DeepPTM: Protein post-translational modification prediction from protein sequences by combining deep protein language model with vision transformers

Name: DeepPTM: Protein post-translational modification prediction from protein sequences by combining deep protein language model with vision transformers
Author: Sefer, Emre, Soylu, Necla Nisa

İsim	DeepPTM: Protein post-translational modification prediction from protein sequences by combining deep protein language model with vision transformers
Yazar	Sefer, Emre, Soylu, Necla Nisa
Basım Tarihi:	2024-02-01
Basım Yeri	- Bentham Science
Konu	Bioinformatics, Protein language model, Deep learning, Vision transformers, Post-translational modification, ProtBERT
Tür	Süreli Yayın
Dil	İngilizce
Dijital	Evet
Yazma	Hayır
Kütüphane:	Özyeğin Üniversitesi
Demirbaş Numarası	1574-8936
Kayıt Numarası	3e32eda5-0f6d-4ac6-a804-358baed58a1e
Lokasyon	Computer Science
Tarih	2024-02-01
Notlar	TÜBİTAK
Örnek Metin	Introduction More recent self-supervised deep language models, such as Bidirectional Encoder Representations from Transformers (BERT), have performed the best on some language tasks by contextualizing word embeddings for a better dynamic representation. Their protein-specific versions, such as ProtBERT, generated dynamic protein sequence embeddings, which resulted in better performance for several bioinformatics tasks. Besides, a number of different protein post-translational modifications are prominent in cellular tasks such as development and differentiation. The current biological experiments can detect these modifications, but within a longer duration and with a significant cost.Methods In this paper, to comprehend the accompanying biological processes concisely and more rapidly, we propose DEEPPTM to predict protein post-translational modification (PTM) sites from protein sequences more efficiently. Different than the current methods, DEEPPTM enhances the modification prediction performance by integrating specialized ProtBERT-based protein embeddings with attention-based vision transformers (ViT), and reveals the associations between different modification types and protein sequence content. Additionally, it can infer several different modifications over different species.Results Human and mouse ROC AUCs for predicting Succinylation modifications were 0.793 and 0.661 respectively, once 10-fold cross-validation is applied. Similarly, we have obtained 0.776, 0.764, and 0.734 ROC AUC scores on inferring ubiquitination, crotonylation, and glycation sites, respectively. According to detailed computational experiments, DEEPPTM lessens the time spent in laboratory experiments while outperforming the competing methods as well as baselines on inferring all 4 modification sites. In our case, attention-based deep learning methods such as vision transformers look more favorable to learning from ProtBERT features than more traditional deep learning and machine learning techniques.Conclusion Additionally, the protein-specific ProtBERT model is more effective than the original BERT embeddings for PTM prediction tasks. Our code and datasets can be found at https://github.com/seferlab/deepptm.
DOI	10.2174/0115748936283134240109054157
Cilt	19

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DeepPTM: Protein post-translational modification prediction from protein sequences by combining deep protein language model with vision transformers

Yazar Sefer, Emre, Soylu, Necla Nisa

Basım Tarihi 2024-02-01

Basım Yeri - Bentham Science

Konu Bioinformatics, Protein language model, Deep learning, Vision transformers, Post-translational modification, ProtBERT

Tür Süreli Yayın

Dil İngilizce

Dijital Evet

Yazma Hayır

Kütüphane Özyeğin Üniversitesi

Demirbaş Numarası 1574-8936

Kayıt Numarası 3e32eda5-0f6d-4ac6-a804-358baed58a1e

Lokasyon Computer Science

Tarih 2024-02-01

Notlar TÜBİTAK

Örnek Metin Introduction More recent self-supervised deep language models, such as Bidirectional Encoder Representations from Transformers (BERT), have performed the best on some language tasks by contextualizing word embeddings for a better dynamic representation. Their protein-specific versions, such as ProtBERT, generated dynamic protein sequence embeddings, which resulted in better performance for several bioinformatics tasks. Besides, a number of different protein post-translational modifications are prominent in cellular tasks such as development and differentiation. The current biological experiments can detect these modifications, but within a longer duration and with a significant cost.Methods In this paper, to comprehend the accompanying biological processes concisely and more rapidly, we propose DEEPPTM to predict protein post-translational modification (PTM) sites from protein sequences more efficiently. Different than the current methods, DEEPPTM enhances the modification prediction performance by integrating specialized ProtBERT-based protein embeddings with attention-based vision transformers (ViT), and reveals the associations between different modification types and protein sequence content. Additionally, it can infer several different modifications over different species.Results Human and mouse ROC AUCs for predicting Succinylation modifications were 0.793 and 0.661 respectively, once 10-fold cross-validation is applied. Similarly, we have obtained 0.776, 0.764, and 0.734 ROC AUC scores on inferring ubiquitination, crotonylation, and glycation sites, respectively. According to detailed computational experiments, DEEPPTM lessens the time spent in laboratory experiments while outperforming the competing methods as well as baselines on inferring all 4 modification sites. In our case, attention-based deep learning methods such as vision transformers look more favorable to learning from ProtBERT features than more traditional deep learning and machine learning techniques.Conclusion Additionally, the protein-specific ProtBERT model is more effective than the original BERT embeddings for PTM prediction tasks. Our code and datasets can be found at https://github.com/seferlab/deepptm.

DOI 10.2174/0115748936283134240109054157

Cilt 19