标题
Key Topics in Molecular Docking for Drug Design
作者
关键词
-
出版物
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
Volume 20, Issue 18, Pages 4574
出版商
MDPI AG
发表日期
2019-09-16
DOI
10.3390/ijms20184574
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。- D3R Grand Challenge 3: blind prediction of protein–ligand poses and affinity rankings
- (2019) Zied Gaieb et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Ultra-large library docking for discovering new chemotypes
- (2019) Jiankun Lyu et al. NATURE
- Identification of New Potent Acetylcholinesterase Inhibitors Using Virtual Screening and In Vitro Approaches
- (2019) El Hassen Mokrani et al. Molecular Informatics
- Computationally driven discovery of phenyl(piperazin-1-yl)methanone derivatives as reversible monoacylglycerol lipase (MAGL) inhibitors
- (2019) Giulio Poli et al. JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY
- In Need of Bias Control: Evaluating Chemical Data for Machine Learning in Structure-Based Virtual Screening
- (2019) Jochen Sieg et al. Journal of Chemical Information and Modeling
- Virtual screening identifies a PIN1 inhibitor with possible antiovarian cancer effects
- (2019) Concetta Russo Spena et al. JOURNAL OF CELLULAR PHYSIOLOGY
- Combating Diseases with Computational Strategies Used for Drug Design and Discovery
- (2019) Farahnaz R. Makhouri et al. CURRENT TOPICS IN MEDICINAL CHEMISTRY
- CompScore: Boosting Structure-Based Virtual Screening Performance by Incorporating Docking Scoring Function Components into Consensus Scoring
- (2019) Yunierkis Perez-Castillo et al. Journal of Chemical Information and Modeling
- Ensemble Docking in Drug Discovery
- (2018) Rommie E. Amaro et al. BIOPHYSICAL JOURNAL
- A selective method for optimizing ensemble docking-based experiments on an InhA Fully-Flexible receptor model
- (2018) Renata De Paris et al. BMC BIOINFORMATICS
- Application of molecular docking for the degradation of organic pollutants in the environmental remediation: A review
- (2018) Zhifeng Liu et al. CHEMOSPHERE
- Structure based virtual screening of the Ebola virus trimeric glycoprotein using consensus scoring
- (2018) Abdulmujeeb T. Onawole et al. COMPUTATIONAL BIOLOGY AND CHEMISTRY
- When fragments link: a bibliometric perspective on the development of fragment-based drug discovery
- (2018) Angelo K.S. Romasanta et al. DRUG DISCOVERY TODAY
- Predictive Power of Different Types of Experimental Restraints in Small Molecule Docking: A Review
- (2018) Darwin Y. Fu et al. Journal of Chemical Information and Modeling
- KDEEP: Protein–Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks
- (2018) José Jiménez et al. Journal of Chemical Information and Modeling
- Consensus scoring model for the molecular docking study of mTOR kinase inhibitor
- (2018) Dong-Dong Li et al. JOURNAL OF MOLECULAR GRAPHICS & MODELLING
- A machine learning approach towards the prediction of protein–ligand binding affinity based on fundamental molecular properties
- (2018) Indra Kundu et al. RSC Advances
- Molecular Insights into the Interaction of RONS and Thieno[3,2-c]pyran Analogs with SIRT6/COX-2: A Molecular Dynamics Study
- (2018) Dharmendra K. Yadav et al. Scientific Reports
- Novel Consensus Docking Strategy to Improve Ligand Pose Prediction
- (2018) Xiaodong Ren et al. Journal of Chemical Information and Modeling
- Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges
- (2018) Duc Duy Nguyen et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Empirical Scoring Functions for Structure-Based Virtual Screening: Applications, Critical Aspects, and Challenges
- (2018) Isabella A. Guedes et al. Frontiers in Pharmacology
- Optimization of a fragment linking hit toward Dengue and Zika virus NS5 methyltransferases inhibitors
- (2018) Jessica Hernandez et al. EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
- A facile consensus ranking approach enhances virtual screening robustness and identifies a cell-active DYRK1α inhibitor
- (2018) Maria E Mavrogeni et al. Future Medicinal Chemistry
- Protein Family-Specific Models Using Deep Neural Networks and Transfer Learning Improve Virtual Screening and Highlight the Need for More Data
- (2018) Fergus Imrie et al. Journal of Chemical Information and Modeling
- A Membrane Protein Complex Docking Benchmark
- (2018) Panagiotis I. Koukos et al. JOURNAL OF MOLECULAR BIOLOGY
- Implicit-descriptor ligand-based virtual screening by means of collaborative filtering
- (2018) Raghuram Srinivas et al. Journal of Cheminformatics
- Task-Specific Scoring Functions for Predicting Ligand Binding Poses and Affinity and for Screening Enrichment
