Visualizing the Residue Interaction Landscape of Proteins by Temporal Network Embedding
Sign Up to like & getrecommendations! Published in 2023 at "Journal of Chemical Theory and Computation"
DOI: 10.1021/acs.jctc.2c01228
Abstract: Characterizing the structural dynamics of proteins with heterogeneous conformational landscapes is crucial to understanding complex biomolecular processes. To this end, dimensionality reduction algorithms are used to produce low-dimensional embeddings of the high-dimensional conformational phase space.… read more here.
Keywords: interaction; network; interaction landscape; residue interaction ... See more keywords
Pattern to Knowledge: Deep Knowledge-Directed Machine Learning for Residue-Residue Interaction Prediction
Sign Up to like & getrecommendations! Published in 2018 at "Scientific Reports"
DOI: 10.1038/s41598-018-32834-z
Abstract: Residue-residue close contact (R2R-C) data procured from three-dimensional protein-protein interaction (PPI) experiments is currently used for predicting residue-residue interaction (R2R-I) in PPI. However, due to complex physiochemical environments, R2R-I incidences, facilitated by multiple factors, are… read more here.
Keywords: residue interaction; knowledge; r2r; deep knowledge ... See more keywords
RING-PyMOL: residue interaction networks of structural ensembles and molecular dynamics
Sign Up to like & getrecommendations! Published in 2023 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btad260
Abstract: Abstract RING-PyMOL is a plugin for PyMOL providing a set of analysis tools for structural ensembles and molecular dynamic simulations. RING-PyMOL combines residue interaction networks, as provided by the RING software, with structural clustering… read more here.
Keywords: structural ensembles; ring pymol; residue interaction; ensembles molecular ... See more keywords
gRINN: a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations
Sign Up to like & getrecommendations! Published in 2018 at "Nucleic Acids Research"
DOI: 10.1093/nar/gky381
Abstract: Abstract Atomistic molecular dynamics (MD) simulations generate a wealth of information related to the dynamics of proteins. If properly analyzed, this information can lead to new insights regarding protein function and assist wet-lab experiments. Aiming… read more here.
Keywords: residue interaction; energy; analysis; grinn ... See more keywords
Prediction of DNA-Binding Protein–Drug-Binding Sites Using Residue Interaction Networks and Sequence Feature
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Bioengineering and Biotechnology"
DOI: 10.3389/fbioe.2022.822392
Abstract: Identification of protein–ligand binding sites plays a critical role in drug discovery. However, there is still a lack of targeted drug prediction for DNA-binding proteins. This study aims at the binding sites of DNA-binding proteins… read more here.
Keywords: residue interaction; drug; binding sites; dna binding ... See more keywords
Inverse Mixed-Solvent Molecular Dynamics for Visualization of the Residue Interaction Profile of Molecular Probes
Sign Up to like & getrecommendations! Published in 2022 at "International Journal of Molecular Sciences"
DOI: 10.3390/ijms23094749
Abstract: To ensure efficiency in discovery and development, the application of computational technology is essential. Although virtual screening techniques are widely applied in the early stages of drug discovery research, the computational methods used in lead… read more here.
Keywords: interaction; inverse mixed; solvent molecular; residue interaction ... See more keywords