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Improving the accuracy of the structure prediction of the third hypervariable loop of the heavy chains of antibodies

Mario Abdel Messih, Rosalba Lepore, Paolo Marcatili, Anna Tramontano
2014 Computer applications in the biosciences : CABIOS  
ACKNOWLEDGEMENTS The authors are grateful to all other members of the Biocomputing Unit for useful discussions.  ...  Antibodies are composed of two identical heavy and light chain pairs.  ...  Three of the loops belong to the variable domain of the light chain, (L1, L2 and L3) and three to the variable domain of the heavy chain (H1, H2 and H3).  ... 
doi:10.1093/bioinformatics/btu194 pmid:24930144 pmcid:PMC4173008 fatcat:6bm7ws2ytzhovm557cd4npx3ii

PIGSPro: prediction of immunoGlobulin structures v2

Rosalba Lepore, Pier P. Olimpieri, Mario A. Messih, Anna Tramontano
2017 Nucleic Acids Research  
; the selection of the main chain conformation of the hypervariable loops according to the canonical structure model, the prediction of the third loop of the heavy chain (H3) for which complete canonical  ...  structures are not available and the packing of the light and heavy chain if derived from different templates.  ...  ACKNOWLEDGEMENTS The authors are grateful to Alessandra Rosi and Paolo Marcatili who contributed to the first version of PIGS and to Anna Chailyan who collaborated to the analysis of the lambda chain canonical  ... 
doi:10.1093/nar/gkx334 pmid:28472367 pmcid:PMC5570210 fatcat:vwzvoefyf5cshpddavofwyhb5m

Antibody structure determination using a combination of homology modeling, energy-based refinement, and loop prediction

Kai Zhu, Tyler Day, Dora Warshaviak, Colleen Murrett, Richard Friesner, David Pearlman
2014 Proteins: Structure, Function, and Bioinformatics  
Our ab initio loop prediction performs well for the H3 loop in the crystal structure context, and allows improved results when refining the H3 loops in the context of homology models.  ...  The ab initio H3 loop predictions yield an average RMSD of 1.28 Å when performed in the context of the crystal structure and 2.67 Å in the context of the homology modeled structure.  ...  Acknowledgments The authors thank Woody Sherman for critical comments and help in the preparation of the manuscript.  ... 
doi:10.1002/prot.24551 pmid:24619874 pmcid:PMC5282925 fatcat:mra5um5hwvgdbnbcb5uexzekci

Conformational changes in antibody Fab fragments upon binding and their consequences on the performance of docking algorithms

Amélie Barozet, Marc Bianciotto, Thierry Siméon, Hervé Minoux, Juan Cortés
2018 Immunology Letters  
First, for a third of the antibodies in our dataset, at least one of the five loops cannot be assigned a canonical class.  ...  Conflict of interest The authors declare no conflict of interest. 18/20 These results confirm that canonical classes give remarkably good results for hypervariable loop structure prediction.  ...  Overall, hypervariable loops in the heavy chain were found to be more flexible than those in the light chain.  ... 
doi:10.1016/j.imlet.2018.06.002 pmid:29885326 fatcat:x5p5h22tnnajhgehd67fh2tztq

Antibodies as a model system for comparative model refinement

Benjamin D. Sellers, Jerome P. Nilmeier, Matthew P. Jacobson
2010 Proteins: Structure, Function, and Bioinformatics  
In this work, we use antibodies as a model system to investigate strategies for more robustly predicting loop conformations when the protein model contains errors in the conformations of side chains and  ...  The new method improves the average accuracy significantly to 1.3 Å RMSD and 3.1 Å RMSD for the shorter and longer loops, respectively.  ...  Our test set of antibody Fv models can be downloaded here:  ... 
doi:10.1002/prot.22757 pmid:20602354 pmcid:PMC2998178 fatcat:qmio32spkveevcv5t4xfq3izta

Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server

Pier Paolo Olimpieri, Anna Chailyan, Anna Tramontano, Paolo Marcatili
2013 Computer applications in the biosciences : CABIOS  
The method, based on the random forest automatic learning techniques, reaches a recall and specificity as high as 80% and is implemented as a free and easy-to-use server, named prediction of Antibody Contacts  ...  Results: In this article, we present a method to identify, on the basis of the antibody sequence alone, which residues of an antibody directly interact with its cognate antigen.  ...  ACKNOWLEDGEMENTS The authors are grateful to all other members of the Biocomputing Unit for useful discussions and for testing the server.  ... 
doi:10.1093/bioinformatics/btt369 pmid:23803466 pmcid:PMC3753563 fatcat:khbc2xgm4jc7zdiyldjr6hosju

Antibody structure prediction using interpretable deep learning [article]

Jeffrey A Ruffolo, Jeremias Sulam, Jeffrey J. Gray
2021 bioRxiv   pre-print
For example, in prediction of one CDR H3 residue conformation, the network attends to proximal aromatics and a key hydrogen bonding interaction that constrain the loop conformation.  ...  Finally, we present a novel mutant scoring metric derived from network confidence and show that for a particular antibody, all ten of the top-ranked mutations improve binding affinity.  ...  The structures predicted by DeepAb and alternative methods for benchmarking will be made available prior to publication.  ... 
doi:10.1101/2021.05.27.445982 fatcat:zxblrtj6zbf7dh5zj4kxju5czi

High-accuracy modeling of antibody structures by a search for minimum-energy recombination of backbone fragments

Christoffer H. Norn, Gideon Lapidoth, Sarel J. Fleishman
2016 Proteins: Structure, Function, and Bioinformatics  
Keywords combinatorial-backbone modeling; loop prediction; protein structure prediction; rosetta; AbDesign Antibodies are the main soluble component of the mammalian immune system.1 Most antibodies comprise  ...  two chains, light and heavy, each of which is generated by random recombination of variable (V) and junctional (J) genomic segments; the heavy chain is further diversified by recombination of diversity  ...  Acknowledgments The authors thank Liam Longo, Lior Zimmerman, and Adi Goldenzweig for testing AbPredict and Shira Warszawski for valuable discussions on antibody loop flexibility.  ... 
doi:10.1002/prot.25185 pmid:27717001 pmcid:PMC5432028 fatcat:bl4urotmwnca5bma2v6nttrxn4

Geometric Potentials from Deep Learning Improve Prediction of CDR H3 Loop Structures [article]

Jeffrey A. Ruffolo, Carlos Guerra, Sai Pooja Mahajan, Jeremias Sulam, Jeffrey J. Gray
2020 bioRxiv   pre-print
experimental CDR H3 loop structure) than the standard Rosetta energy function for 30, 13, and 6 targets, respectively, and improved the average RMSD of predictions by 21.3% (0.48 A).  ...  This work proposes DeepH3, a deep residual neural network that learns to predict inter-residue distances and orientations from antibody heavy and light chain sequence.  ...  However, the third CDR loop of the heavy chain (H3) is observed in a diverse set of conformations and remains a challenge to model [3] [4] [5] [6] [7] [8] [9] .  ... 
doi:10.1101/2020.02.09.940254 fatcat:ohbk4fpalnf77bljmytbpfxutq

Sequencing and modeling of anti-DNA immunoglobulin Fv domains. Comparison with crystal structures

M M Barry, C D Mol, W F Anderson, J S Lee
1994 Journal of Biological Chemistry  
Models for the third complementarity-determining region of the heavy chain were constructed from known immunoglobulin loops of similar length and sequence.  ...  Biol. 196, 901), model loops were selected from immunoglobulin domains of known structure for five of the six antibody hypervariable regions.  ...  Acknowledgments-The sequencing expertise of Brenda Haug and Jamshid Tanha is gratefully acknowledged.  ... 
pmid:8106407 fatcat:7tqz4lednbeknhlozgh5aujkom

Fine Tuning of the Specificity of an Anti-progesterone Antibody by First and Second Sphere Residue Engineering

