HADDOCK2.4 Antibody - Antigen tutorial using PDB-tools webserver
This tutorial demonstrates the use of HADDOCK2.4 for predicting the structure of an antibody-antigen complex. It also includes our newly developed PDB-tools and ProABC-2 webservers. We will be following the protocol described in Ambrosetti, et al ArXiv, 2020 .
Enhanced antibody-antigen structure prediction from molecular docking …
2023年9月13日 · Antibody-antigen docking simulations were performed with the ProPOSE 4, ZDOCK 2 and PIPER 3 methods using as input the protein structures in their bound-backbone and unbound-backbone...
Fast, accurate antibody structure prediction from deep learning …
2023年4月25日 · In the meantime, IgFold will provide immediate benefits to existing antibody-antigen docking methods. For traditional docking methods, the improvements to speed and accuracy by IgFold should be...
[2207.06616] Antibody-Antigen Docking and Design via …
2022年7月14日 · In this paper, we propose a new model called Hierarchical Equivariant Refinement Network (HERN) for paratope docking and design. During docking, HERN employs a hierarchical message passing network to predict atomic forces and use them to refine a binding complex in an iterative, equivariant manner.
The ClusPro AbEMap web server for the prediction of antibody …
2023年5月15日 · ClusPro, a leading protein–protein docking server, together with its template-based modeling version, ClusPro-TBM, have been re-purposed to map epitopes for specific antibody–antigen ...
Modeling Immunity with Rosetta: Methods for Antibody and Antigen …
2021年3月11日 · Structure-based antibody and antigen design has advanced greatly in recent years, due not only to the increasing availability of experimentally determined structures but also to improved computational methods for both prediction and design.
An expanded benchmark for antibody-antigen docking and …
2021年6月3日 · Initial assessments of docking and affinity prediction tools highlight the challenges posed by this diverse set of cases, which includes camelid nanobodies, therapeutic monoclonal antibodies, and broadly neutralizing antibodies targeting viral glycoproteins.
An expanded benchmark for antibody-antigen docking and …
Computational antibody-antigen docking and design are major challenges. •. Major benchmark expansion, total of 67 non-redundant docking cases, 51 affinities. •. Camelid, therapeutic, and broadly neutralizing antiviral antibodies. •. Enables docking and design algorithm developments, insights into interface features. Summary.
An expanded benchmark for antibody-antigen docking and …
2021年6月3日 · Through a systematic search for high-resolution structures of antibody-antigen complexes and unbound antibody and antigen structures, in conjunction with identification of experimentally determined binding affinities, we have assembled a non-redundant set of test cases for antibody-antigen docking and affinity prediction.
Fast and accurate modeling and design of antibody-antigen
2024年2月8日 · Combined with specially designed modules such as the AI-driven flexible docking module, it achieves superior performance and significantly enhanced speed in predicting both antibody (1.6% RMSD reduction in the CDR-H3 region, thousand times faster) and antibody-antigen complex structures (37% increase in DockQ score, over 10 times faster), compar...