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AbDb: antibody structure database—a database of PDB-derived antibody structures

Saba Ferdous, Andrew C R Martin
2018 Database: The Journal of Biological Databases and Curation  
We have created an automatically updated resource, AbDb, which collects the Fv regions from antibody structures using information from our SACS database which summarises antibody structures from the PDB  ...  In order to analyze structures of proteins of a particular class, these need to be extracted from the Protein Data Bank (PDB).  ...  A detailed breakdown of the content of the AbDb database as of October 2017 is shown in The SACS database which provides lists of antibodies to be processed by AbDb is a cumulative resource (listing PDB  ... 
doi:10.1093/database/bay040 pmid:29718130 pmcid:PMC5925428 fatcat:yghl2v7m2jb43f4ggmlfprukzm

SAbDab in the age of biotherapeutics: updates including SAbDab-nano, the nanobody structure tracker

Constantin Schneider, Matthew I J Raybould, Charlotte M Deane
2021 Nucleic Acids Research  
In 2013, we released the Structural Antibody Database (SAbDab), a publicly available repository of experimentally determined antibody structures.  ...  These include the development of SAbDab-nano, a sub-database that tracks nanobodies (heavy chain-only antibodies) which have seen a particular growth in attention from both the academic and pharmaceutical  ...  Zavrtanik and Hadži (16) compiled a static, non-redundant set of 123 nanobody structures in complex with antigens, derived from 217 PDB deposited structures.  ... 
doi:10.1093/nar/gkab1050 pmid:34986602 pmcid:PMC8728266 fatcat:nfqd6lt4lvhw7k63xuf6j7xh24

Extracting human antibody sequences from public databases for antibody humanization: high frequency of species assignment errors

Andrew C.R. Martin, Anthony R. Rees
2016 Protein Engineering Design & Selection  
In antibody humanization, CDRs from a 'donor' antibody are often grafted onto a human framework selected by high sequence identity with the donor.  ...  Here we take three mouse antibodies and perform BLAST searches against sequences annotated as being human.  ...  A local BLAST database was created containing sequences annotated as human from Kabat, IMGT, EMBLIG (derived from EMBL-ENA) and the PDB.  ... 
doi:10.1093/protein/gzw018 pmid:27274090 fatcat:p62jxhfn6vfehcsaxxz7hhjso4

Improving CDR-H3 modelling in antibodies

Benjamin Blundell, Andrew Martin
2019 Zenodo  
The variable domain of the antibody is responsible for binding to an antigen and contains polypeptide loops, each referred to as a 'Complemen- tarity Determining Region (CDR)'.  ...  Antibodies - key molecules of the immune system - are increasingly used as ther- apeutic drugs.  ...  Both sets of PDB files were entered into a database for ease of batching and examination. AbDb dataset The initial dataset we consider is derived from AbDb [18] .  ... 
doi:10.5281/zenodo.2549566 fatcat:zu5nehrr3rgopaenguvnat6u6q

Effective rational humanization of a PASylated anti-galectin-3 Fab for the sensitive PET imaging of thyroid cancer in vivo

Emanuel Peplau, Francesco De Rose, Andreas Eichinger, Sybille Reder, Markus Mittelhäuser, Giorgia Scafetta, Markus Schwaiger, Wolfgang A. Weber, Armando Bartolazzi, Calogero D'Alessandria, Arne Skerra
2021 Scientific Reports  
We previously developed a human-chimeric αhGal3 Fab fragment derived from the rat monoclonal antibody (mAb) M3/38 with optimized clearance characteristics using PASylation technology.  ...  AbstractThe lack of a non-invasive test for malignant thyroid nodules makes the diagnosis of thyroid cancer (TC) challenging.  ...  Acknowledgements The authors wish to thank Stefan Achatz (TUM) for ESI-MS measurements as well as help with the database analysis and Christian Feiler for technical support at BESSY beamline 14.1 of the  ... 
doi:10.1038/s41598-021-86641-0 pmid:33795750 pmcid:PMC8016950 fatcat:ulrto3kjoffnvpqcpx7yq6zuye

NanoNet: Rapid end-to-end nanobody modeling by deep learning at sub angstrom resolution [article]

Tomer Cohen, Matan Halfon, Dina Schneidman-Duhovny
2021 bioRxiv   pre-print
Antibodies are a rapidly growing class of therapeutics.  ...  NanoNet runtimes allow generation of ~1M nanobody structures in less than an hour on a standard CPU computer enabling high-throughput structure modeling.  ...  The antibody structures were obtained from abYbank/AbDb 40 and SAbDab 41, 42 ; a total of 2,085 non-redundant structures of Nbs (319) and mAb heavy chains (1,766) were used.  ... 
doi:10.1101/2021.08.03.454917 fatcat:vxhixb33crgc7de2weuursbye4

A finite vocabulary of antibody-antigen interaction enables predictability of paratope-epitope binding [article]

Rahmad Akbar, Jeliazko R Jeliazkov, Philippe A Robert, Igor Snapkov, Milena Pavlović, Andrei Slabodkin, Cédric R. Weber, Yana Safanova, Geir Kjetil Sandve, Victor Greiff
2019 bioRxiv   pre-print
A fundamental premise for the predictability of paratope-epitope binding is the existence of structural units that are universally shared among antibody-antigen binding complexes.  ...  Here, we identified structural interaction motifs, which together compose a vocabulary of paratope-epitope binding that is shared among investigated antibody-antigen complexes.  ...  (A) We characterized antibody-antigen interaction using publicly available 3D structures deposited in the Antibody Database (AbDb) (see Methods), a total of 825 antibody-antigen complexes (dark/light blue  ... 
doi:10.1101/759498 fatcat:xkgqan33zjb4jc2xmfoscc5btq

