Related papers: Predicting non-neutral missense mutations and thei…

Figuring out small molecule binding sites in target proteins, in the resolution of either pocket or residue, is critical in many virtual and real drug-discovery scenarios. Since it is not always easy to find such binding sites based on…

Various machine-learning models, including deep neural network models, have already been developed to predict deleteriousness of missense (non-synonymous) mutations. Potential improvements to the current state of the art, however, may still…

Amino-acid substitutions are implicated in a wide range of human diseases, many of which are lethal. Distinguishing such mutations from polymorphisms without significant effect on human health is a necessary step in understanding the…

Understanding how protein mutations affect protein-nucleic acid binding is critical for unraveling disease mechanisms and advancing therapies. Current experimental approaches are laborious, and computational methods remain limited in…

Elucidating the functional effect of missense variants is of crucial importance, yet challenging. To understand the impact of such variants, we fine-tuned the ESM2 protein language model to classify 20 protein features at amino acid…

A mutation in a protein-coding gene in DNA can alter the protein structure coded by the same gene. Structurally altered proteins usually lose their functions and sometimes gain an undesirable function instead. These types of mutations and…

Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of…

Motivation: Site directed mutagenesis is widely used to understand the structure and function of biomolecules. Computational prediction of protein mutation impacts offers a fast, economical and potentially accurate alternative to laboratory…

When nanoparticles (NPs) are introduced into a biological solution, layers of biomolecules form on their surface, creating a corona. Understanding how the structure of the protein evolves into the corona is essential for evaluating the…

Protein-protein bindings play a key role in a variety of fundamental biological processes, and thus predicting the effects of amino acid mutations on protein-protein binding is crucial. To tackle the scarcity of annotated mutation data,…

Deep learning has been widely used for protein engineering. However, it is limited by the lack of sufficient experimental data to train an accurate model for predicting the functional fitness of high-order mutants. Here, we develop SESNet,…

It is increasingly common clinically for cancer specimens to be examined using techniques that identify somatic mutations. In principle these mutational profiles can be used to diagnose the tissue of origin, a critical task for the 3-5% of…

The innovation of next-generation sequencing (NGS) techniques has significantly reduced the price of genome sequencing, lowering barriers to future medical research; it is now feasible to apply genome sequencing to studies where it would…

Many applications of machine learning methods involve an iterative protocol in which data are collected, a model is trained, and then outputs of that model are used to choose what data to consider next. For example, one data-driven approach…

The noval method for mutational disease prediction using bioinformatics tools and datasets for diagnosis the malignant mutations with powerful Artificial Neural Network (Backpropagation Network) for classifying these malignant mutations are…

Accurately determining a change in protein binding affinity upon mutations is important for the discovery and design of novel therapeutics and to assist mutagenesis studies. Determination of change in binding affinity upon mutations…

Post-translational modifications (PTMs) have vital roles in extending the functional diversity of proteins and as a result, regulating diverse cellular processes in prokaryotic and eukaryotic organisms. Phosphorylation modification is a…

In cancer therapeutics, protein-metal binding mechanisms critically govern the pharmacokinetics and targeting efficacy of drugs, thereby fundamentally shaping the rational design of anticancer metallodrugs. While conventional laboratory…

Multiple sequence alignment (MSA) data play a crucial role in the study of protein mutations, with contact prediction being a notable application. Existing methods are often model-based or algorithmic and typically do not incorporate…

Protein-ligand binding prediction is a fundamental problem in AI-driven drug discovery. Prior work focused on supervised learning methods using a large set of binding affinity data for small molecules, but it is hard to apply the same…