- (2017) Hossam M. Ashtawy 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
- Protein–Ligand Scoring with Convolutional Neural Networks
- (2017) Matthew Ragoza et al. Journal of Chemical Information and Modeling
- Fragment-Based Discovery and Optimization of Enzyme Inhibitors by Docking of Commercial Chemical Space
- (2017) Axel Rudling et al. JOURNAL OF MEDICINAL CHEMISTRY
- Dynamic Docking: A Paradigm Shift in Computational Drug Discovery
- (2017) Dario Gioia et al. MOLECULES
- Performance of machine-learning scoring functions in structure-based virtual screening
- (2017) Maciej Wójcikowski et al. Scientific Reports
- RADER: a RApid DEcoy Retriever to facilitate decoy based assessment of virtual screening
- (2016) Ling Wang et al. BIOINFORMATICS
- Fragment-based drug discovery of potent and selective MKK3/6 inhibitors
- (2016) Mark Adams et al. BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
- Enhancing Scoring Performance of Docking-Based Virtual Screening Through Machine Learning
- (2016) Cândida G. Silva et al. Current Bioinformatics
- Boosting Docking-Based Virtual Screening with Deep Learning
- (2016) Janaina Cruz Pereira et al. Journal of Chemical Information and Modeling
- Reliability analysis and optimization of the consensus docking approach for the development of virtual screening studies
- (2016) Giulio Poli et al. JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY
- Application of Fragment-Based de Novo Design to the Discovery of Selective Picomolar Inhibitors of Glycogen Synthase Kinase-3 Beta
- (2016) Hwangseo Park et al. JOURNAL OF MEDICINAL CHEMISTRY
- Identifying Interactions that Determine Fragment Binding at Protein Hotspots
- (2016) Chris J. Radoux et al. JOURNAL OF MEDICINAL CHEMISTRY
- Empirical Scoring Functions for Affinity Prediction of Protein-ligand Complexes
- (2016) Lukas P. Pason et al. Molecular Informatics
- Computational protein–ligand docking and virtual drug screening with the AutoDock suite
- (2016) Stefano Forli et al. Nature Protocols
- CSM-lig: a web server for assessing and comparing protein–small molecule affinities
- (2016) Douglas E.V. Pires et al. NUCLEIC ACIDS RESEARCH
- 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
- Insights into regioselective metabolism of mefenamic acid by cytochrome P450 BM3 mutants through crystallography, docking, molecular dynamics, and free energy calculations
- (2016) Luigi Capoferri et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- vSDC: a method to improve early recognition in virtual screening when limited experimental resources are available
- (2016) Ludovic Chaput et al. Journal of Cheminformatics
- Identification of DNA primase inhibitors via a combined fragment-based and virtual screening
- (2016) Stefan Ilic et al. Scientific Reports
- Machine learning in computational docking
- (2015) Mohamed A. Khamis et al. ARTIFICIAL INTELLIGENCE IN MEDICINE
- A potent and selective inhibitor for the UBLCP1 proteasome phosphatase
- (2015) Yantao He et al. BIOORGANIC & MEDICINAL CHEMISTRY
- Machine-learning scoring functions for identifying native poses of ligands docked to known and novel proteins
- (2015) Hossam M Ashtawy et al. BMC BIOINFORMATICS
- A Comparative Assessment of Predictive Accuracies of Conventional and Machine Learning Scoring Functions for Protein-Ligand Binding Affinity Prediction
- (2015) Hossam M. Ashtawy et al. IEEE-ACM Transactions on Computational Biology and Bioinformatics
- Comparative Modeling and Benchmarking Data Sets for Human Histone Deacetylases and Sirtuin Families
- (2015) Jie Xia et al. Journal of Chemical Information and Modeling
- Structural Insight into Tetrameric hTRPV1 from Homology Modeling, Molecular Docking, Molecular Dynamics Simulation, Virtual Screening, and Bioassay Validations
- (2015) Zhiwei Feng et al. Journal of Chemical Information and Modeling
- Neural-Network Scoring Functions Identify Structurally Novel Estrogen-Receptor Ligands
- (2015) Jacob D. Durrant 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
- Updates to the Integrated Protein–Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2
- (2015) Thom Vreven et al. JOURNAL OF MOLECULAR BIOLOGY
- Improving AutoDock Vina Using Random Forest: The Growing Accuracy of Binding Affinity Prediction by the Effective Exploitation of Larger Data Sets
- (2015) Hongjian Li et al. Molecular Informatics
- PubChem Substance and Compound databases
- (2015) Sunghwan Kim et al. NUCLEIC ACIDS RESEARCH
- MLViS: A Web Tool for Machine Learning-Based Virtual Screening in Early-Phase of Drug Discovery and Development
- (2015) Selcuk Korkmaz et al. PLoS One
