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 · These improvements, obtained without any calibration or novel methodologies, led to a notable level of performance in antibody-antigen unbound docking that was never achieved previously.
ABAG-docking benchmark: a non-redundant structure benchmark …
2024年1月22日 · Accurate prediction of antibody-antigen complex structures is pivotal in drug discovery, vaccine design and disease treatment and can facilitate the development of more effective therapies and diagnostics. In this work, we first review the antibody-antigen docking (ABAG-docking) datasets.
[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.
2024年11月6日 · We utilized AI-guided antibody modeling tools to generate ensembles displaying diversity in the complementarity-determining region (CDR) and integrated those into our previously published AlphaFold2-rescored docking pipeline, a strategy called AI-augmented physics-based docking.
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 and docking of antibody structures with Rosetta
2017年1月26日 · We describe Rosetta-based computational protocols for predicting the 3D structure of an antibody from sequence (RosettaAntibody) and then docking the antibody to protein antigens (SnugDock).
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.
Modeling Antibody-Antigen Complexes by Information-Driven Docking …
2020年1月7日 · Antibody-antigen docking was performed following three different scenarios in order to mimic different levels of information that can be obtained about the antibody and antigen residues involved in the binding.
An expanded benchmark for antibody-antigen docking and …
2021年6月3日 · An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants
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