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Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15

To enhance the AlphaFold-Multimer-based protein complex structure prediction, we developed a quaternary structure prediction system (MULTICOM) to improve the input fed to AlphaFold-Multimer and evaluate and refine its outputs. MULTICOM samples diverse multiple sequence alignments (MSAs) and template...

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Autores principales: Liu, Jian, Guo, Zhiye, Wu, Tianqi, Roy, Raj S., Quadir, Farhan, Chen, Chen, Cheng, Jianlin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10638423/
https://www.ncbi.nlm.nih.gov/pubmed/37949999
http://dx.doi.org/10.1038/s42003-023-05525-3
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author Liu, Jian
Guo, Zhiye
Wu, Tianqi
Roy, Raj S.
Quadir, Farhan
Chen, Chen
Cheng, Jianlin
author_facet Liu, Jian
Guo, Zhiye
Wu, Tianqi
Roy, Raj S.
Quadir, Farhan
Chen, Chen
Cheng, Jianlin
author_sort Liu, Jian
collection PubMed
description To enhance the AlphaFold-Multimer-based protein complex structure prediction, we developed a quaternary structure prediction system (MULTICOM) to improve the input fed to AlphaFold-Multimer and evaluate and refine its outputs. MULTICOM samples diverse multiple sequence alignments (MSAs) and templates for AlphaFold-Multimer to generate structural predictions by using both traditional sequence alignments and Foldseek-based structure alignments, ranks structural predictions through multiple complementary metrics, and refines the structural predictions via a Foldseek structure alignment-based refinement method. The MULTICOM system with different implementations was blindly tested in the assembly structure prediction in the 15(th) Critical Assessment of Techniques for Protein Structure Prediction (CASP15) in 2022 as both server and human predictors. MULTICOM_qa ranked 3(rd) among 26 CASP15 server predictors and MULTICOM_human ranked 7(th) among 87 CASP15 server and human predictors. The average TM-score of the first predictions submitted by MULTICOM_qa for CASP15 assembly targets is ~0.76, 5.3% higher than ~0.72 of the standard AlphaFold-Multimer. The average TM-score of the best of top 5 predictions submitted by MULTICOM_qa is ~0.80, about 8% higher than ~0.74 of the standard AlphaFold-Multimer. Moreover, the Foldseek Structure Alignment-based Multimer structure Generation (FSAMG) method outperforms the widely used sequence alignment-based multimer structure generation.
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spelling pubmed-106384232023-11-11 Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15 Liu, Jian Guo, Zhiye Wu, Tianqi Roy, Raj S. Quadir, Farhan Chen, Chen Cheng, Jianlin Commun Biol Article To enhance the AlphaFold-Multimer-based protein complex structure prediction, we developed a quaternary structure prediction system (MULTICOM) to improve the input fed to AlphaFold-Multimer and evaluate and refine its outputs. MULTICOM samples diverse multiple sequence alignments (MSAs) and templates for AlphaFold-Multimer to generate structural predictions by using both traditional sequence alignments and Foldseek-based structure alignments, ranks structural predictions through multiple complementary metrics, and refines the structural predictions via a Foldseek structure alignment-based refinement method. The MULTICOM system with different implementations was blindly tested in the assembly structure prediction in the 15(th) Critical Assessment of Techniques for Protein Structure Prediction (CASP15) in 2022 as both server and human predictors. MULTICOM_qa ranked 3(rd) among 26 CASP15 server predictors and MULTICOM_human ranked 7(th) among 87 CASP15 server and human predictors. The average TM-score of the first predictions submitted by MULTICOM_qa for CASP15 assembly targets is ~0.76, 5.3% higher than ~0.72 of the standard AlphaFold-Multimer. The average TM-score of the best of top 5 predictions submitted by MULTICOM_qa is ~0.80, about 8% higher than ~0.74 of the standard AlphaFold-Multimer. Moreover, the Foldseek Structure Alignment-based Multimer structure Generation (FSAMG) method outperforms the widely used sequence alignment-based multimer structure generation. Nature Publishing Group UK 2023-11-10 /pmc/articles/PMC10638423/ /pubmed/37949999 http://dx.doi.org/10.1038/s42003-023-05525-3 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Liu, Jian
Guo, Zhiye
Wu, Tianqi
Roy, Raj S.
Quadir, Farhan
Chen, Chen
Cheng, Jianlin
Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15
title Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15
title_full Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15
title_fullStr Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15
title_full_unstemmed Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15
title_short Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15
title_sort enhancing alphafold-multimer-based protein complex structure prediction with multicom in casp15
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10638423/
https://www.ncbi.nlm.nih.gov/pubmed/37949999
http://dx.doi.org/10.1038/s42003-023-05525-3
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