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PyIgClassify: a database of antibody CDR structural classifications

Jared Adolf-Bryfogle, Qifang Xu, Benjamin North, Andreas Lehmann, Roland L. Dunbrack
2014 Nucleic Acids Research  
We present PyIgClassify (for Pythonbased immunoglobulin classification; available at http://dunbrack2.fccc.edu/pyigclassify/), a database and web server that provides access to assignments of all CDR structures  ...  Classification of the structures of the complementarity determining regions (CDRs) of antibodies is critically important for antibody structure prediction and computational design.  ...  Because of this, we have implemented automatic assignments of CDR structures in the PDB to our CDR structure classification system (14) , and in this paper, we present a comprehensive database and server  ... 
doi:10.1093/nar/gku1106 pmid:25392411 pmcid:PMC4383924 fatcat:j5kavqxkdngind4w2b5i5pqoie

Non-H3 CDR template selection in antibody modeling through machine learning

Xiyao Long, Jeliazko R. Jeliazkov, Jeffrey J. Gray
2019 PeerJ  
We compare the classification results using the GBM method to that of RosettaAntibody in a 3-repeat 10-fold cross-validation (CV) scheme on the cluster-annotated antibody database PyIgClassify and we observe  ...  The homology modeling of non-H3 CDRs is more accurate because non-H3 CDR loops of the same length and type can be grouped into a few structural clusters.  ...  Roland Dunbrack (ORCID 0000-0001-7674-6667) and Jared Adolf-Bryfogle for help with the PyIgClassify database. ADDITIONAL INFORMATION AND DECLARATIONS Funding Xiyao Long, Jeliazko R.  ... 
doi:10.7717/peerj.6179 pmid:30648015 pmcid:PMC6330961 fatcat:s3tfhyujrfb4dj6axf4etbausm

RosettaAntibodyDesign (RAbD): A general framework for computational antibody design

Jared Adolf-Bryfogle, Oleks Kalyuzhniy, Michael Kubitz, Brian D. Weitzner, Xiaozhen Hu, Yumiko Adachi, William R. Schief, Roland L. Dunbrack, Nir Ben-Tal
2018 PLoS Computational Biology  
A structural-bioinformatics-based computational methodology has been developed for the design of antibodies to targets of interest.  ...  The program samples antibody sequences and structures by grafting structures from updated canonical clusters of CDRs (North et al., J. Mol.  ...  From this classification, we developed the PyIgClassify database [53] , which is updated monthly and contains CDR sequences and cluster identifications for all antibodies in the PDB.  ... 
doi:10.1371/journal.pcbi.1006112 pmid:29702641 pmcid:PMC5942852 fatcat:ca5dpandm5hsnergjqeritdyv4

RosettaAntibodyDesign (RAbD): A General Framework for Computational Antibody Design [article]

Jared Adolf-Bryfogle, Oleks Kalyuzhniy, Michael Kubitz, Brian D. Weitzner, Xiaozhen Hu, Yumiko Adachi, William R. Schief, Roland L. Dunbrack
2017 bioRxiv   pre-print
The program samples antibody sequences and structures by grafting structures from a widely accepted set of the canonical clusters of CDRs (North et al., J. Mol. Biol., 406:228-256, 2011).  ...  A structural-bioinformatics-based computational methodology and framework have been developed for the design of antibodies to targets of interest.  ...  From this classification, we developed the PyIgClassify database [54] , which is updated monthly and contains CDR sequences and cluster identifications for all antibodies in the PDB.  ... 
doi:10.1101/183350 fatcat:pnhsg4fgjnbufhufpfxd6fxqcq

Coevolved Canonical Loops Conformations of Single-Domain Antibodies: A Tale of Three Pockets Playing Musical Chairs

Francis Gaudreault, Christopher R. Corbeil, Enrico O. Purisima, Traian Sulea
2022 Frontiers in Immunology  
Single-domain antibodies (sdAbs) are a promising class of biotherapeutics with unique structural traits within their paratope region.  ...  We outline a game of musical chairs that is necessary to maintain the integrity of the antibody structures that arose during evolution.  ...  The classification is updated periodically with newly deposited antibody structures from the PDB based on a dedicated database called PyIgClassify (33) .  ... 
doi:10.3389/fimmu.2022.884132 pmid:35720356 pmcid:PMC9203998 fatcat:ejxolpmolbahhgiovv5wqhnqfu

Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction

Akhila Melarkode Vattekatte, Nicolas Ken Shinada, Tarun J Narwani, Floriane Noël, Olivier Bertrand, Jean-Philippe Meyniel, Alain Malpertuy, Jean-Christophe Gelly, Frédéric Cadet, Alexandre G de Brevern
2020 PeerJ  
Members of the family Camelidae have a modified form of immunoglobulin gamma (IgG) with only heavy chains, called Heavy Chain only Antibodies (HCAb).  ...  Antigen binding by antibodies requires precise orientation of the complementarity- determining region (CDR) loops in the variable domain to establish the correct contact surface.  ...  CDRs were analysed using PyIgClassify classification (http://dunbrack2.fccc.edu/pyigclassify/) (Adolf-Bryfogle et al., 2015) (described in greater detail below).  ... 
doi:10.7717/peerj.8408 pmid:32185102 pmcid:PMC7061911 fatcat:ovj42chiq5gxrpc7cnaucky244

Understanding the Significance and Implications of Antibody Numbering and Antigen-Binding Surface/Residue Definition

Mathieu Dondelinger, Patrice Filée, Eric Sauvage, Birgit Quinting, Serge Muyldermans, Moreno Galleni, Marylène S. Vandevenne
2018 Frontiers in Immunology  
The recently generated deep-sequencing data and the increasing number of solved three-dimensional structures of antibodies from human and non-human origins have led to the emergence of numerous databases  ...  Despite the emergence of techniques allowing the development of fully human antibodies such as transgenic Xeno-mice, antibody humanization remains a standard procedure for therapeutic antibodies.  ...  In conjunction, these studies suggest that the structural classification of the CDRs based on structure prediction from the CDR sequences can be a very useful tool for antibody engineering.  ... 
doi:10.3389/fimmu.2018.02278 fatcat:haxad3vokjfxjbaukprptfcs6a

ASAP-SML: An Antibody Sequence Analysis Pipeline Using Statistical Testing and Machine Learning [article]

Xinmeng Li, James A. Van Deventer, Soha Hassoun
2020 arXiv   pre-print
The fingerprints represent germline, CDR canonical structure, isoelectric point and frequent positional motifs.  ...  We develop a pipeline, Antibody Sequence Analysis Pipeline using Statistical testing and Machine Learning (ASAP-SML), to identify features that distinguish one set of antibody sequences from antibody sequences  ...  Acknowledgements We appreciate the contribution of Niroshan Anadasivam, funded under NSF REU award 1560388, in running the isoelectric point calculations for the CDR-H3 region.  ... 
arXiv:2003.03811v1 fatcat:7rzvmxveozdpblontkhwxkioge

ASAP-SML: An antibody sequence analysis pipeline using statistical testing and machine learning

Xinmeng Li, James A. Van Deventer, Soha Hassoun, Dario Ghersi
2020 PLoS Computational Biology  
The fingerprints represent germline, CDR canonical structure, isoelectric point and frequent positional motifs.  ...  We develop a pipeline, Antibody Sequence Analysis Pipeline using Statistical testing and Machine Learning (ASAP-SML), to identify features that distinguish one set of antibody sequences from antibody sequences  ...  Acknowledgments We appreciate the contribution of Niroshan Anadasivam, funded under NSF REU award 1560388, in running the isoelectric point calculations for the CDR-H3 region. Author Contributions  ... 
doi:10.1371/journal.pcbi.1007779 pmid:32339164 fatcat:hrfnaeknybhbbj7aplu5qvpgie

Crystal structures of a llama VHH antibody BCD090-M2 targeting human ErbB3 receptor

Igor E. Eliseev, Anna N. Yudenko, Vera V. Vysochinskaya, Anna A. Svirina, Anna V. Evstratyeva, Maria S. Drozhzhachih, Elena A. Krendeleva, Anna K. Vladimirova, Timofey A. Nemankin, Viktoria M. Ekimova, Andrey B. Ulitin, Maria I. Lomovskaya (+5 others)
2018 F1000Research  
.: PyIgClassify: a database of antibody CDR structural classifications. Nucleic Acids Res. 2015; 43(Database issue): D432-D438. PubMed Abstract | Publisher Full Text | Free Full Text 26.  ...  Here we report the expression, purification and structural analysis of a new anti-ErbB3 single-chain antibody.  ...  We then used a PyIgClassify 25 to analyze the structures of BCD090-M2 CDRs using a comprehensive database of antibody CDR loop conformations.  ... 
doi:10.12688/f1000research.13612.1 fatcat:xp2uwq2cy5f7vlfmr3dtjihbti

