AI Medical Compendium Journal:
Protein science : a publication of the Protein Society

Showing 11 to 20 of 35 articles

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 Jan 1, 2025
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...
Software Molecular Docking Simulation Machine Learning Databases, Protein Ligands Protein Binding Proteins
View on PubMed DOI

ThermoLink: Bridging disulfide bonds and enzyme thermostability through database construction and machine learning prediction.

Protein science : a publication of the Protein Society Sep 1, 2024
Disulfide bonds, covalently formed by sulfur atoms in cysteine residues, play a crucial role in protein folding and structure stability. Considering their significance, artificial disulfide bonds are often introduced to enhance protein thermostabilit...
Protein Folding Databases, Protein Models, Molecular Enzyme Stability Disulfides Machine Learning
View on PubMed DOI

De novo synthetic antimicrobial peptide design with a recurrent neural network.

Protein science : a publication of the Protein Society Aug 1, 2024
Antibiotic resistance is recognized as an imminent and growing global health threat. New antimicrobial drugs are urgently needed due to the decreasing effectiveness of conventional small-molecule antibiotics. Antimicrobial peptides (AMPs), a class of...
Antimicrobial Peptides Escherichia coli Staphylococcus aureus Neural Networks, Computer Anti-Bacterial Agents Drug Design Microbial Sensitivity Tests
View on PubMed DOI

EFG-CS: Predicting chemical shifts from amino acid sequences with protein structure prediction using machine learning and deep learning models.

Protein science : a publication of the Protein Society Aug 1, 2024
Nuclear magnetic resonance (NMR) crystallography is one of the main methods in structural biology for analyzing protein stereochemistry and structure. The chemical shift of the resonance frequency reflects the effect of the protons in a molecule prod...
Machine Learning Proteins Models, Molecular Software Deep Learning Nuclear Magnetic Resonance, Biomolecular Amino Acid Sequence Protein Conformation
View on PubMed DOI

Structure-aware deep learning model for peptide toxicity prediction.

Protein science : a publication of the Protein Society Jul 1, 2024
Antimicrobial resistance is a critical public health concern, necessitating the exploration of alternative treatments. While antimicrobial peptides (AMPs) show promise, assessing their toxicity using traditional wet lab methods is both time-consuming...
Antimicrobial Peptides Deep Learning Neural Networks, Computer Hemolysis
View on PubMed DOI

Knot or not? Identifying unknotted proteins in knotted families with sequence-based Machine Learning model.

Protein science : a publication of the Protein Society Jul 1, 2024
Knotted proteins, although scarce, are crucial structural components of certain protein families, and their roles continue to be a topic of intense research. Capitalizing on the vast collection of protein structure predictions offered by AlphaFold (A...
Amino Acid Sequence Protein Conformation Models, Molecular Machine Learning Proteins Databases, Protein
View on PubMed DOI

ProkDBP: Toward more precise identification of prokaryotic DNA binding proteins.

Protein science : a publication of the Protein Society Jun 1, 2024
Prokaryotic DNA binding proteins (DBPs) play pivotal roles in governing gene regulation, DNA replication, and various cellular functions. Accurate computational models for predicting prokaryotic DBPs hold immense promise in accelerating the discovery...
DNA-Binding Proteins Computational Biology Bacterial Proteins Machine Learning Algorithms
View on PubMed DOI

An ensemble machine learning model generates a focused screening library for the identification of CDK8 inhibitors.

Protein science : a publication of the Protein Society Jun 1, 2024
The identification of an effective inhibitor is an important starting step in drug development. Unfortunately, many issues such as the characterization of protein binding sites, the screening library, materials for assays, etc., make drug screening a...
Cyclin-Dependent Kinase 8 Small Molecule Libraries Humans Drug Evaluation, Preclinical Machine Learning Protein Kinase Inhibitors Molecular Docking Simulation
View on PubMed DOI

Int&in: A machine learning-based web server for active split site identification in inteins.

Protein science : a publication of the Protein Society Jun 1, 2024
Inteins are proteins that excise themselves out of host proteins and ligate the flanking polypeptides in an auto-catalytic process called protein splicing. In nature, inteins are either contiguous or split. In the case of split inteins, the two fragm...
Software Internet Catalytic Domain Inteins Machine Learning Protein Splicing
View on PubMed DOI

KCD: A prediction web server of knowledge-based circular dichroism.

Protein science : a publication of the Protein Society Apr 1, 2024
We present a web server that predicts the far-UV circular dichroism (CD) spectra of proteins by utilizing their three-dimensional (3D) structures from the Protein Data Bank (PDB). The main algorithm is based on the classical theory of optical activit...
Amino Acids Circular Dichroism Algorithms Artificial Intelligence Proteins
View on PubMed DOI
Popular Topics
Popular Journals