Comparing AutoDock and Vina in Ligand/Decoy Discrimination for Virtual Screening

Dynamics and binding interactions of peptide inhibitors of dengue virus entry

(2019) Diyana Mohd Isa et al.   JOURNAL OF BIOLOGICAL PHYSICS

Ligity: A Non-Superpositional, Knowledge-Based Approach to Virtual Screening

(2019) Jean-Paul Ebejer et al.   Journal of Chemical Information and Modeling

Molecular Docking Guided Grid-Independent Descriptor Analysis to Probe the Impact of Water Molecules on Conformational Changes of hERG Inhibitors in Drug Trapping Phenomenon

(2019) Saba Munawar et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

DLIGAND2: an improved knowledge-based energy function for protein–ligand interactions using the distance-scaled, finite, ideal-gas reference state

(2019) Pin Chen et al.   Journal of Cheminformatics

Improving the Virtual Screening Ability of Target-Specific Scoring Functions Using Deep Learning Methods

(2019) Dingyan Wang et al.   Frontiers in Pharmacology

Multiple grid arrangement improves ligand docking with unknown binding sites: Application to the inverse docking problem

(2018) Tomohiro Ban et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Importance of protein flexibility in molecular recognition: a case study on Type-I1/2 inhibitors of ALK

(2018) Xiaotian Kong et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

FINDSITEcomb2.0: A New Approach for Virtual Ligand Screening of Proteins and Virtual Target Screening of Biomolecules

(2018) Hongyi Zhou et al.   Journal of Chemical Information and Modeling

Machine Learning Consensus Scoring Improves Performance Across Targets in Structure-Based Virtual Screening

(2017) Spencer S. Ericksen et al.   Journal of Chemical Information and Modeling

DockingApp: a user friendly interface for facilitated docking simulations with AutoDock Vina

(2017) Elena Di Muzio et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Recent Advances and Applications of Molecular Docking to G Protein-Coupled Receptors

(2017) Damian Bartuzi et al.   MOLECULES

LEADS-PEP: A Benchmark Data Set for Assessment of Peptide Docking Performance

(2016) Alexander Sebastian Hauser et al.   Journal of Chemical Information and Modeling

1001 Ways to run AutoDock Vina for virtual screening

(2016) Mohammad Mahdi Jaghoori et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Docking and ADMET prediction of few GSK-3 inhibitors divulges 6-bromoindirubin-3-oxime as a potential inhibitor

(2016) Chaluveelaveedu Murleedharan Nisha et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking

(2016) Shota Uehara et al.   MOLECULES

Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: the prediction accuracy of sampling power and scoring power

(2016) Zhe Wang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

AutoDock VinaXB: implementation of XBSF, new empirical halogen bond scoring function, into AutoDock Vina

(2016) Mathew R. Koebel et al.   Journal of Cheminformatics

vSDC: a method to improve early recognition in virtual screening when limited experimental resources are available

(2016) Ludovic Chaput et al.   Journal of Cheminformatics

Vinardo: A Scoring Function Based on Autodock Vina Improves Scoring, Docking, and Virtual Screening

(2016) Rodrigo Quiroga et al.   PLoS One

Receptor-based virtual screening protocol for drug discovery

(2015) Nuno M.F.S.A. Cerqueira et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Docking small peptides remains a great challenge: an assessment using AutoDock Vina

(2015) R. Rentzsch et al.   BRIEFINGS IN BIOINFORMATICS

DOCK 6: Impact of new features and current docking performance

(2015) William J. Allen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Comparing sixteen scoring functions for predicting biological activities of ligands for protein targets

(2015) Weijun Xu et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Molecular Docking and Structure-Based Drug Design Strategies

(2015) Leonardo Ferreira et al.   MOLECULES

MTiOpenScreen: a web server for structure-based virtual screening

(2015) Céline M. Labbé et al.   NUCLEIC ACIDS RESEARCH

AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility

(2015) Pradeep Anand Ravindranath et al.   PLoS Computational Biology

Drug repositioning by structure-based virtual screening

(2013) Dik-Lung Ma et al.   CHEMICAL SOCIETY REVIEWS

Protein-Ligand Docking in the New Millennium – A Retrospective of 10 Years in the Field

(2013) S.F. Sousa et al.   CURRENT MEDICINAL CHEMISTRY

Ligand Pose and Orientational Sampling in Molecular Docking

(2013) Ryan G. Coleman et al.   PLoS One

Structure-Based Virtual Screening for Drug Discovery: a Problem-Centric Review

(2012) Tiejun Cheng et al.   AAPS Journal

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

(2012) Michael M. Mysinger et al.   JOURNAL OF MEDICINAL CHEMISTRY

Quantifying Water-Mediated Protein–Ligand Interactions in a Glutamate Receptor: A DFT Study

(2011) Michelle A. Sahai et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Virtual Screening in Drug Design and Development

(2010) Sergio F. Sousa et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

Advances and Challenges in Protein-Ligand Docking

(2010) Sheng-You Huang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

(2009) Oleg Trott et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis

(2009) Sarah L. Kinnings et al.   PLoS Computational Biology

Flexible ligand docking to multiple receptor conformations: a practical alternative

(2008) Maxim Totrov et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY