GalaxyDock BP2 score: a hybrid scoring function for accurate protein–ligand docking
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Computer-Aided Molecular Design"
DOI: 10.1007/s10822-017-0030-9
Abstract: Protein–ligand docking is a useful tool for providing atomic-level understanding of protein functions in nature and design principles for artificial ligands or proteins with desired properties. The ability to identify the true binding pose of… read more here.
Keywords: protein; scoring function; galaxydock bp2; score ... See more keywords
Development of Postprocessing Method of Protein-Ligand Docking using Interaction Fingerprint
Sign Up to like & getrecommendations! Published in 2017 at "Biophysical Journal"
DOI: 10.1016/j.bpj.2016.11.2423
Abstract: Protein-ligand docking is an important method in Structure-based Drug Discovery [1]. Although many programs have been developed for docking [2], the accuracy is still insufficient due to the difficulty in the scoring function [3]. Interaction… read more here.
Keywords: protein; chemistry; method; interaction ... See more keywords
Modeling ligand docking to RNA in the design of RNA-based nanostructures.
Sign Up to like & getrecommendations! Published in 2019 at "Current opinion in biotechnology"
DOI: 10.1016/j.copbio.2019.10.010
Abstract: RNA has grown in biological importance as the discovery of its many functional roles in the cellular machinery has revealed the potential for targeting it to disrupt cancer pathways. RNA structure underlies its functionality and… read more here.
Keywords: design rna; based nanostructures; rna; rna based ... See more keywords
Deep Learning Model for Efficient Protein-Ligand Docking with Implicit Side-Chain Flexibility
Sign Up to like & getrecommendations! Published in 2023 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.2c01436
Abstract: Protein-ligand docking is an essential tool in structure-based drug design with applications ranging from virtual high-throughput screening to pose prediction for lead optimization. Most docking programs for pose prediction are optimized for redocking to an… read more here.
Keywords: ligand docking; ligand; deep learning; model ... See more keywords
FitDock: protein-ligand docking by template fitting.
Sign Up to like & getrecommendations! Published in 2022 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbac087
Abstract: Protein-ligand docking is an essential method in computer-aided drug design and structural bioinformatics. It can be used to identify active compounds and reveal molecular mechanisms of biological processes. A successful docking usually requires thorough conformation… read more here.
Keywords: ligand docking; fitdock protein; docking template; protein ligand ... See more keywords
PLIDflow: an open-source workflow for the online analysis of protein-ligand docking using galaxy
Sign Up to like & getrecommendations! Published in 2020 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btaa481
Abstract: MOTIVATION Molecular docking is aimed at predicting the conformation of small-molecule (ligands) within an identified binding site in a target protein (receptor). Protein-ligand docking plays an important role in modern drug discovery and biochemistry for… read more here.
Keywords: protein; analysis; binding site; protein ligand ... See more keywords
ViTScore: a novel three-dimensional Vision Transformer method for accurate prediction of protein-ligand docking poses.
Sign Up to like & getrecommendations! Published in 2023 at "IEEE transactions on nanobioscience"
DOI: 10.1109/tnb.2023.3274640
Abstract: Protein-ligand interactions (PLIs) are essential for cellular activities and drug discovery, and due to the complexity and high cost of experimental methods, there is a great demand for computational approaches, such as protein-ligand docking, to… read more here.
Keywords: native poses; ligand docking; near native; set poses ... See more keywords
Diversity-guided Lamarckian random drift particle swarm optimization for flexible ligand docking
Sign Up to like & getrecommendations! Published in 2020 at "BMC Bioinformatics"
DOI: 10.1186/s12859-020-03630-2
Abstract: Background Protein-ligand docking has emerged as a particularly important tool in drug design and development, and flexible ligand docking is a widely used method for docking simulations. Many docking software packages can simulate flexible ligand… read more here.
Keywords: flexible ligand; swarm optimization; particle swarm; ligand ... See more keywords
PlaceWaters: Real-time, explicit interface water sampling during Rosetta ligand docking
Sign Up to like & getrecommendations! Published in 2022 at "PLoS ONE"
DOI: 10.1371/journal.pone.0269072
Abstract: Water molecules at the protein-small molecule interface often form hydrogen bonds with both the small molecule ligand and the protein, affecting the structural integrity and energetics of a binding event. The inclusion of these ‘bridging… read more here.
Keywords: explicit interface; ligand docking; water; rosetta ... See more keywords
Comparative Analysis of Electrostatic Models for Ligand Docking
Sign Up to like & getrecommendations! Published in 2019 at "Frontiers in Molecular Biosciences"
DOI: 10.3389/fmolb.2019.00052
Abstract: The precise modeling of molecular interactions remains an important goal among molecular modeling techniques. Some of the challenges in the field include the precise definition of a Hamiltonian for biomolecular systems, together with precise parameters… read more here.
Keywords: energies computed; models ligand; model; coulomb model ... See more keywords