NanoNet: Rapid and accurate end-to-end nanobody modeling by deep learning

Tomer Cohen, Matan Halfon, Dina Schneidman-Duhovny
2022 Frontiers in Immunology  
Antibodies are a rapidly growing class of therapeutics.  ...  NanoNet run times allow generation of ∼1M nanobody structures in less than 4 hours on a standard CPU computer enabling high-throughput structure modeling.  ...  The antibody structures were obtained from abYbank/AbDb (53) and SAbDab (54, 55) ; a total of 2,085 non-redundant structures of Nbs (319) and mAb heavy chains (1,766) were used.  ... 
doi:10.3389/fimmu.2022.958584 pmid:36032123 pmcid:PMC9411858 fatcat:s5dmmoa6tvasfkvyjnulf27vke

Ig-VAE: Generative Modeling of Immunoglobulin Proteins by Direct 3D Coordinate Generation [article]

Raphael R Eguchi, Namrata Anand, Christian Andrew Choe, Po-Ssu Huang
2020 bioRxiv   pre-print
Our model is torsion- and distance-aware, learns a high-resolution embedding of the dataset, and generates novel, high-quality structures compatible with existing design tools.  ...  problem in the latent space of a generative model.  ...  of General Medical Sciences of the National Institutes of Health under Award Number T32GM120007.  ... 
doi:10.1101/2020.08.07.242347 fatcat:kvxzk7jierfnlbxcwykci2ay2q

BCEPS: A Web Server to Predict Linear B Cell Epitopes with Enhanced Immunogenicity and Cross-Reactivity

Alvaro Ras-Carmona, Hector F. Pelaez-Prestel, Esther M. Lafuente, Pedro A. Reche
2021 Cells  
BCEPS implements various machine learning models trained on a dataset including 555 linearized conformational B cell epitopes that were mined from antibody–antigen protein structures.  ...  In an independent dataset consisting of B cell epitopes retrieved from the Immune Epitope Database (IEDB), this model achieved an accuracy of 67.05%.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/cells10102744 pmid:34685724 pmcid:PMC8534968 fatcat:xfkuhg2vsnakzaz2pzrlkoknlm

Augmenting adaptive immunity: progress and challenges in the quantitative engineering and analysis of adaptive immune receptor repertoires [article]

Alex J. Brown, Igor Snapkov, Rahmad Akbar, Milena Pavlović, Enkelejda Miho, Geir K. Sandve, Victor Greiff
2019 arXiv   pre-print
A long-standing dream of immunoengineers has been, therefore, to mechanistically understand how the immune system sees, reacts and remembers antigens.  ...  The adaptive immune system is a natural diagnostic and therapeutic. It recognizes threats earlier than clinical symptoms manifest and neutralizes antigen with exquisite specificity.  ...  Given a fasta file of antibody sequences (may be unpaired), SAAB maps the full sequences, frameworks, and CDRs to the high-quality antibody structures currently available in the Protein Data Bank (PDB)  ... 
arXiv:1904.04105v2 fatcat:4dxyjc2aevd5zeue2cjlhgkoju

Deep Learning in Protein Structural Modeling and Design

Wenhao Gao, Sai Pooja Mahajan, Jeremias Sulam, Jeffrey J. Gray
2020 Patterns  
of a protein, is critical to understand and engineer biological systems at the molecular level.  ...  We argue for the central importance of structure, following the "sequence → structure → function" paradigm.  ...  Protein Data Bank (PDB) 3D structural data of biomolecules, such as proteins and nucleic acids $160,000 Nucleic Acid Database (NDB) structure of nucleic acids and complex  ... 
doi:10.1016/j.patter.2020.100142 pmid:33336200 pmcid:PMC7733882 fatcat:qhjfidyusbfothv4kxdthodv6q

G-VAE, a Geometric Convolutional VAE for ProteinStructure Generation [article]

Hao Huang, Boulbaba Ben Amor, Xichan Lin, Fan Zhu, Yi Fang
2021 arXiv   pre-print
Analyzing the structure of proteins is a key part of understanding their functions and thus their role in biology at the molecular level.  ...  We test the effectiveness of our models by generating novel protein structures and predicting completions of corrupted protein structures.  ...  Their VAE is trained on AbDb, an antibody structure database [13] including 10,768 immunoglobulins spanning 4,154 non-sequence-redundant structures.  ... 
arXiv:2106.11920v1 fatcat:j3w4mnswavbwvgupoqux64agay

Protein design via deep learning

Wenze Ding, Kenta Nakai, Haipeng Gong
2022 Briefings in Bioinformatics  
Recent introduction of deep learning into design methods exhibits a transformative influence and is expected to represent a promising and exciting future direction.  ...  We not only describe deep learning developments in structure-based protein design and direct sequence design, but also highlight recent applications of deep reinforcement learning in protein design.  ...  of 100 amino acids substitution step of a simulated annealing trajectory [93] Generate coordinates of immunoglobulin Antibody structures from AbDb database VAE backbones [39] Generate protein sequence  ... 
doi:10.1093/bib/bbac102 pmid:35348602 pmcid:PMC9116377 fatcat:xicmholegnf3jbakjlb3p6hlca

Structural Determinants of DNA-binding Specificity for Hox Proteins

Peng Liu
Our work leads to a new understanding of the structural basis of specific DNA-binding for Drosophila Hox proteins, linking preference of DNA-binding sites to DNA minor groove shape.  ...  We have identified DNA minor groove shape as a structural determinant for Hox specificity.  ...  This is facilitated by a database of pre-compiled structures and an annotation map in MarkUs. Every protein-DNA structure in the database has its DNA-contacting residues characterized.  ... 
doi:10.7916/d8x0654j fatcat:ea57o27pknhpvicf7kzy27szgu
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