AIMC Topic: Models, Molecular

Clear Filters Showing 611 to 620 of 759 articles

AlphaFold modeling uncovers global structural features of class I and class II fungal hydrophobins.

Protein science : a publication of the Protein Society Sep 1, 2025
Hydrophobins are a family of small fungal proteins that self-assemble at hydrophobic-hydrophilic interfaces. Hydrophobins not only play crucial roles in filamentous fungal growth and development but also have attracted substantial attention due to th...
Databases, Protein Computational Biology Models, Molecular Protein Conformation Protein Folding Hydrophobic and Hydrophilic Interactions Fungal Proteins
View on PubMed DOI

Unambiguous assignment of kinked-β sheets leads to insights into molecular grammar of reversibility in biomolecular condensates.

Protein science : a publication of the Protein Society Sep 1, 2025
Kinked- sheets are short peptide motifs that appear as distortions in strands and often mediate formation of reversible amyloid fibrils in prion-like proteins. Standard methods for assigning secondary structures cannot distinguish these esoteric mo...
Amyloid Machine Learning Models, Molecular Protein Conformation, beta-Strand Biomolecular Condensates
View on PubMed DOI

BindUP-Alpha: A Webserver for Predicting DNA-and RNA-binding Proteins based on Experimental and Computational Structural Models☆.

Journal of molecular biology Sep 1, 2025
Structural data provides important information on the proteins' function. Recent development of advanced machine learning and artificial intelligence tools, such as AlphaFold, have led to an explosion of predicted protein structures. However, many of...
Models, Molecular Software Internet Algorithms Protein Conformation DNA-Binding Proteins RNA-Binding Proteins Support Vector Machine Protein Binding Computational Biology
View on PubMed DOI

Generating a vast chemical space for high polar surface area triphenylamine polymers by machine learning-DFT calculations assisted reverse engineering for photovoltaics.

Journal of molecular graphics & modelling Sep 1, 2025
The total polar surface area (TPSA) is a crucial parameter in photovoltaic (PV) materials, as it directly influences their solubility, processability, and device performance. This study leverages machine learning-assisted reverse engineering to gener...
Density Functional Theory Polymers Machine Learning Models, Molecular Aniline Compounds Solar Energy Algorithms
View on PubMed DOI

DSSP 4: FAIR annotation of protein secondary structure.

Protein science : a publication of the Protein Society Aug 1, 2025
Protein secondary structure annotation is essential for understanding protein architecture, serving as a cornerstone for structural classification, alignment, visualization, and machine learning applications. The Define Secondary Structure of Protein...
Proteins Databases, Protein Molecular Sequence Annotation Protein Structure, Secondary Models, Molecular Software Algorithms
View on PubMed DOI

Artificial intelligence and first-principle methods in protein redesign: A marriage of convenience?

Protein science : a publication of the Protein Society Aug 1, 2025
Since AlphaFold2's rise, many deep learning methods for protein design have emerged. Here, we validate widely used and recognized tools, compare them with first-principle methods, and explore their combinations, focusing on their effectiveness in pro...
Proteins Databases, Protein Artificial Intelligence Deep Learning Protein Engineering Protein Folding Models, Molecular Protein Conformation
View on PubMed DOI

HAIRpred: Prediction of human antibody interacting residues in an antigen from its primary structure.

Protein science : a publication of the Protein Society Aug 1, 2025
In the past, several methods have been developed for predicting conformational B-cell epitopes in antigens that are not specific to any host. Our primary analysis of antibody-antigen complexes indicated a need to develop host-specific B-cell epitopes...
Humans Antigen-Antibody Complex Machine Learning Epitopes, B-Lymphocyte Models, Molecular Antigens Software
View on PubMed DOI

Harnessing computational technologies to facilitate antibody-drug conjugate development.

Nature chemical biology Aug 1, 2025
Antibody-drug conjugates (ADCs) represent a powerful therapeutic approach for the treatment of a range of cancers. They merge the toxicity of known chemical agents with the specificity of monoclonal antibodies, thereby maximizing efficacy while minim...
Humans Models, Molecular Immunoconjugates Machine Learning Drug Development Drug Design Antibodies, Monoclonal
View on PubMed DOI

Discovery of novel potential 11β-HSD1 inhibitors through combining deep learning, molecular modeling, and bio-evaluation.

Molecular diversity Aug 1, 2025
11β-Hydroxysteroid dehydrogenase type 1 (11β-HSD1) has been shown to play an important role in the treatment of impaired glucose tolerance, insulin resistance, dyslipidemia, and obesity and is a promising drug target. In this study, we built a gated ...
Deep Learning Models, Molecular Molecular Docking Simulation Humans Drug Discovery 11-beta-Hydroxysteroid Dehydrogenase Type 1 Molecular Dynamics Simulation Enzyme Inhibitors
View on PubMed DOI

Relationship between immunogenicity and protein structure at amino acid substitution sites of blood group antigens.

Blood Jul 24, 2025
Polypeptide blood group antigens, many of which are created by single exofacial amino acid substitutions, have varying immunogenicities. Why some amino acid substitutions are more immunogenic than others is little understood. Using AlphaFold2, an art...
Amino Acid Substitution Blood Group Antigens Models, Molecular Humans Protein Conformation
View on PubMed DOI
Popular Topics
Recent Journals