Anna M Herz, Maicol Bissaro, Carmen Esposito, Julien Michel
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Modular and Interoperable Workflows for Benchmarking Alchemical Binding Free Energy Calculation Methodologies.
Alchemical free energy methods are gaining traction in computer-aided drug discovery. An expanding array of methodologies is available for the setup, execution, and analysis of relative binding free energy (RBFE) calculations. However, the sharing of algorithms and protocols developed by different organizations is often impeded by incompatible software and outdated file formats. In this work, we leveraged the BioSimSpace framework to build modular and interoperable RBFE workflows. We assessed the performance of various setup, simulation, and analysis tools developed by the community on a benchmark set of six protein-ligand congeneric series, providing recommendations on best practices for the reliable application of RBFE methods in drug discovery.
期刊介绍：
The Journal of Chemical Information and Modeling publishes papers reporting new methodology and/or important applications in the fields of chemical informatics and molecular modeling. Specific topics include the representation and computer-based searching of chemical databases, molecular modeling, computer-aided molecular design of new materials, catalysts, or ligands, development of new computational methods or efficient algorithms for chemical software, and biopharmaceutical chemistry including analyses of biological activity and other issues related to drug discovery.
Astute chemists, computer scientists, and information specialists look to this monthly’s insightful research studies, programming innovations, and software reviews to keep current with advances in this integral, multidisciplinary field.
As a subscriber you’ll stay abreast of database search systems, use of graph theory in chemical problems, substructure search systems, pattern recognition and clustering, analysis of chemical and physical data, molecular modeling, graphics and natural language interfaces, bibliometric and citation analysis, and synthesis design and reactions databases.
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