Molegro Virtual Docker for Docking Screens.

No abstract is available for this paper.

• Publication year

  2026

• Venue

  Methods in molecular biology

• Publication date

  Unknown publication date

• Fields of study

  Medicine, Computer Science

• Identifiers
  DOI 10.1007/978-1-0716-4949-7_10PMID 41075090
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Beyond AlphaFold2: The Impact of AI for the Further Improvement of Protein Structure Prediction.

  2025cited by this paper
• Cyclin Dependent Kinases in Antiviral Drug Discovery.

  2025cited by this paper
• Predicting Inhibition of CDK2 with SAnDReS: The Application of Machine Learning to Navigate the Scoring Function Space.

  2024cited by this paper
• The Art and Science of Molecular Docking.

  2024cited by this paper
• BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data

  2024cited by this paper
• Machine Learning Meets Physics-based Modeling: A Mass-spring System to Predict Protein-ligand Binding Affinity.

  2024cited by this paper
• SAnDReS 2.0: Development of machine‐learning models to explore the scoring function space

  2024cited by this paper
• Addressing docking pose selection with structure-based deep learning: Recent advances, challenges and opportunities

  2024cited by this paper
• Are protein-ligand docking programs good enough to predict experimental poses of noncovalent ligands bound to the SARS-CoV-2 main protease?

  2024cited by this paper
• Exploring Scoring Function Space: Developing Computational Models for Drug Discovery.

  2023cited by this paper
• Roles of Virtual Screening and Molecular Dynamics Simulations in Discovering and Understanding Antimalarial Drugs

  2023cited by this paper
• SGNet: Sequence-Based Convolution and Ligand Graph Network for Protein Binding Affinity Prediction

  2023cited by this paper
• Scoring Functions for Protein-Ligand Binding Affinity Prediction Using Structure-based Deep Learning: A Review

  2022cited by this paper
• PlayMolecule Glimpse: Understanding Protein–Ligand Property Predictions with Interpretable Neural Networks

  2022cited by this paper
• RDPSOVina: the random drift particle swarm optimization for protein–ligand docking

  2022cited by this paper
• Benchmarking AlphaFold‐enabled molecular docking predictions for antibiotic discovery

  2022cited by this paper
• Protein–Ligand Docking in the Machine-Learning Era

  2022cited by this paper
• 3,5,7-Substituted Pyrazolo[4,3-d]Pyrimidine Inhibitors of Cyclin-Dependent Kinases and Cyclin K Degraders.

  2022cited by this paper
• Delta Machine Learning to Improve Scoring-Ranking-Screening Performances of Protein-Ligand Scoring Functions

  2022cited by this paper
• AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings

  2021cited by this paper
• Application of Machine Learning Techniques for Drug Discovery.

  2021cited by this paper
• Computational Prediction of Binding Affinity for CDK2-ligand Complexes. A Protein Target for Cancer Drug Discovery.

  2021cited by this paper
• Highly accurate protein structure prediction with AlphaFold

  2021cited by this paper
• Protein-ligand Docking Simulations with AutoDock4 Focused on the Main Protease of SARS-CoV-2.

  2021cited by this paper
• Overview of PCTK3/CDK18: A Cyclin-Dependent Kinase Involved in Specific Functions in Post-Mitotic Cells.

  2021cited by this paper
• Electrostatic Potential Energy in Protein-Drug Complexes.

  2021cited by this paper
• Recent Advances in Molecular Docking for the Research and Discovery of Potential Marine Drugs

  2020cited by this paper
• Computational Analysis of Dipyrone Metabolite 4-Aminoantipyrine as a Cannabinoid Receptor 1 Agonist.

  2020cited by this paper
• ZINC20 - A Free Ultralarge-Scale Chemical Database for Ligand Discovery

  2020cited by this paper
• In silico study examining new phenylpropanoids targets with antidepressant activity.

  2020cited by this paper
• Cryo-EM as a powerful tool for drug discovery

  2020cited by this paper
• Antinociceptive Activity of Chemical Components of Essential Oils That Involves Docking Studies: A Review

  2020cited by this paper
• How Docking Programs Work.

  2019cited by this paper
• Exploring the Scoring Function Space.

  2019cited by this paper
• Hydrogen Bonds in Protein-Ligand Complexes.

  2019cited by this paper
• Docking with SwissDock.

  2019cited by this paper
• Advances in the Understanding of the Cannabinoid Receptor 1 - Focusing on the Inverse Agonists Interactions

  2019cited by this paper
• Cyclin-Dependent Kinase 2 in Cellular Senescence and Cancer. A Structural and Functional Review.

  2019cited by this paper
• Docking with AutoDock4.

  2019cited by this paper
• Molecular Docking Simulations with ArgusLab.

  2019cited by this paper
• Machine Learning to Predict Binding Affinity.

  2019cited by this paper
• Building Machine-Learning Scoring Functions for Structure-Based Prediction of Intermolecular Binding Affinity.

  2019cited by this paper
• Docking with GemDock.

  2019cited by this paper
• Homology Modeling of Protein Targets with MODELLER.

  2019cited by this paper
• Taba: A Tool to Analyze the Binding Affinity

  2019cited by this paper
• Molegro Virtual Docker for Docking.

  2019cited by this paper
• Van der Waals Potential in Protein Complexes.

