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Protein Binding

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Applying deep learning to iterative screening of medium-sized molecules for protein-protein interaction-targeted drug discovery.

Chemical communications (Cambridge, England) May 30, 2023
We combined a library of medium-sized molecules with iterative screening using multiple machine learning algorithms that were ligand-based, which resulted in a large increase of the hit rate against a protein-protein interaction target. This was demo...
Drug Discovery Deep Learning Protein Binding NF-E2-Related Factor 2 Kelch-Like ECH-Associated Protein 1
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Identification of SH2 domain-containing proteins and motifs prediction by a deep learning method.

Computers in biology and medicine May 29, 2023
The Src Homology 2 (SH2) domain plays an important role in the signal transmission mechanism in organisms. It mediates the protein-protein interactions based on the combination between phosphotyrosine and motifs in SH2 domain. In this study, we desig...
Binding Sites Signal Transduction Phosphotyrosine Proteins Deep Learning src Homology Domains Protein Binding
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Targeting protein-protein interactions with low molecular weight and short peptide modulators: insights on disease pathways and starting points for drug discovery.

Expert opinion on drug discovery May 29, 2023
INTRODUCTION: Protein-protein interactions (PPIs) have been often considered undruggable targets although they are attractive for the discovery of new therapeutics. The spread of artificial intelligence and machine learning complemented with experime...
Protein Binding Proteins Humans Peptides Artificial Intelligence Molecular Weight Drug Discovery
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Machine learning-based drug design for identification of thymidylate kinase inhibitors as a potential anti-Mycobacterium tuberculosis.

Journal of biomolecular structure & dynamics May 26, 2023
The rise of antibiotic-resistant Mycobacterium tuberculosis (Mtb) has reduced the availability of medications for tuberculosis therapy, resulting in increased morbidity and mortality globally. Tuberculosis spreads from the lungs to other parts of the...
Molecular Docking Simulation Nucleoside-Phosphate Kinase Drug Design Antitubercular Agents Mycobacterium tuberculosis Protein Binding Machine Learning Humans Molecular Dynamics Simulation Protein Kinase Inhibitors Algorithms
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: A Web Server for Machine Learning-Based Prediction of Protein-Protein and Antibody-Protein Antigen Binding Affinities.

Journal of chemical information and modeling May 26, 2023
Protein-Protein binding affinity reflects the binding strength between the binding partners. The prediction of protein-protein binding affinity is important for elucidating protein functions and also for designing protein-based therapeutics. The geom...
Computers Protein Binding Machine Learning Amino Acids Proteins
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Machine learning and classical MD simulation to identify inhibitors against the P37 envelope protein of monkeypox virus.

Journal of biomolecular structure & dynamics May 23, 2023
Monkeypox virus (MPXV) outbreak is a serious public health concern that requires international attention. P37 of MPXV plays a pivotal role in DNA replication and acts as one of the promising targets for antiviral drug design. In this study, we intent...
Monkeypox virus Binding Sites Viral Envelope Proteins Antiviral Agents Protein Binding Hydrophobic and Hydrophilic Interactions Hydrogen Bonding Molecular Dynamics Simulation Machine Learning Molecular Docking Simulation
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Discovery of novel PARP-1 inhibitors using tandem studies: integrated docking, e-pharmacophore, deep learning based de novo and molecular dynamics simulation approach.

Journal of biomolecular structure & dynamics May 22, 2023
Cancer accounts for the majority of deaths worldwide, and the increasing incidence of breast cancer is a matter of grave concern. Poly (ADP-ribose) polymerase-1 (PARP-1) has emerged as an attractive target for the treatment of breast cancer as it has...
Ligands Poly (ADP-Ribose) Polymerase-1 Protein Binding Molecular Dynamics Simulation Poly(ADP-ribose) Polymerase Inhibitors Pharmacophore Artificial Intelligence Female Molecular Docking Simulation Deep Learning Breast Neoplasms Humans
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Predicting Protein-Peptide Interactions: Benchmarking Deep Learning Techniques and a Comparison with Focused Docking.

Journal of chemical information and modeling May 11, 2023
The accurate prediction of protein structures achieved by deep learning (DL) methods is a significant milestone and has deeply impacted structural biology. Shortly after its release, AlphaFold2 has been evaluated for predicting protein-peptide intera...
Molecular Docking Simulation Software Proteins Protein Binding Peptides Deep Learning Protein Conformation
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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...
Protein Binding Proteins Databases, Protein Machine Learning Molecular Docking Simulation Ligands
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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...
Protein Binding Proteins Protein Engineering Deep Learning
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