Cuturello F, Celoria M, Ansuini A, Cazzaniga A. Enhancing predictions of protein stability changes induced by single mutations using MSA-based Language Models.
Bioinformatics 2024;
40:btae447. [PMID:
39012369 PMCID:
PMC11269464 DOI:
10.1093/bioinformatics/btae447]
[Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/19/2024] [Accepted: 07/10/2024] [Indexed: 07/17/2024] Open
Abstract
MOTIVATION
Protein Language Models offer a new perspective for addressing challenges in structural biology, while relying solely on sequence information. Recent studies have investigated their effectiveness in forecasting shifts in thermodynamic stability caused by single amino acid mutations, a task known for its complexity due to the sparse availability of data, constrained by experimental limitations. To tackle this problem, we introduce two key novelties: leveraging a Protein Language Model that incorporates Multiple Sequence Alignments to capture evolutionary information, and using a recently released mega-scale dataset with rigorous data pre-processing to mitigate overfitting.
RESULTS
We ensure comprehensive comparisons by fine-tuning various pre-trained models, taking advantage of analyses such as ablation studies and baselines evaluation. Our methodology introduces a stringent policy to reduce the widespread issue of data leakage, rigorously removing sequences from the training set when they exhibit significant similarity with the test set. The MSA Transformer emerges as the most accurate among the models under investigation, given its capability to leverage co-evolution signals encoded in aligned homologous sequences. Moreover, the optimized MSA Transformer outperforms existing methods and exhibits enhanced generalization power, leading to a notable improvement in predicting changes in protein stability resulting from point mutations.
AVAILABILITY AND IMPLEMENTATION
Code and data at https://github.com/RitAreaSciencePark/PLM4Muts.
SUPPLEMENTARY INFORMATION
Supplementary Information is available at Bioinformatics online.
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