Length-independent structural similarities enrich the antibody CDR canonical class model

Jaroslaw Nowak, Terry Baker, Guy Georges, Sebastian Kelm, Stefan Klostermann, Jiye Shi, Sudharsan Sridharan, Charlotte M. Deane
2016 mAbs  
Complementarity-determining regions (CDRs) are antibody loops that make up the antigen binding site. Here, we show that all CDR types have structurally similar loops of different lengths.  ...  This suggests that our length-independent canonical classes might be a highly prevalent feature of antibody space, and could substantially improve our ability to accurately predict the structure of novel  ...  This clustering is available as an online database (http://dunbrack2.fccc.edu/PyIgClassify/). 19 There have also been studies of canonical shapes that involved only a subset of available structures.  ... 
doi:10.1080/19420862.2016.1158370 pmid:26963563 pmcid:PMC4966832 fatcat:lleh7xoyqnespcfkkwtqy5jnzq

Antibody CDR loops as ensembles in solution vs. canonical clusters from X-ray structures

Monica L Fernández-Quintero, Martin C Heiss, Nancy D Pomarici, Barbara A Math, Klaus R Liedl
2020 mAbs  
Here, we present a kinetic classification of CDR loop structures as ensembles in solution.  ...  conformational ensemble in solution as a new paradigm in the field of antibody structure design.Abbreviations: CDR: Complementary-determining region; Fv: Antibody variable fragment; PCCA: Perron cluster  ...  With the substantial rise in the number of antibody crystal structures, the number of antibody databases and sequence-based classification servers has also increased significantly.  ... 
doi:10.1080/19420862.2020.1744328 pmid:32264741 pmcid:PMC7153821 fatcat:2e7iwzpql5eivobxq6htmyb35a

Hiding in plain sight: structure and sequence analysis reveals the importance of the antibody DE loop for antibody-antigen binding [article]

Simon P. Kelow, Jared Adolf-Bryfogle, Roland Dunbrack
2020 bioRxiv   pre-print
Our structural classification of the DE loop uncovers its influence on CDR1 and CDR2 conformations, which in turn affect antibody binding.  ...  Length-8 L4 CDRs from a subset of λ5/λ6 germlines all have a backbone conformation very similar to that of the H4 length 8 cluster.  ...  Acknowledgements This work was funded by NIH grant R35 GM122517 (to R.L.D.) as well as the NIH T32 Structural Biology and Molecular Biophysics training grant awarded by the Department of Biochemistry and  ... 
doi:10.1101/2020.02.12.946350 fatcat:lvfvzcyimjevvewcp4grxmowdm

ANARCI: antigen receptor numbering and receptor classification

James Dunbar, Charlotte M. Deane
2015 Bioinformatics  
Such annotations are valuable for antibody sequence comparison, protein structure modelling and engineering.  ...  Results: ANARCI is a tool to classify and number antibody and T-cell receptor amino-acid variable domain sequences.  ...  Acknowledgements We would like to thank Dominic Kelly, Anna Fowler and Jake Galson for providing the benchmark set of VH sequences.  ... 
doi:10.1093/bioinformatics/btv552 pmid:26424857 pmcid:PMC4708101 fatcat:reqkes6yivhizb667x43mpbsw4

CoV3D: a database of high resolution coronavirus protein structures

Ragul Gowthaman, Johnathan D Guest, Rui Yin, Jared Adolf-Bryfogle, William R Schief, Brian G Pierce
2020 Nucleic Acids Research  
structure-based classification of spike conformations, generated by unsupervised clustering.  ...  To assist structure-based design of vaccines and therapeutics against SARS-CoV-2 and other coronaviruses, we have developed CoV3D, a database and resource for coronavirus protein structures, which is updated  ...  ACKNOWLEDGEMENTS We are grateful to the structural biologists and researchers whose work resulted in the structures enabling the development of this database.  ... 
doi:10.1093/nar/gkaa731 pmid:32890396 fatcat:cm5ersfz2nhlpdzzc27trakg5y
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