AIMC Topic: Proteins

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Structure-Based Prediction of lncRNA-Protein Interactions by Deep Learning.

Methods in molecular biology (Clifton, N.J.)
The interactions between long noncoding RNA (lncRNA) and protein play crucial roles in various biological processes. Computational methods are essential for predicting lncRNA-protein interactions and deciphering their mechanisms. In this chapter, we ...

SG-ML-PLAP: A structure-guided machine learning-based scoring function for protein-ligand binding affinity prediction.

Protein science : a publication of the Protein Society
Computational methods to predict binding affinity of protein-ligand complex have been used extensively to design inhibitors for proteins selected as drug targets. In recent years machine learning (ML) is being increasingly used for design of drugs/in...

Beyond AlphaFold2: The Impact of AI for the Further Improvement of Protein Structure Prediction.

Methods in molecular biology (Clifton, N.J.)
Protein structure prediction is fundamental to molecular biology and has numerous applications in areas such as drug discovery and protein engineering. Machine learning techniques have greatly advanced protein 3D modeling in recent years, particularl...

Machine Learning Techniques to Infer Protein Structure and Function from Sequences: A Comprehensive Review.

Methods in molecular biology (Clifton, N.J.)
The elucidation of protein structure and function plays a pivotal role in understanding biological processes and facilitating drug discovery. With the exponential growth of protein sequence data, machine learning techniques have emerged as powerful t...

DDGemb: predicting protein stability change upon single- and multi-point variations with embeddings and deep learning.

Bioinformatics (Oxford, England)
MOTIVATION: The knowledge of protein stability upon residue variation is an important step for functional protein design and for understanding how protein variants can promote disease onset. Computational methods are important to complement experimen...

Improving generalizability of drug-target binding prediction by pre-trained multi-view molecular representations.

Bioinformatics (Oxford, England)
MOTIVATION: Most drugs start on their journey inside the body by binding the right target proteins. This is the reason that numerous efforts have been devoted to predicting the drug-target binding during drug development. However, the inherent divers...

DPAM-AI: a domain parser for AlphaFold models powered by artificial intelligence.

Bioinformatics (Oxford, England)
MOTIVATION: Due to the breakthrough in protein structure prediction by AlphaFold, the scientific community has access to 200 million predicted protein structures with near-atomic accuracy from the AlphaFold protein structure DataBase (AFDB), covering...

TPepPro: a deep learning model for predicting peptide-protein interactions.

Bioinformatics (Oxford, England)
MOTIVATION: Peptides and their derivatives hold potential as therapeutic agents. The rising interest in developing peptide drugs is evidenced by increasing approval rates by the FDA of USA. To identify the most potential peptides, study on peptide-pr...

[AcidBasePred: a protein acid-base tolerance prediction platform based on deep learning].

Sheng wu gong cheng xue bao = Chinese journal of biotechnology
The structures and activities of enzymes are influenced by pH of the environment. Understanding and distinguishing the adaptation mechanisms of enzymes to extreme pH values is of great significance for elucidating the molecular mechanisms and promoti...

Improved prediction of post-translational modification crosstalk within proteins using DeepPCT.

Bioinformatics (Oxford, England)
MOTIVATION: Post-translational modification (PTM) crosstalk events play critical roles in biological processes. Several machine learning methods have been developed to identify PTM crosstalk within proteins, but the accuracy is still far from satisfa...