AIMC Topic: Protein Binding

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A Small Step Toward Generalizability: Training a Machine Learning Scoring Function for Structure-Based Virtual Screening.

Journal of chemical information and modeling May 11, 2023
Over the past few years, many machine learning-based scoring functions for predicting the binding of small molecules to proteins have been developed. Their objective is to approximate the distribution which takes two molecules as input and outputs th...
Databases, Protein Ligands Protein Binding Proteins Machine Learning Molecular Docking Simulation
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Improving de novo protein binder design with deep learning.

Nature communications May 6, 2023
Recently it has become possible to de novo design high affinity protein binding proteins from target structural information alone. There is, however, considerable room for improvement as the overall design success rate is low. Here, we explore the au...
Proteins Protein Engineering Deep Learning Protein Binding
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De novo design of protein interactions with learned surface fingerprints.

Nature Apr 26, 2023
Physical interactions between proteins are essential for most biological processes governing life. However, the molecular determinants of such interactions have been challenging to understand, even as genomic, proteomic and structural data increase. ...
Humans Computer Simulation Proteins Synthetic Biology Binding Sites Protein Binding Proteomics Deep Learning Protein Interaction Maps
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Targeting Protein-Protein Interfaces with Peptides: The Contribution of Chemical Combinatorial Peptide Library Approaches.

International journal of molecular sciences Apr 25, 2023
Protein-protein interfaces play fundamental roles in the molecular mechanisms underlying pathophysiological pathways and are important targets for the design of compounds of therapeutic interest. However, the identification of binding sites on protei...
Membrane Proteins Binding Sites Protein Binding Peptide Library Peptides Artificial Intelligence
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Modulation of DNA-protein Interactions by Proximal Genetic Elements as Uncovered by Interpretable Deep Learning.

Journal of molecular biology Apr 24, 2023
Transcription factors (TF) recognize specific motifs in the genome that are typically 6-12 bp long to regulate various aspects of the cellular machinery. Presence of binding motifs and favorable genome accessibility are key drivers for a consistent T...
Deep Learning Binding Sites Transcription Factors DNA Protein Binding
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PeSTo: parameter-free geometric deep learning for accurate prediction of protein binding interfaces.

Nature communications Apr 18, 2023
Proteins are essential molecular building blocks of life, responsible for most biological functions as a result of their specific molecular interactions. However, predicting their  binding  interfaces remains a challenge. In this study, we present a ...
Deep Learning Protein Binding Computational Biology Proteins Molecular Dynamics Simulation
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Artificial intelligence assisted identification of potential tau aggregation inhibitors: ligand- and structure-based virtual screening, in silico ADME, and molecular dynamics study.

Molecular diversity Apr 6, 2023
Alzheimer's disease (AD) is a severe, growing, multifactorial disorder affecting millions of people worldwide characterized by cognitive decline and neurodegeneration. The accumulation of tau protein into paired helical filaments is one of the major ...
tau Proteins Protein Aggregates Alzheimer Disease Ligands Molecular Dynamics Simulation Drug Evaluation, Preclinical Computer Simulation Molecular Docking Simulation Drug Discovery Protein Binding Humans Artificial Intelligence
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Self-Attention Based Neural Network for Predicting RNA-Protein Binding Sites.

IEEE/ACM transactions on computational biology and bioinformatics Apr 3, 2023
Proteins binding to Ribonucleic Acid (RNA) inside cells are called RNA-binding proteins (RBP), which play a crucial role in gene regulation. The identification of RNA-protein binding sites helps to understand the function of RBP better. Although many...
Neural Networks, Computer Binding Sites Protein Binding RNA
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HAC-Net: A Hybrid Attention-Based Convolutional Neural Network for Highly Accurate Protein-Ligand Binding Affinity Prediction.

Journal of chemical information and modeling Mar 29, 2023
Applying deep learning concepts from image detection and graph theory has greatly advanced protein-ligand binding affinity prediction, a challenge with enormous ramifications for both drug discovery and protein engineering. We build upon these advanc...
Proteins Ligands Software Protein Binding Neural Networks, Computer
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HeadTailTransfer: An efficient sampling method to improve the performance of graph neural network method in predicting sparse ncRNA-protein interactions.

Computers in biology and medicine Mar 15, 2023
Noncoding RNA (ncRNA) is a functional RNA derived from DNA transcription, and most transcribed genes are transcribed into ncRNA. ncRNA is not directly involved in the translation of proteins, but it can participate in gene expression in cells and aff...
RNA, Untranslated Protein Binding Proteins Neural Networks, Computer Machine Learning
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