- Predictiveness curves in virtual screening
- (2015) Charly Empereur-mot et al. Journal of Cheminformatics
- Machine-learning scoring functions to improve structure-based binding affinity prediction and virtual screening
- (2015) Qurrat Ul Ain et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- Creating Novel Activated Factor XI Inhibitors through Fragment Based Lead Generation and Structure Aided Drug Design
- (2015) Ola Fjellström et al. PLoS One
- Increasing Chemical Space Coverage by Combining Empirical and Computational Fragment Screens
- (2014) Sarah Barelier et al. ACS Chemical Biology
- Synthesis, Biological Evaluation, and Computational Studies of Tri- and Tetracyclic Nitrogen-Bridgehead Compounds as Potent Dual-Acting AChE Inhibitors and hH3 Receptor Antagonists
- (2014) Fouad H. Darras et al. ACS Chemical Neuroscience
- Improved protein–ligand binding affinity prediction by using a curvature-dependent surface-area model
- (2014) Yang Cao et al. BIOINFORMATICS
- Discovery of BRD4 bromodomain inhibitors by fragment-based high-throughput docking
- (2014) Hongtao Zhao et al. BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
- Integrating docking scores, interaction profiles and molecular descriptors to improve the accuracy of molecular docking: Toward the discovery of novel Akt1 inhibitors
- (2014) Wenhu Zhan et al. EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
- A dynamic niching genetic algorithm strategy for docking highly flexible ligands
- (2014) Camila Silva de Magalhães et al. INFORMATION SCIENCES
- Does a More Precise Chemical Description of Protein–Ligand Complexes Lead to More Accurate Prediction of Binding Affinity?
- (2014) Pedro J. Ballester et al. Journal of Chemical Information and Modeling
- Extensive Consensus Docking Evaluation for Ligand Pose Prediction and Virtual Screening Studies
- (2014) Tiziano Tuccinardi et al. Journal of Chemical Information and Modeling
- A comparative study of family-specific protein–ligand complex affinity prediction based on random forest approach
- (2014) Yu Wang et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- NRLiSt BDB, the Manually Curated Nuclear Receptors Ligands and Structures Benchmarking Database
- (2014) Nathalie Lagarde et al. JOURNAL OF MEDICINAL CHEMISTRY
- Recent improvements to Binding MOAD: a resource for protein–ligand binding affinities and structures
- (2014) Aqeel Ahmed et al. NUCLEIC ACIDS RESEARCH
- Combining Machine Learning Systems and Multiple Docking Simulation Packages to Improve Docking Prediction Reliability for Network Pharmacology
- (2014) Kun-Yi Hsin et al. PLoS One
- The use of virtual screening and differential scanning fluorimetry for the rapid identification of fragments active against MEK1
- (2013) Kwame Amaning et al. BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
- Fragment-based hit identification: thinking in 3D
- (2013) Andrew D. Morley et al. DRUG DISCOVERY TODAY
- Computation of Binding Energies Including Their Enthalpy and Entropy Components for Protein–Ligand Complexes Using Support Vector Machines
- (2013) Chaitanya A. K. Koppisetty et al. Journal of Chemical Information and Modeling
- Binding Affinity Prediction for Protein–Ligand Complexes Based on β Contacts and B Factor
- (2013) Qian Liu et al. Journal of Chemical Information and Modeling
- ID-Score: A New Empirical Scoring Function Based on a Comprehensive Set of Descriptors Related to Protein–Ligand Interactions
- (2013) Guo-Bo Li et al. Journal of Chemical Information and Modeling
- SFCscoreRF: A Random Forest-Based Scoring Function for Improved Affinity Prediction of Protein–Ligand Complexes
- (2013) David Zilian et al. Journal of Chemical Information and Modeling
- Evaluation and Optimization of Virtual Screening Workflows with DEKOIS 2.0 – A Public Library of Challenging Docking Benchmark Sets
- (2013) Matthias R. Bauer et al. Journal of Chemical Information and Modeling
- CSAR Data Set Release 2012: Ligands, Affinities, Complexes, and Docking Decoys
- (2013) James B. Dunbar et al. Journal of Chemical Information and Modeling
- Consensus Docking: Improving the Reliability of Docking in a Virtual Screening Context
- (2013) Douglas R. Houston et al. Journal of Chemical Information and Modeling
- Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise
- (2013) David Ryan Koes et al. Journal of Chemical Information and Modeling
- Latest developments in molecular docking: 2010-2011 in review
- (2013) Elizabeth Yuriev et al. JOURNAL OF MOLECULAR RECOGNITION
- The 'rule of three' for fragment-based drug discovery: where are we now?
