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   Articles with "ligand docking" as a keyword



GalaxyDock BP2 score: a hybrid scoring function for accurate protein–ligand docking

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recommendations! 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

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recommendations! 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.

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recommendations! 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

Advancing Ligand Docking through Deep Learning: Challenges and Prospects in Virtual Screening.

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recommendations! Published in 2024 at "Accounts of chemical research"

DOI: 10.1021/acs.accounts.4c00093

Abstract: ConspectusMolecular docking, also termed ligand docking (LD), is a pivotal element of structure-based virtual screening (SBVS) used to predict the binding conformations and affinities of protein-ligand complexes. Traditional LD methodologies rely on a search and… read more here.

Keywords: deep learning; virtual screening; speed; ligand ... See more keywords

Deep Learning Model for Efficient Protein-Ligand Docking with Implicit Side-Chain Flexibility

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recommendations! 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

Interformer: an interaction-aware model for protein-ligand docking and affinity prediction

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recommendations! Published in 2024 at "Nature Communications"

DOI: 10.1038/s41467-024-54440-6

Abstract: In recent years, the application of deep learning models to protein-ligand docking and affinity prediction, both vital for structure-based drug design, has garnered increasing interest. However, many of these models overlook the intricate modeling of… read more here.

Keywords: affinity prediction; affinity; protein ligand; model ... See more keywords

FitDock: protein-ligand docking by template fitting.

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recommendations! 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

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recommendations! 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.

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recommendations! 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

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recommendations! 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

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recommendations! 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