Olivier Dubreuil, Marc Bossus, Marc Graille, Maëlle Bilous, Alexandra Savatier, Michel Jolivet, André Ménez, Enrico Stura, Frédéric Ducancel
2005 Journal of Biological Chemistry  
The improvements are partly linked to a change in the canonical class of the light chain third hypervariable loop.  ...  The specificity of anti-progesterone P15G12C12G11 antibody was improved by combination of in vitro scanning saturation mutagenesis and error-prone PCR.  ...  Genevieve Sibaï, Nicole Poirot-Battail, Yu-Ping, and Loïc Martin for contributions to the different aspects of this work.  ... 
doi:10.1074/jbc.m500048200 pmid:15878862 fatcat:p4j3rr3vobbepltrpya2ye2yru

How B-Cell Receptor Repertoire Sequencing Can Be Enriched with Structural Antibody Data

Aleksandr Kovaltsuk, Konrad Krawczyk, Jacob D. Galson, Dominic F. Kelly, Charlotte M. Deane, Johannes Trück
2017 Frontiers in Immunology  
Within each of the VL and VH chains lie three hypervariable loops, the complementarity determining regions (CDRs), which are the most Frontiers in Immunology |  ...  The variable region (Fv) is composed of two domains called the heavy (VH) and light (VL) chains.  ...  These improved predictions are only possible if a native structure or an accurate model of the antibody is available.  ... 
doi:10.3389/fimmu.2017.01753 pmid:29276518 pmcid:PMC5727015 fatcat:w5zqlbyvkvejbesfrybp23caem

Fully automated antibody structure prediction using BIOVIA tools: Validation study

Helen Kemmish, Marc Fasnacht, Lisa Yan, Andrew C. Gill
2017 PLoS ONE  
We describe the methodology and results from our validation study of the fully automated antibody structure prediction tool available in the BIOVIA (formerly Accelrys) protein modeling suite.  ...  Our analysis provides improved guidelines of best practices for using our protocol to build antibody structures.  ...  Acknowledgments The authors thank Kenneth Butenhof and Hughes-Olivier Bertrand for their critical comments and help in the preparation of the article.  ... 
doi:10.1371/journal.pone.0177923 pmid:28542300 pmcid:PMC5436848 fatcat:7tb46mniwjafvk7dtgh6qz3qra

Toward high-resolution homology modeling of antibody Fvregions and application to antibody-antigen docking

Arvind Sivasubramanian, Aroop Sircar, Sidhartha Chaudhury, Jeffrey J. Gray
2009 Proteins: Structure, Function, and Bioinformatics  
Initial Low rmsd NatRec Homology NatRec Homology Low score Low rmsd ACKNOWLEDGMENTS We thank Eric Kim for developing the antibody structure prediction server and David Masica for comments on the manuscript  ...  Protein structures were created using PyMOL, 76 plots were generated using the R statistical package 77 and rmsd was calculated using ProFit (Martin, A. C.  ...  The CDR loops of the native structure are blue, the non-H3 CDR loops of the homology model antibody are cyan, and the CDR H3 of the homology model antibody is red. future efforts to improve antibody structural  ... 
doi:10.1002/prot.22309 pmid:19062174 pmcid:PMC2909601 fatcat:rxgs2dch65cnvgh7txe3oohuqi

Modeling Antibody-Antigen Complexes by Information-Driven Docking

Francesco Ambrosetti, Brian Jiménez-García, Jorge Roel-Touris, Alexandre M.J.J. Bonvin
2019 Structure  
Understanding the structural basis of antibody-antigen interactions is therefore crucial for improving our ability to design efficient biological drugs.  ...  HADDOCK, which includes information to drive the docking, is shown to perform best in terms of both success rate and quality of the generated models in both the presence and absence of information about  ...  This work has been carried out with the financial support of the European Union Horizon  ... 
doi:10.1016/j.str.2019.10.011 pmid:31727476 fatcat:pmfkdu65rrasteycdwoey5nh3i
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