AIMC Topic: Molecular Conformation

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A deep autoencoder framework for discovery of metastable ensembles in biomacromolecules.

The Journal of chemical physics Sep 21, 2021
Biomacromolecules manifest dynamic conformational fluctuation and involve mutual interconversion among metastable states. A robust mapping of their conformational landscape often requires the low-dimensional projection of the conformational ensemble ...
Molecular Conformation Neural Networks, Computer Molecular Dynamics Simulation Macromolecular Substances Proteins
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A spatial-temporal gated attention module for molecular property prediction based on molecular geometry.

Briefings in bioinformatics Sep 2, 2021
MOTIVATION: Geometry-based properties and characteristics of drug molecules play an important role in drug development for virtual screening in computational chemistry. The 3D characteristics of molecules largely determine the properties of the drug ...
Neural Networks, Computer Software Humans Drug Discovery Deep Learning Protein Binding Algorithms Reproducibility of Results Pharmaceutical Preparations Ligands Models, Molecular Molecular Conformation Computational Biology Molecular Structure Proteins
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A sequence-based deep learning approach to predict CTCF-mediated chromatin loop.

Briefings in bioinformatics Sep 2, 2021
Three-dimensional (3D) architecture of the chromosomes is of crucial importance for transcription regulation and DNA replication. Various high-throughput chromosome conformation capture-based methods have revealed that CTCF-mediated chromatin loops a...
Datasets as Topic Humans Gene Expression Regulation Neural Networks, Computer Genome, Human Software Nucleotide Motifs MCF-7 Cells Molecular Conformation Chromatin K562 Cells CCCTC-Binding Factor
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Antibody Clustering Using a Machine Learning Pipeline that Fuses Genetic, Structural, and Physicochemical Properties.

Advances in experimental medicine and biology Jan 1, 2020
Antibody V domain clustering is of paramount importance to a repertoire of immunology-related areas. Although several approaches have been proposed for antibody clustering, still no consensus has been reached. Numerous attempts use information from g...
Complementarity Determining Regions Molecular Conformation Antigen-Antibody Complex Cluster Analysis Amino Acid Sequence Machine Learning
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Bacillus methylotrophicus ASWU-C2, a strain inhabiting hot desert soil, a new source for antibacterial bacillopyrone, pyrophen, and cyclopeptides.

Zeitschrift fur Naturforschung. C, Journal of biosciences Dec 19, 2018
A strain of Bacillus methylotrophicus was isolated from a soil sample collected in Aswan eastern desert, which is known for its extremely arid climate. After fermentation of the strain in liquid culture and subsequent extraction, a bioassay-guided is...
Pyrones Peptides, Cyclic Soil Microbiology Anti-Bacterial Agents Bacillus Staphylococcus aureus Chromobacterium Molecular Conformation Microbial Sensitivity Tests Phenylalanine
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Approaching Pharmacological Space: Events and Components.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2018
With a view to introducing the concept of pharmacological space and its potential applications in investigating and predicting the toxic mechanisms of xenobiotics, this opening chapter describes the logical relations between conformational behavior, ...
Ligands Molecular Conformation Static Electricity Fuzzy Logic Quantitative Structure-Activity Relationship Molecular Docking Simulation Molecular Dynamics Simulation Drug Discovery
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A systematic approach to prioritize drug targets using machine learning, a molecular descriptor-based classification model, and high-throughput screening of plant derived molecules: a case study in oral cancer.

Molecular bioSystems Dec 1, 2015
Systems-biology inspired identification of drug targets and machine learning-based screening of small molecules which modulate their activity have the potential to revolutionize modern drug discovery by complementing conventional methods. To utilize ...
Mouth Neoplasms High-Throughput Screening Assays Machine Learning Binding Sites Drug Discovery Protein Interaction Mapping Receptors, CXCR4 Humans Molecular Conformation Models, Molecular Gene Expression Regulation, Neoplastic Gene Regulatory Networks Cell Line, Tumor Protein Binding Antineoplastic Agents, Phytogenic ROC Curve Computational Biology
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