AIMC Topic: Proteins

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Toward Building Protein Force Fields by Residue-Based Systematic Molecular Fragmentation and Neural Network.

Journal of chemical theory and computation Jan 7, 2019
Accurate force fields are crucial for molecular dynamics investigation of complex biological systems. Building accurate protein force fields from quantum mechanical (QM) calculations is challenging due to the complexity of proteins and high computati...
Peptides Proteins Models, Chemical Neural Networks, Computer Dipeptides Static Electricity Thermodynamics Amino Acids Molecular Dynamics Simulation Quantum Theory
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Extracting chemical-protein interactions from literature using sentence structure analysis and feature engineering.

Database : the journal of biological databases and curation Jan 1, 2019
Information about the interactions between chemical compounds and proteins is indispensable for understanding the regulation of biological processes and the development of therapeutic drugs. Manually extracting such information from biomedical litera...
Software Computational Biology Proteins Semantics Databases, Protein Humans Databases, Chemical Pharmaceutical Preparations Machine Learning Data Mining
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Convolutional neural network based on SMILES representation of compounds for detecting chemical motif.

BMC bioinformatics Dec 31, 2018
BACKGROUND: Previous studies have suggested deep learning to be a highly effective approach for screening lead compounds for new drugs. Several deep learning models have been developed by addressing the use of various kinds of fingerprints and graph ...
Neural Networks, Computer Models, Chemical Software Pharmaceutical Preparations Deep Learning Binding Sites Protein Binding Humans Proteins DNA
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Gene ontology improves template selection in comparative protein docking.

Proteins Dec 27, 2018
Structural characterization of protein-protein interactions is essential for our ability to study life processes at the molecular level. Computational modeling of protein complexes (protein docking) is important as the source of their structure and a...
Binding Sites Protein Interaction Mapping Structural Homology, Protein Models, Molecular Humans Protein Conformation Software Gene Ontology Computational Biology Proteins Molecular Docking Simulation Databases, Protein Protein Interaction Maps Protein Binding
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Toward Achieving Efficient and Accurate Ligand-Protein Unbinding with Deep Learning and Molecular Dynamics through RAVE.

Journal of chemical theory and computation Dec 24, 2018
In this work, we demonstrate how to leverage our recent iterative deep learning-all atom molecular dynamics (MD) technique "Reweighted autoencoded variational Bayes for enhanced sampling (RAVE)" (Ribeiro, Bravo, Wang, Tiwary, J. Chem. Phys. 2018, 149...
Thermodynamics Proteins Molecular Dynamics Simulation Ligands Deep Learning Protein Binding
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Practical Model Selection for Prospective Virtual Screening.

Journal of chemical information and modeling Dec 18, 2018
Virtual (computational) high-throughput screening provides a strategy for prioritizing compounds for experimental screens, but the choice of virtual screening algorithm depends on the data set and evaluation strategy. We consider a wide range of liga...
Protein Conformation User-Computer Interface Proteins Drug Evaluation, Preclinical Machine Learning Algorithms Molecular Docking Simulation
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iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations.

Proteins Dec 3, 2018
Quantitative evaluation of binding affinity changes upon mutations is crucial for protein engineering and drug design. Machine learning-based methods are gaining increasing momentum in this field. Due to the limited number of experimental data, using...
Machine Learning Protein Binding Models, Molecular Mutation Protein Domains Computational Biology Evolution, Molecular Proteins Proto-Oncogene Proteins c-mdm2 Tumor Suppressor Protein p53 Thermodynamics Binding, Competitive
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BetaDL: A protein beta-sheet predictor utilizing a deep learning model and independent set solution.

Computers in biology and medicine Dec 2, 2018
The sequence-based prediction of beta-residue contacts and beta-sheet structures contain key information for protein structure prediction. However, the determination of beta-sheet structures poses numerous challenges due to long-range beta-residue in...
Software Deep Learning Computational Biology Proteins Databases, Protein Protein Conformation, beta-Strand Models, Molecular
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Computational prediction of inter-species relationships through omics data analysis and machine learning.

BMC bioinformatics Nov 20, 2018
BACKGROUND: Antibiotic resistance and its rapid dissemination around the world threaten the efficacy of currently-used medical treatments and call for novel, innovative approaches to manage multi-drug resistant infections. Phage therapy, i.e., the us...
Computational Biology Bacteriophages Proteins Machine Learning Species Specificity Algorithms Data Analysis Genomics Bacteria
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Gene Ontology-based function prediction of long non-coding RNAs using bi-random walk.

BMC medical genomics Nov 20, 2018
BACKGROUND: With the development of sequencing technology, more and more long non-coding RNAs (lncRNAs) have been identified. Some lncRNAs have been confirmed that they play an important role in the process of development through the dosage compensat...
Computational Biology MicroRNAs RNA, Long Noncoding Stomach Neoplasms Humans Proteins Protein Interaction Maps Algorithms Gene Ontology Gene Regulatory Networks
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