AI Medical Compendium Topic:
Protein Binding

Clear Filters Showing 421 to 430 of 812 articles

IConMHC: a deep learning convolutional neural network model to predict peptide and MHC-I binding affinity.

Immunogenetics Jun 24, 2020
Tumor-specific neoantigens are mutated self-peptides presented by tumor cell major histocompatibility complex (MHC) molecules and are necessary to elicit host's anti-cancer cytotoxic T cell responses. It could be specifically recognized by neoantigen...
Peptides Deep Learning Protein Binding Antigens, Neoplasm Neural Networks, Computer Computer Simulation Reproducibility of Results Amino Acid Sequence Databases, Protein Alleles Histocompatibility Antigens Class I Humans
View on PubMed DOI

Immunopeptidomic Data Integration to Artificial Neural Networks Enhances Protein-Drug Immunogenicity Prediction.

Frontiers in immunology Jun 23, 2020
Recombinant DNA technology has, in the last decades, contributed to a vast expansion of the use of protein drugs as pharmaceutical agents. However, such biological drugs can lead to the formation of anti-drug antibodies (ADAs) that may result in adve...
Mass Spectrometry Peptides Humans Neural Networks, Computer CD4-Positive T-Lymphocytes Dendritic Cells Antirheumatic Agents Epitopes, T-Lymphocyte Infliximab Protein Binding Rituximab Proteomics Histocompatibility Antigens Class II
View on PubMed DOI

CoRNeA: A Pipeline to Decrypt the Inter-Protein Interfaces from Amino Acid Sequence Information.

Biomolecules Jun 22, 2020
Decrypting the interface residues of the protein complexes provides insight into the functions of the proteins and, hence, the overall cellular machinery. Computational methods have been devised in the past to predict the interface residues using ami...
Machine Learning Protein Binding Computational Biology Proteins Databases, Protein Amino Acid Sequence Humans
View on PubMed DOI

Direct Comparison of Total Clearance Prediction: Computational Machine Learning Model versus Bottom-Up Approach Using In Vitro Assay.

Molecular pharmaceutics Jun 12, 2020
The in vitro-in vivo extrapolation (IVIVE) approach for predicting total plasma clearance (CL) has been widely used to rank order compounds early in discovery. More recently, a computational machine learning approach utilizing physicochemical descrip...
Humans Machine Learning Animals Membranes, Artificial Administration, Intravenous Plasma Metabolic Clearance Rate Dogs Models, Biological Madin Darby Canine Kidney Cells Microsomes, Liver Hepatocytes Permeability Pharmacokinetics Rats, Sprague-Dawley Male Protein Binding Liver Rats Blood Proteins Pharmaceutical Preparations
View on PubMed DOI

Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies.

Journal of chemical theory and computation Jun 4, 2020
Calculating absolute binding free energies is challenging and important. In this paper, we test some recently developed metadynamics-based methods and develop a new combination with a Hamiltonian replica-exchange approach. The methods were tested on ...
Humans Machine Learning Algorithms Ligands Thermodynamics Protein Structure, Tertiary Epoxide Hydrolases Drug Design Protein Binding Molecular Dynamics Simulation
View on PubMed DOI

Using machine learning to improve ensemble docking for drug discovery.

Proteins May 25, 2020
Ensemble docking has provided an inexpensive method to account for receptor flexibility in molecular docking for virtual screening. Unfortunately, as there is no rigorous theory to connect the docking scores from multiple structures to measured activ...
Protein Structure, Secondary Protein Binding Support Vector Machine Bayes Theorem Ligands Humans ErbB Receptors Protein Kinase Inhibitors Molecular Docking Simulation Binding Sites Drug Discovery User-Computer Interface
View on PubMed DOI

GPS-PBS: A Deep Learning Framework to Predict Phosphorylation Sites that Specifically Interact with Phosphoprotein-Binding Domains.

Cells May 20, 2020
Protein phosphorylation is essential for regulating cellular activities by modifying substrates at specific residues, which frequently interact with proteins containing phosphoprotein-binding domains (PPBDs) to propagate the phosphorylation signaling...
Phosphoproteins Statistics as Topic Binding Sites Humans Algorithms Animals Signal Transduction Deep Learning Databases, Protein Protein Binding Phosphorylation Proteome Protein Domains
View on PubMed DOI

CNN-Peaks: ChIP-Seq peak detection pipeline using convolutional neural networks that imitate human visual inspection.

Scientific reports May 13, 2020
ChIP-seq is one of the core experimental resources available to understand genome-wide epigenetic interactions and identify the functional elements associated with diseases. The analysis of ChIP-seq data is important but poses a difficult computation...
Protein Binding Computational Biology Epigenesis, Genetic Epigenomics Histones Binding Sites Nucleotide Motifs Humans Databases, Nucleic Acid Neural Networks, Computer Transcription Initiation Site Software Chromatin Immunoprecipitation Sequencing Algorithms
View on PubMed DOI

Improving Docking-Based Virtual Screening Ability by Integrating Multiple Energy Auxiliary Terms from Molecular Docking Scoring.

Journal of chemical information and modeling May 11, 2020
Virtual Screening (VS) based on molecular docking is an efficient method used for retrieving novel hit compounds in drug discovery. However, the accuracy of the current docking scoring function (SF) is usually insufficient. In this study, in order to...
Protein Binding Proteins Ligands Machine Learning Molecular Docking Simulation
View on PubMed DOI

Binding Affinity Prediction by Pairwise Function Based on Neural Network.

Journal of chemical information and modeling May 11, 2020
We present a new approach to estimate the binding affinity from given three-dimensional poses of protein-ligand complexes. In this scheme, every protein-ligand atom pair makes an additive free-energy contribution. The sum of these pairwise contributi...
Ligands Molecular Docking Simulation Drug Design Protein Binding Neural Networks, Computer
View on PubMed DOI
Popular Topics
Recent Journals