The LightDock Server: Artificial Intelligence-powered modeling of macromolecular interactions.

Brian Jiménez-García; Jorge Roel-Touris; Didier Barradas Bautista

doi:10.1093/nar/gkad327

The LightDock Server: Artificial Intelligence-powered modeling of macromolecular interactions.

Brian Jiménez-García, Jorge Roel-Touris, Didier Barradas Bautista

Research output: Contribution to journal › Article › peer-review

8 Scopus citations

Abstract

Computational docking is an instrumental method of the structural biology toolbox. Specifically, integrative modeling software, such as LightDock, arise as complementary and synergetic methods to experimental structural biology techniques. Ubiquitousness and accessibility are fundamental features to promote ease of use and to improve user experience. With this goal in mind, we have developed the LightDock Server, a web server for the integrative modeling of macromolecular interactions, along with several dedicated usage modes. The server builds upon the LightDock macromolecular docking framework, which has proved useful for modeling medium-to-high flexible complexes, antibody-antigen interactions, or membrane-associated protein assemblies.

Original language	English (US)
Journal	Nucleic acids research
DOIs	https://doi.org/10.1093/nar/gkad327
State	Published - May 4 2023

Bibliographical note

KAUST Repository Item: Exported on 2023-05-08
Acknowledgements: J.R.T. acknowledges funding from the European Molecular Biology Organization (EMBO) [ALTF 145-2021]; B.J.G. is employed by Zymvol Biomodeling by a project which received funding from the European Union's Horizon 2020 research and innovation programme under Marie Skłodowska-Curie [801342] (Tecniospring INDUSTRY); Government of Catalonia's Agency for Business Competitiveness (ACCIÓ); D.B.B. was supported by funding from the AI Initiative at KAUST. Funding for open access charge: European Union's Horizon 2020 research and innovation programme under Marie Skłodowska-Curie [801342] (Tecniospring INDUSTRY); Government of Catalonia's Agency for Business Competitiveness (ACCIÓ). The authors would like to thank all users from more than 50 countries who participated in the open beta version of the server providing valuable feedback. D.B.B. thanks the Supercomputing Laboratory at KAUST for technical support and access to the HPC facilities. Our warmest thanks are extended to Dr. Maria Fatima Lucas for helping in revising the content of this manuscript.

ASJC Scopus subject areas

Genetics

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10.1093/nar/gkad327

https://repository.kaust.edu.sa/bitstream/10754/691541/1/gkad327.pdf

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title = "The LightDock Server: Artificial Intelligence-powered modeling of macromolecular interactions.",

abstract = "Computational docking is an instrumental method of the structural biology toolbox. Specifically, integrative modeling software, such as LightDock, arise as complementary and synergetic methods to experimental structural biology techniques. Ubiquitousness and accessibility are fundamental features to promote ease of use and to improve user experience. With this goal in mind, we have developed the LightDock Server, a web server for the integrative modeling of macromolecular interactions, along with several dedicated usage modes. The server builds upon the LightDock macromolecular docking framework, which has proved useful for modeling medium-to-high flexible complexes, antibody-antigen interactions, or membrane-associated protein assemblies.",

author = "Brian Jim{\'e}nez-Garc{\'i}a and Jorge Roel-Touris and {Barradas Bautista}, Didier",

note = "KAUST Repository Item: Exported on 2023-05-08 Acknowledgements: J.R.T. acknowledges funding from the European Molecular Biology Organization (EMBO) [ALTF 145-2021]; B.J.G. is employed by Zymvol Biomodeling by a project which received funding from the European Union's Horizon 2020 research and innovation programme under Marie Sk{\l}odowska-Curie [801342] (Tecniospring INDUSTRY); Government of Catalonia's Agency for Business Competitiveness (ACCI{\'O}); D.B.B. was supported by funding from the AI Initiative at KAUST. Funding for open access charge: European Union's Horizon 2020 research and innovation programme under Marie Sk{\l}odowska-Curie [801342] (Tecniospring INDUSTRY); Government of Catalonia's Agency for Business Competitiveness (ACCI{\'O}). The authors would like to thank all users from more than 50 countries who participated in the open beta version of the server providing valuable feedback. D.B.B. thanks the Supercomputing Laboratory at KAUST for technical support and access to the HPC facilities. Our warmest thanks are extended to Dr. Maria Fatima Lucas for helping in revising the content of this manuscript.",

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The LightDock Server: Artificial Intelligence-powered modeling of macromolecular interactions.

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