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PyIgClassify: a database of antibody CDR structural classifications
2014
Nucleic Acids Research
Preserved Fulltext
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
2019
PeerJ
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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
2018
PLoS Computational Biology
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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]
2017
bioRxiv
pre-print
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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
2022
Frontiers in Immunology
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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
2020
PeerJ
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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
2018
Frontiers in Immunology
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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]
2020
arXiv
pre-print
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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
2020
PLoS Computational Biology
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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
2018
F1000Research
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.: 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
2016
mAbs
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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
2020
mAbs
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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]
2020
bioRxiv
pre-print
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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
2015
Bioinformatics
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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
2020
Nucleic Acids Research
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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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