标题
MetaDOCK: A Combinatorial Molecular Docking Approach
作者
关键词
-
出版物
ACS Omega
Volume -, Issue -, Pages -
出版商
American Chemical Society (ACS)
发表日期
2023-02-01
DOI
10.1021/acsomega.2c07619
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- Benchmarking the Ability of Common Docking Programs to Correctly Reproduce and Score Binding Modes in SARS-CoV-2 Protease Mpro
- (2021) Shani Zev et al. Journal of Chemical Information and Modeling
- gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS
- (2021) Mario S. Valdés-Tresanco et al. Journal of Chemical Theory and Computation
- End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design
- (2019) Ercheng Wang et al. CHEMICAL REVIEWS
- Molecular Docking: Shifting Paradigms in Drug Discovery
- (2019) Luca Pinzi et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- Comparative Assessment of Seven Docking Programs on a Nonredundant Metalloprotein Subset of the PDBbind Refined
- (2019) Süleyman Selim Çınaroğlu et al. Journal of Chemical Information and Modeling
- Inhibition activities of catechol diether based non-nucleoside inhibitors against the HIV reverse transcriptase variants: Insights from molecular docking and ONIOM calculations
- (2017) Pabitra Narayan Samanta et al. JOURNAL OF MOLECULAR GRAPHICS & MODELLING
- Identification of potential inhibitors against the Zika virus using consensus scoring
- (2017) Abdulmujeeb T. Onawole et al. JOURNAL OF MOLECULAR GRAPHICS & MODELLING
- Identification of new 2,5-diketopiperazine derivatives as simultaneous effective inhibitors of αβ-tubulin and BCRP proteins: Molecular docking, Structure−Activity Relationships and virtual consensus docking studies
- (2017) Najmeh Fani et al. JOURNAL OF MOLECULAR STRUCTURE
- Efficient conformational sampling and weak scoring in docking programs? Strategy of the wisdom of crowds
- (2017) Ludovic Chaput et al. Journal of Cheminformatics
- Prediction of Protein–Ligand Binding Poses via a Combination of Induced Fit Docking and Metadynamics Simulations
- (2016) Anthony J. Clark et al. Journal of Chemical Theory and Computation
- The “Gatekeeper” Residue Influences the Mode of Binding of Acetyl Indoles to Bromodomains
- (2016) Andrea Unzue et al. JOURNAL OF MEDICINAL CHEMISTRY
- Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein–Ligand Binding Free Energy
- (2016) Lili Duan et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- 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
- The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities
- (2015) Samuel Genheden et al. Expert Opinion on Drug Discovery
- POSIT: Flexible Shape-Guided Docking For Pose Prediction
- (2015) Brian P. Kelley et al. Journal of Chemical Information and Modeling
- DOCK 6: Impact of new features and current docking performance
- (2015) William J. Allen et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Beware of docking!
- (2015) Yu-Chian Chen TRENDS IN PHARMACOLOGICAL SCIENCES
- Extensive Consensus Docking Evaluation for Ligand Pose Prediction and Virtual Screening Studies
- (2014) Tiziano Tuccinardi et al. Journal of Chemical Information and Modeling
- Efficient calculation of relative binding free energies by umbrella sampling perturbation
- (2014) Fabian Zeller et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids
- (2014) Sergio Ruiz-Carmona et al. PLoS Computational Biology
- Discovery of ZAP70 inhibitors by high-throughput docking into a conformation of its kinase domain generated by molecular dynamics
- (2013) Hongtao Zhao et al. BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
- Automated Large-Scale File Preparation, Docking, and Scoring: Evaluation of ITScore and STScore Using the 2012 Community Structure–Activity Resource Benchmark
- (2013) Sam Z. Grinter et al. Journal of Chemical Information and Modeling
- CSAR Benchmark Exercise 2011–2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series
- (2013) Kelly L. Damm-Ganamet et al. Journal of Chemical Information and Modeling
- Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery
- (2012) Xuan-Yu Meng et al. Current Computer-Aided Drug Design
- FIPSDock: A new molecular docking technique driven by fully informed swarm optimization algorithm
- (2012) Yu Liu et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Variability in docking success rates due to dataset preparation
- (2012) Christopher R. Corbeil et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Surflex-Dock: Docking benchmarks and real-world application
- (2012) Russell Spitzer et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Docking and scoring with ICM: the benchmarking results and strategies for improvement
- (2012) Marco A. C. Neves et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking
- (2012) Michael M. Mysinger et al. JOURNAL OF MEDICINAL CHEMISTRY
- FRED Pose Prediction and Virtual Screening Accuracy
- (2011) Mark McGann Journal of Chemical Information and Modeling
- SwissDock, a protein-small molecule docking web service based on EADock DSS
- (2011) A. Grosdidier et al. NUCLEIC ACIDS RESEARCH
- Metadynamics
- (2011) Alessandro Barducci et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database
- (2010) Dariusz Plewczynski et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Assessing the Stability of Alzheimer’s Amyloid Protofibrils Using Molecular Dynamics
- (2010) Justin A. Lemkul et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Empirical Scoring Functions for Advanced Protein−Ligand Docking with PLANTS
- (2009) Oliver Korb et al. Journal of Chemical Information and Modeling
- 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
- Medicinal Chemistry and the Molecular Operating Environment (MOE): Application of QSAR and Molecular Docking to Drug Discovery
- (2008) Santiago Vilar et al. CURRENT TOPICS IN MEDICINAL CHEMISTRY
Discover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversationAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started