A molecular evolution algorithm for ligand design in DOCK
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.26993
Abstract: As a complement to virtual screening, de novo design of small molecules is an alternative approach for identifying potential drug candidates. Here, we present a new 3D genetic algorithm to evolve molecules through breeding, mutation,… read more here.
Keywords: algorithm; dock; design; fitness ... See more keywords
ProBiS-Dock: A Hybrid Multitemplate Homology Flexible Docking Algorithm Enabled by Protein Binding Site Comparison
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.1c01176
Abstract: The protein data bank (PDB) is a rich source of protein ligand structures, but ligands are not explicitly used in current docking algorithms. We have developed ProBiS-Dock, a docking algorithm complementary to the ProBiS-Dock Database… read more here.
Keywords: probis dock; docking algorithm; binding site; dock ... See more keywords
Large-Scale Docking in the Cloud
Sign Up to like & getrecommendations! Published in 2023 at "Journal of Chemical Information and Modeling"
DOI: 10.1021/acs.jcim.3c00031
Abstract: Molecular docking is a pragmatic approach to exploit protein structures for new ligand discovery, but the growing size of available chemical space is increasingly challenging to screen on in-house computer clusters. We have therefore developed… read more here.
Keywords: large scale; cost; dock; scale docking ... See more keywords
Uni-Dock: GPU-Accelerated Docking Enables Ultralarge Virtual Screening.
Sign Up to like & getrecommendations! Published in 2023 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.2c01145
Abstract: Molecular docking, a structure-based virtual screening method, is a reliable tool to enrich potential bioactive molecules from molecular databases. With the rapid expansion of compound library sizes, the speed of existing molecular docking programs becomes… read more here.
Keywords: virtual screening; gpu accelerated; dock; accelerated docking ... See more keywords
Docking of peptides to GPCRs using a combination of CABS-dock with FlexPepDock refinement
Sign Up to like & getrecommendations! Published in 2020 at "Briefings in Bioinformatics"
DOI: 10.1093/bib/bbaa109
Abstract: Abstract The structural description of peptide ligands bound to G protein-coupled receptors (GPCRs) is important for the discovery of new drugs and deeper understanding of the molecular mechanisms of life. Here we describe a three-stage… read more here.
Keywords: peptides gpcrs; docking peptides; dock; cabs dock ... See more keywords
Liquid dispensing in the adhesive hairy pads of dock beetles
Sign Up to like & getrecommendations! Published in 2020 at "Journal of the Royal Society Interface"
DOI: 10.1098/rsif.2020.0024
Abstract: Many insects can climb on smooth inverted substrates using adhesive hairy pads on their legs. The hair–surface contact is often mediated by minute volumes of liquid, which form capillary bridges in the contact zones and… read more here.
Keywords: liquid; hairy; dock; hairy pads ... See more keywords
A Deformable Spatial Attention Mechanism-Based Method and a Benchmark for Dock Detection
Sign Up to like & getrecommendations! Published in 2023 at "IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing"
DOI: 10.1109/jstars.2023.3265700
Abstract: Dock is a significant site in the shipbuilding industry. The detection of docks contributes to many important fields. With the abundant methods and datasets, the deep learning-based object detection in remote sensing images has received… read more here.
Keywords: dock detection; spatial attention; dock; detection ... See more keywords
Tandem C2 domains mediate dynamic organelle targeting of a DOCK family guanine nucleotide exchange factor.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of cell science"
DOI: 10.1242/jcs.259825
Abstract: Multicellular organisms use DOCK family guanine nucleotide exchange factors to activate Rac/Rho-of-Plants small GTPases and coordinate cell shape change. In developing tissues, DOCK signals integrate cell-cell interactions with cytoskeleton remodeling, and the GEFs cluster reversibly… read more here.
Keywords: guanine nucleotide; dock family; family guanine; cell ... See more keywords
Docking cholesterol to integral membrane proteins with Rosetta
Sign Up to like & getrecommendations! Published in 2023 at "PLOS Computational Biology"
DOI: 10.1371/journal.pcbi.1010947
Abstract: Lipid molecules such as cholesterol interact with the surface of integral membrane proteins (IMP) in a mode different from drug-like molecules in a protein binding pocket. These differences are due to the lipid molecule’s shape,… read more here.
Keywords: integral membrane; membrane proteins; dock; docking cholesterol ... See more keywords
Comparative Assessment of Docking Programs for Docking and Virtual Screening of Ribosomal Oxazolidinone Antibacterial Agents
Sign Up to like & getrecommendations! Published in 2023 at "Antibiotics"
DOI: 10.3390/antibiotics12030463
Abstract: Oxazolidinones are a broad-spectrum class of synthetic antibiotics that bind to the 50S ribosomal subunit of Gram-positive and Gram-negative bacteria. Many crystal structures of the ribosomes with oxazolidinone ligands have been reported in the literature,… read more here.
Keywords: oxazolidinone; virtual screening; dock; docking programs ... See more keywords