AIMC Topic: Proteins

Clear Filters Showing 1161 to 1170 of 1979 articles

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...
Protein Binding Proteins Molecular Dynamics Simulation Deep Learning Ligands Thermodynamics
View on PubMed DOI

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...
User-Computer Interface Drug Evaluation, Preclinical Protein Conformation Machine Learning Proteins Algorithms Molecular Docking Simulation
View on PubMed DOI

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...
Evolution, Molecular Proteins Models, Molecular Protein Binding Machine Learning Computational Biology Protein Domains Thermodynamics Binding, Competitive Tumor Suppressor Protein p53 Mutation Proto-Oncogene Proteins c-mdm2
View on PubMed DOI

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...
Computational Biology Proteins Databases, Protein Software Deep Learning Protein Conformation, beta-Strand Models, Molecular
View on PubMed DOI

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...
Proteins Bacteria Species Specificity Machine Learning Algorithms Computational Biology Bacteriophages Data Analysis Genomics
View on PubMed DOI

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...
RNA, Long Noncoding Proteins Stomach Neoplasms Gene Ontology Humans Protein Interaction Maps Algorithms Computational Biology Gene Regulatory Networks MicroRNAs
View on PubMed DOI

Computational discovery of direct associations between GO terms and protein domains.

BMC bioinformatics Nov 20, 2018
BACKGROUND: Families of related proteins and their different functions may be described systematically using common classifications and ontologies such as Pfam and GO (Gene Ontology), for example. However, many proteins consist of multiple domains, a...
Algorithms Computational Biology Databases, Protein Area Under Curve Proteins Protein Domains Gene Ontology Amino Acid Sequence Molecular Sequence Annotation
View on PubMed DOI

Learning protein binding affinity using privileged information.

BMC bioinformatics Nov 15, 2018
BACKGROUND: Determining protein-protein interactions and their binding affinity are important in understanding cellular biological processes, discovery and design of novel therapeutics, protein engineering, and mutagenesis studies. Due to the time an...
Ligands Proteins Amino Acid Sequence Reproducibility of Results ROC Curve Algorithms Computational Biology Support Vector Machine Machine Learning Protein Binding
View on PubMed DOI

Two New Heuristic Methods for Protein Model Quality Assessment.

IEEE/ACM transactions on computational biology and bioinformatics Nov 9, 2018
Protein tertiary structure prediction is an important open challenge in bioinformatics and requires effective methods to accurately evaluate the quality of protein 3-D models generated computationally. Many quality assessment (QA) methods have been p...
Computational Biology Proteins Protein Structure, Tertiary Computer Heuristics Models, Molecular Software Algorithms
View on PubMed DOI

Improving Protein Gamma-Turn Prediction Using Inception Capsule Networks.

Scientific reports Oct 24, 2018
Protein gamma-turn prediction is useful in protein function studies and experimental design. Several methods for gamma-turn prediction have been developed, but the results were unsatisfactory with Matthew correlation coefficients (MCC) around 0.2-0.4...
Protein Structure, Secondary Computational Biology Neural Networks, Computer Proteins Algorithms Amino Acid Sequence
View on PubMed DOI
Popular Topics
Recent Journals