Help and About

Dunbar, J., Krawczyk, K. et al (2014). Nucleic Acids Res. 42. D1140-D1146

What is:

  • an antibody? - an immunoprotein responsible for specifically recognising and binding to potentially pathogenic molecules.
  • an antigen? - the molecule that the antibody targets.
  • a heavy chain? - the longer antibody chain. This folds to form one variable domain (VH) and three or more constant domains (CH1, CH2 and CH3).
  • a light chain? - the shorter antibody chain. This folds to form one variable domain (VL) and one constant domain (CL1).
  • a variable domain (VH or VL)? - the variable part of the antibody.
  • a CDR? - a Complimentarity Determining Region. These are generally characterised by six hypervariable loops: three on VH (H1, H2 and H3) and three on VL (L1, L2 and L3). Diversity in the sequence and structure of the CDRs are the main determinants of antigen specificity and affinity.
  • the framework region? - the collective name for the residues in VH or VL that are not CDRs.
  • an Fv? - a variable fragment. The collective name for a paired VH and VL.
  • an Fab?- an antigen binding fragment. The same as an Fv but also including the first constant domains of each chain, CH1 and CL1. Typically an antibody will have two Fab arms (see above). Most structures in SAbDab contain only these fragments.
  • a numbering scheme? - a system to annotate equivalent positions in antibodies. A scheme can often be applied by examining the sequence of the antibody only.

  • J. Leem, J. Dunbar, G. Georges, J. Shi, C.M. Deane. ABodyBuilder: automated antibody structure prediction with data-driven accuracy estimation., mAbs, 2016, doi: 10.1080/19420862.2016.1205773, [Paper Link]

  • J. Dunbar, K. Krawczyk, J. Leem, C. Marks, J. Nowak, C. Regep, G. Georges, S. Kelm, B. Popovic and C.M. Deane. SAbPred: a structure-based antibody prediction server, Nucleic Acids Res., 2016, doi: 10.1093/nar/gkw361, [Paper Link]

  • J. Nowak, T. Baker, G. Georges, S. Kelm, S. Klostermann, J. Shi, S. Sridharan and C.M. Deane. Length-independent structural similarities enrich the antibody CDR canonical class model, MAbs, 2016, [Paper Link]

  • J. Dunbar and CM. Deane ANARCI: Antigen receptor numbering and receptor classification., Bioinformatics, 2016, 32(2), 298-300 [Paper Link]

  • A. Bujotzek, J. Dunbar, F. Lipsmeier, W. Schäfer, I.Antes, C.M. Deane and G. Georges. Prediction of VH-VL domain orientation for antibody variable domain modeling, Proteins, 2015, 83(4), 681-695 [Paper Link]

  • J. Dunbar, B. Knapp, A. Fuchs, J. Shi and CM. Deane. Examining variable domain orientations in antigen receptors gives insight into TCR-like antibody design, PLOS Comp. Bio., 2014, 10(9), e1003852 [Paper Link]

  • K Krawczyk, X Liu, T Baker, J Shi, CM Deane, Improving B-cell epitope prediction and its application to global antibody-antigen docking, Bioinformatics, 2014, 30(16), 2288-2294 [Paper Link]

  • J. Dunbar, K. Krawczyk, J. Leem, T. Baker, A. Fuchs, G. Georges, J. Shi and CM. Deane, SAbDab: the Structural Antibody Database, Nucleic Acids Res., 2014, 42, D1140-D1146 [Paper Link]

  • Konrad Krawczyk, Terry Baker, Jiye Shi, Charlotte M. Deane, Antibody i-Patch prediction of the antibody binding site improves rigid local antibody antigen docking, PEDS, 2013, 26(10), 621-629 [Paper Link]

  • J. Dunbar, A. Fuchs, J. Shi, CM. Deane, ABangle: Characterising the VH-VL orientation in antibodies, Protein Eng. Des. & Sel., 2013, 26(10), 611-620 [Paper Link]

  • Choi Y, Deane CM, Predicting antibody complementarity determining region structures without classification, Mol. BioSyst., 2011, 7(12), 3327-34 [Paper Link]

  • Choi Y, Deane CM, FREAD revisited: Accurate loop structure prediction using a database search algorithm, Proteins, 2010, 78(6), 1431-40 [Paper Link]

  • SAbDab and SAbPred are built and maintained by the Oxford Protein Informatics Group (OPIG)
  • Please see the FAQ and topics on the help pages (SAbDab, SAbPred) for more information.
  • For any further queries please use our query form or contact us directly: opig <~at~>