AIMC Topic: Models, Molecular

Clear Filters Showing 111 to 120 of 657 articles

Classifying and Predicting the Thermal Expansion Properties of Metal-Organic Frameworks: A Data-Driven Approach.

Journal of chemical information and modeling Jun 26, 2024
Metal-organic frameworks (MOFs) are versatile materials for a wide variety of potential applications. Tunable thermal expansion properties promote the application of MOFs in thermally sensitive composite materials; however, they are currently availab...
Models, Molecular Machine Learning Temperature Metal-Organic Frameworks
View on PubMed DOI

TransfIGN: A Structure-Based Deep Learning Method for Modeling the Interaction between HLA-A*02:01 and Antigen Peptides.

Journal of chemical information and modeling Jun 26, 2024
The intricate interaction between major histocompatibility complexes (MHCs) and antigen peptides with diverse amino acid sequences plays a pivotal role in immune responses and T cell activity. In recent years, deep learning (DL)-based models have eme...
Amino Acid Sequence HLA-A2 Antigen Protein Binding Protein Conformation Models, Molecular Peptides Humans Deep Learning
View on PubMed DOI

Accurate prediction of CDR-H3 loop structures of antibodies with deep learning.

eLife Jun 26, 2024
Accurate prediction of the structurally diverse complementarity determining region heavy chain 3 (CDR-H3) loop structure remains a primary and long-standing challenge for antibody modeling. Here, we present the H3-OPT toolkit for predicting the 3D st...
Deep Learning Models, Molecular Humans Single-Domain Antibodies Protein Conformation Antibodies, Monoclonal Complementarity Determining Regions
View on PubMed DOI

Protein loop structure prediction by community-based deep learning and its application to antibody CDR H3 loop modeling.

PLoS computational biology Jun 24, 2024
As of now, more than 60 years have passed since the first determination of protein structures through crystallography, and a significant portion of protein structures can be predicted by computers. This is due to the groundbreaking enhancement in pro...
Humans Neural Networks, Computer Antibodies Protein Conformation Computational Biology Algorithms Databases, Protein Complementarity Determining Regions Deep Learning Models, Molecular
View on PubMed DOI

Computational design of soluble and functional membrane protein analogues.

Nature Jun 19, 2024
De novo design of complex protein folds using solely computational means remains a substantial challenge. Here we use a robust deep learning pipeline to design complex folds and soluble analogues of integral membrane proteins. Unique membrane topolog...
Amino Acid Motifs Models, Molecular Solubility Proof of Concept Study Protein Folding Protein Stability Membrane Proteins Receptors, G-Protein-Coupled Deep Learning Proteome Humans Computer-Aided Design
View on PubMed DOI

Highly accurate carbohydrate-binding site prediction with DeepGlycanSite.

Nature communications Jun 17, 2024
As the most abundant organic substances in nature, carbohydrates are essential for life. Understanding how carbohydrates regulate proteins in the physiological and pathological processes presents opportunities to address crucial biological problems a...
Humans Neural Networks, Computer Deep Learning Models, Molecular Binding Sites Protein Binding Carbohydrates Proteins
View on PubMed DOI

EGG: Accuracy Estimation of Individual Multimeric Protein Models Using Deep Energy-Based Models and Graph Neural Networks.

International journal of molecular sciences Jun 6, 2024
Reliable and accurate methods of estimating the accuracy of predicted protein models are vital to understanding their respective utility. Discerning how the quaternary structure conforms can significantly improve our collective understanding of cell ...
Computational Biology Proteins Models, Molecular Neural Networks, Computer Protein Conformation Protein Multimerization
View on PubMed DOI

Folding the human proteome using BioNeMo: A fused dataset of structural models for machine learning purposes.

Scientific data Jun 6, 2024
Human proteins are crucial players in both health and disease. Understanding their molecular landscape is a central topic in biological research. Here, we present an extensive dataset of predicted protein structures for 42,042 distinct human proteins...
Protein Folding Models, Molecular Protein Conformation Humans Proteome Machine Learning Databases, Protein
View on PubMed DOI

RhoMax: Computational Prediction of Rhodopsin Absorption Maxima Using Geometric Deep Learning.

Journal of chemical information and modeling Jun 3, 2024
Microbial rhodopsins (MRs) are a diverse and abundant family of photoactive membrane proteins that serve as model systems for biophysical techniques. Optogenetics utilizes genetic engineering to insert specialized proteins into specific neurons or br...
Deep Learning Models, Molecular Optogenetics Rhodopsin Amino Acid Sequence Rhodopsins, Microbial Protein Conformation
View on PubMed DOI

Equivariant score-based generative diffusion framework for 3D molecules.

BMC bioinformatics May 30, 2024
BACKGROUND: Molecular biology is crucial for drug discovery, protein design, and human health. Due to the vastness of the drug-like chemical space, depending on biomedical experts to manually design molecules is exceedingly expensive. Utilizing gener...
Computational Biology Drug Discovery Algorithms Models, Molecular Drug Design Deep Learning
View on PubMed DOI
Popular Topics
Recent Journals