 2018, J Comput Biol)
ISMBLab-PPI link Protein contact prediction, applied to paratopes (Peng et al., 2014, PNAS)
Rapberger et al 2007 link Ab-specific epitope prediction (Rapberger et al., 2007, J Mol Recognit)
PEASE link Ab-specific epitope prediction (Sela-Culang et al., 2015, Bioinformatics)
EpiPred link Ab-specific Epitope Prediction (Krawczyk et al., 2014, Bioinformatics)
Jespersen et al. link Ab-specific Epitope Prediction (Jespersen et al., 2019, Front Immun)
EpiScope link Ab-specific Epitope Prediction (Hua et al., 2017, eLife)
MabTope link Ab-specific Epitope Prediction (Bourquard et al., 2018)
ASEP link Ab-specific Epitope Prediction (Soga et al., 2010, Protein Eng Des Sel)
BEPAR link Ab-specific Epitope Prediction (Zhao and Li, 2010, BMC Struct Biol)
ABEPAR link Ab-specific Epitope Prediction (Zhao et al., 2011, IEEE/ACM Trans)
ClusPro link Ab-specific docking (Brenke et al., 2012, Bioinformatics), (Kozakov et al., 2017, Nat Prot)
surFit link Ab-specific docking (Shimba et al., 2016, J Chem Inf Model)
SnugDock link Ab-specific docking (Sircar and Gray, 2010, Plos Comp Bio)
FRODOCK link Ab-specfic docking (Ramírez-Aportela et al., 2016, Bioinformatics)
DockSorter (ab-specific scoring) link Ab-specific docking scoring (Krawczyk et al., 2013, Prot Eng Des Sel)
Hex link Docking, not antibody specific (Macindoe et al., 2010, NAR)
ZDOCK link Docking, not antibody specific. (Chen et al., 2003, Proteins)
HADDOCK link Docking, not antibody specific. (Dominguez et al., 2003, J Am Chem Soc), (De Vries et al., 2007, Proteins)
ATTRACT link Docking, not antibody specific (De Vries et al., 2015, Biophys J)
GRAMM-X link Docking, not antibody specific (Tovchigrechko and Vakser, 2006, NAR)
pyDockWeb (pyDock, FTDock) link Docking, not antibody specific (Jiménez-García et al., 2013, Bioinformatics)
Swarmdock link Docking, not antibody specific. (Torchala et al., 2013, Bioinformatics)
PatchDock link Docking, not antibody specific. (Schneidman-Duhovny et al., 2005, NAR)
OPTCDR link Design Protocol (Pantazes and Maranas, 2010, Prot Eng Des Sel)
OPTMaven link Design Protocol (Li et al., 2014; Plos ONE), (Chowdhury et al., 2018, Antibodies)
RosettaAntibodyDesign link Design Protocol (Adolf-Bryfogle et al., 2018, Plos Comp Bio)
AbDesign link Design Protocol (Baran et al., 2017, PNAS), (Lapidoth et al., 2015, Proteins)
Humanness Score link Humanization (Abhinandan and Martin, 2007, J Mol Biol)
Humanizer link Humanization (Chowdhury et al., 2018, Antibodies)
Tabhu link Humanization (Olimpieri et al., 2015, Bioinformatics)
Human String Content link Humanization (Lazar et al., 2007, Mol Immunol)
T20 Score link Humanization (Gao et al., 2013, BMC Biotechnol)
CODah link Humanization (Choi et al., 2015, MAbs)
Developability Index link Developability (Lauer et al., 2012, J Pharm Sci)
Delayed HIC retention prediction link Developability (Jain, Boland, et al., 2017, Bioinformatics)
Therapeutic Antibody Profiler link Developability (Raybould et al., 2019, PNAS)
Lonza Predictor link Developability (Obrezanova et al., 2015, MAbs)