Antibody Design Platform Tools and Databases

Resource Type Resource Name PMID Description
Database TABS n/a Database of therapeutic antibodies
PDB 10592235 Database of protein structures
In house DB n/a Database of human ig sequences
OAS 30217829 Compendium of ig sequences gathered from large ngs studies
SAbDab 24214988 Antibody structures in pdb
SAbDab-Thera 31555805 Database of antibody therapeutics
Andrew Martin’s Antibody Resources n/a Database of sequence- and structure-based bioinformatics tools
IMGT 15608269 Database on genome, proteome, genetics and structure of ig, tcr and mhc
Abysis 27561707 Database of sequence- and structure-based bioinformatics tools
Immune Epitope Database 30357391 Database on antibody and t cell epitopes
Antibody Sequence Assessment Abnum 18614234 Tool to number antibody vh and vl sequence
MUSCLE 15034147 Tool for sequence alignment
CLUSTALW 12824352 Tool for sequence alignment
Jalview 19151095 Analysis and visualization of multiple sequence alignments
NetMHCIIpan 32308001 Tool to predict binding sites of mhc ii molecules
Therapeutic Antibody Profiler 30765520 In silico assessment of antibody developability
Humanness Score 17442342 Assess the degree of “humanness” of antibodies
Parapred 29672675 Sequence-based algorithm for paratope prediction
Geneious n/a Tool for phylogeny and sequence analysis
NetNGlyc – 1.0 n/a Tool to predict n-glycosylation sites in human proteins
Antibody Structural Assessment Swiss-model 29788355 3d modeling of antibodies
PIGS 25375991 3d modeling of antibodies
ABodyBuilder 27392298 3d modeling of antibodies
PyMOL 21053052 Molecular visualization and assessment
SWISS PDBViewer 19517507 Integrated suite of tools for structural assessment of proteins
AbAngle 23708320 Tool to compute relative orientation between the variable domains (vh and vl)
Protein-Protein Docking ZDOCK 12784371 Protein-protein docking
HADDOCK 12580598 Protein-protein docking
pyDockWeb 23661696 Protein-protein docking
Network Analysis SIN server Tool to compute quantitative network scores of residues in a 3d protein structure
CDR Redesign AIF 23569282 Distribution of pairwise contact in ag-ab interface
EPCN 26189681 2d network of epitope-paratope contacts
Discovery Studio/CHARMM Energy Minimization n/a Integrated suite of tools for life sciences
RosettaAntibodyDesign 29702641 Framework for ab initio design of antibodies
Literature/Patent PubMed  12438481 Archive of biomedical and life sciences journal literature at NLM/NIH
USPTO n/a Patent database
EPO n/a Patent database