flexx docking algorithm (Astex Inc)
90
Structured Review
Astex Inc
flexx docking algorithm
Flexx Docking Algorithm, supplied by Astex Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/docking+algorithms+flexx/easydock/pm22203423-47-35-6
Average 90 stars, based on 1 article reviews
Flexx Docking Algorithm, supplied by Astex Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/docking+algorithms+flexx/easydock/pm22203423-47-35-6
Average 90 stars, based on 1 article reviews
flexx docking algorithm - by Bioz Stars,
2026-10
90/100 stars
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other:Article Title: Chaos-embedded particle swarm optimization approach for protein-ligand docking and virtual screening Article Snippet: Following the procedure in Ref. [8, 11], a default docking box size of 22.5 Å in all three dimensions was created for Article Title: A consistent description of HYdrogen bond and DEhydration energies in protein-ligand complexes: methods behind the HYDE scoring function. Article Snippet: The estimation of free energy of binding is a key problem in structure-based design.. We developed the scoring function HYDE based on a consistent description of HYdrogen bond and DEhydration energies in protein– ligand complexes.. HYDE is applicable to all types of protein targets since it is not calibrated on experimental binding affinity data or protein–ligand complexes. Biomarker Discovery:Article Title: Expanded interaction fingerprint method for analyzing ligand binding modes in docking and structure-based drug design. Article Snippet: An expanded interaction fingerprint method has been developed for analyzing the binding modes of ligands in docking and structure-based design methods.. Taking the basic premise of representing a ligand in terms of a binary string that denotes its interactions with a target protein, we have expanded the method to include additional interaction-specific information.. By considering the hydrogen-bonding strength and/or accessibility of the hydrogen bonding groups within a binding site as well as their geometric arrangement we aim to provide a better representation of a ligand-protein interaction. Generated:Article Title: A novel interaction fingerprint derived from per atom score contributions: exhaustive evaluation of interaction fingerprint performance in docking based virtual screening Article Snippet: .. In order to evaluate the performance of PADIF in pose recovery, 100 diverse docking poses (inter pose RMSD > 1.5 Å) per ligand were generated for a suitable subset of 61 complexes of the Article Title: A novel interaction fingerprint derived from per atom score contributions: exhaustive evaluation of interaction fingerprint performance in docking based virtual screening Article Snippet: .. In order to evaluate the performance of PADIF in pose recovery, 100 diverse docking poses (inter pose RMSD > 1.5 Å) per ligand were generated for a suitable subset of 61 complexes of the Produced:Article Title: Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function. Article Snippet: The HYDE scoring function consistently describes hydrogen bonding, the hydrophobic effect and desolvation.. It relies on HYdration and DEsolvation terms which are calibrated using octanol/water partition coefficients of small molecules.. We do not use affinity data for calibration, therefore HYDE is generally applicable to all protein targets. Article Title: Protein-ligand docking against non-native protein conformers. Article Snippet: In the validation of protein-ligand docking protocols, performance is mostly measured against native protein conformers, i.e. each ligand is docked into the protein conformation from the structure that contained that ligand.. In real-life applications, however, ligands are docked against non-native conformations of the protein, i.e. the apo structure or a structure of a different protein-ligand complex.. Here, we have constructed an extensive test set for assessing docking performance against non-native protein conformations. Transformation Assay:Article Title: Power transformations improve interpolation of grids for molecular mechanics interaction energies Article Snippet: .. RMSEs (kcal/mol) between the direct and interpolated LJ repulsive (top) and attractive (bottom) energies as a function of grid spacing (x-axis) and inverse transformation power (y-axis) for atoms from docking poses to the |