  2019cited by this paper
• Application of Machine Learning Techniques to Predict Binding Affinity for Drug Targets. A Study of Cyclin-Dependent Kinase 2.

  2019cited by this paper
• Development of a machine-learning model to predict Gibbs free energy of binding for protein-ligand complexes.

  2018cited by this paper
• KDEEP: Protein-Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks

  2018cited by this paper
• Pre-clinical effects of metformin and aspirin on the cell lines of different breast cancer subtypes

  2018cited by this paper
• High throughput nonparametric probability density estimation

  2018cited by this paper
• Development of CDK-targeted scoring functions for prediction of binding affinity.

  2018cited by this paper
• Protein-Ligand Docking in Drug Design: Performance Assessment and Binding-Pose Selection.

  2018cited by this paper
• GPCR drug discovery: integrating solution NMR data with crystal and cryo-EM structures

  2018cited by this paper
• Development of machine learning models to predict inhibition of 3‐dehydroquinate dehydratase

  2018cited by this paper
• Improving classical scoring functions using random forest: The non‐additivity of free energy terms’ contributions in binding

  2018cited by this paper
• Supervised Machine Learning Methods Applied to Predict Ligand- Binding Affinity.

  2017cited by this paper
• Optimized Virtual Screening Workflow: Towards Target-Based Polynomial Scoring Functions for HIV-1 Protease.

  2017cited by this paper
• Supervised machine learning techniques to predict binding affinity. A study for cyclin-dependent kinase 2.

  2017cited by this paper
• Understanding the Structural Basis for Inhibition of Cyclin-Dependent Kinases. New Pieces in the Molecular Puzzle.

  2017cited by this paper
• Computational protein–ligand docking and virtual drug screening with the AutoDock suite

  2016cited by this paper
• SAnDReS a Computational Tool for Statistical Analysis of Docking Results and Development of Scoring Functions.

  2016cited by this paper
• Computational methods in drug discovery

  2016cited by this paper
• DOCK 6: Impact of new features and current docking performance

  2015cited by this paper
• Opinion Paper: Targeting Multiple Cyclin-Dependent Kinases (CDKs): A New Strategy for Molecular Docking Studies.

  2015cited by this paper
• A lupane-triterpene isolated from Combretum leprosum Mart. fruit extracts that interferes with the intracellular development of Leishmania (L.) amazonensis in vitro

  2015cited by this paper
• Shikimate kinase, a protein target for drug design.

  2014cited by this paper
• Challenges, Applications, and Recent Advances of Protein-Ligand Docking in Structure-Based Drug Design

  2014cited by this paper
• One Size Does Not Fit All: The Limits of Structure-Based Models in Drug Discovery

  2013cited by this paper
• Targeting imidazoline site on monoamine oxidase B through molecular docking simulations

  2012cited by this paper
• Anti-Trypanosoma cruzi activity of nicotinamide.

  2012cited by this paper
• Identification of new potential Mycobacterium tuberculosis shikimate kinase inhibitors through molecular docking simulations

  2012cited by this paper
• SwissDock, a protein-small molecule docking web service based on EADock DSS

  2011cited by this paper
• Antimalarial activity of physalins B, D, F, and G.

  2011cited by this paper
• Bio-inspired algorithms applied to molecular docking simulations.

  2011cited by this paper
• Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

  2011cited by this paper
• Structure-based virtual screening.

  2010cited by this paper
• MolDock applied to structure-based virtual screening.

  2010cited by this paper
• A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking

  2010cited by this paper
• Empirical Scoring Functions for Advanced Protein-Ligand Docking with PLANTS

  2009cited by this paper
• AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

  2009cited by this paper
• AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

  2009cited by this paper
• Molecular docking algorithms.

  2008cited by this paper
• CDK9 a potential target for drug development.

  2008cited by this paper
• Evaluation of ligand-binding affinity using polynomial empirical scoring functions.

  2008cited by this paper
• Computational methods for calculation of ligand-binding affinity.

  2008cited by this paper
• Evaluation of molecular docking using polynomial empirical scoring functions.

  2008cited by this paper
• 4-arylazo-3,5-diamino-1H-pyrazole CDK inhibitors: SAR study, crystal structure in complex with CDK2, selectivity, and cellular effects.

  2006cited by this paper
• Development and validation of a modular, extensible docking program: DOCK 5

  2006cited by this paper
• BindingDB: a web-accessible database of experimentally determined protein–ligand binding affinities

  2006cited by this paper
• Structure-based drug design of a highly potent CDK1,2,4,6 inhibitor with novel macrocyclic quinoxalin-2-one structure.

  2006cited by this paper
• MolDock: a new technique for high-accuracy molecular docking.

  2006cited by this paper
• Binding MOAD (Mother Of All Databases)

  2005cited by this paper
• Automated NMR structure determination and disulfide bond identification of the myotoxin crotamine from Crotalus durissus terrificus.

  2005cited by this paper
• PostDOCK: a structural, empirical approach to scoring protein ligand complexes.

  2005cited by this paper
• A pharmacophore‐based evolutionary approach for screening selective estrogen receptor modulators

  2005cited by this paper
• Parmodel: a web server for automated comparative modeling of proteins.

  2004cited by this paper
• Molecular models of cyclin-dependent kinase 1 complexed with inhibitors.

  2004cited by this paper
• Prospects for atomic resolution and neutron crystallography in drug design.

  2004cited by this paper

• No citing papers are available for this paper.