- (2013) Harren Jhoti et al. NATURE REVIEWS DRUG DISCOVERY
- Optimization of molecular docking scores with support vector rank regression
- (2013) Wei Wang et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- wFReDoW: A Cloud-Based Web Environment to Handle Molecular Docking Simulations of a Fully Flexible Receptor Model
- (2013) Renata De Paris et al. Biomed Research International
- Fragment-Based Approaches in Drug Discovery and Chemical Biology
- (2012) Duncan E. Scott et al. BIOCHEMISTRY
- DecoyFinder: an easy-to-use python GUI application for building target-specific decoy sets
- (2012) Adrià Cereto-Massagué et al. BIOINFORMATICS
- Potential and Limitations of Ensemble Docking
- (2012) Oliver Korb et al. Journal of Chemical Information and Modeling
- Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking
- (2012) Michael M. Mysinger et al. JOURNAL OF MEDICINAL CHEMISTRY
- H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations
- (2012) R. Anandakrishnan et al. NUCLEIC ACIDS RESEARCH
- Application of Consensus Scoring and Principal Component Analysis for Virtual Screening against β-Secretase (BACE-1)
- (2012) Shu Liu et al. PLoS One
- Avogadro: an advanced semantic chemical editor, visualization, and analysis platform
- (2012) Marcus D Hanwell et al. Journal of Cheminformatics
- Molecular complexity and fragment-based drug discovery: ten years on
- (2011) Andrew R Leach et al. CURRENT OPINION IN CHEMICAL BIOLOGY
- Support Vector Regression Scoring of Receptor–Ligand Complexes for Rank-Ordering and Virtual Screening of Chemical Libraries
- (2011) Liwei Li et al. Journal of Chemical Information and Modeling
- DEKOIS: Demanding Evaluation Kits for Objectivein SilicoScreening — A Versatile Tool for Benchmarking Docking Programs and Scoring Functions
- (2011) Simon M. Vogel et al. Journal of Chemical Information and Modeling
- CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring Functions
- (2011) Richard D. Smith et al. Journal of Chemical Information and Modeling
- A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing
- (2011) Sarah L. Kinnings et al. Journal of Chemical Information and Modeling
- Ligand and Decoy Sets for Docking to G Protein-Coupled Receptors
- (2011) Edgar A. Gatica et al. Journal of Chemical Information and Modeling
- Virtual Decoy Sets for Molecular Docking Benchmarks
- (2011) Izhar Wallach et al. Journal of Chemical Information and Modeling
- FRED Pose Prediction and Virtual Screening Accuracy
- (2011) Mark McGann Journal of Chemical Information and Modeling
- Combining Global and Local Measures for Structure-Based Druggability Predictions
- (2011) Andrea Volkamer et al. Journal of Chemical Information and Modeling
- CSCORE: A SIMPLE YET EFFECTIVE SCORING FUNCTION FOR PROTEIN–LIGAND BINDING AFFINITY PREDICTION USING MODIFIED CMAC LEARNING ARCHITECTURE
- (2011) XUCHANG OUYANG et al. Journal of Bioinformatics and Computational Biology
- A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking
- (2010) Pedro J. Ballester et al. BIOINFORMATICS
- NNScore: A Neural-Network-Based Scoring Function for the Characterization of Protein−Ligand Complexes
- (2010) Jacob D. Durrant et al. Journal of Chemical Information and Modeling
- Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database
- (2010) Dariusz Plewczynski et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- VoteDock: Consensus docking method for prediction of protein-ligand interactions
- (2010) Dariusz Plewczynski et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Virtual Screening for HIV Protease Inhibitors: A Comparison of AutoDock 4 and Vina
- (2010) Max W. Chang et al. PLoS One
- Maximum Unbiased Validation (MUV) Data Sets for Virtual Screening Based on PubChem Bioactivity Data
- (2009) Sebastian G. Rohrer et al. Journal of Chemical Information and Modeling
- 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
- Fragment-based ligand discovery
- (2009) M. Fischer et al. MOLECULAR INTERVENTIONS
- Molecular docking and ligand specificity in fragment-based inhibitor discovery
- (2009) Yu Chen et al. Nature Chemical Biology
- Flexible ligand docking to multiple receptor conformations: a practical alternative
- (2008) Maxim Totrov et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection?
- (2008) Andrew C. Good et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection—What can we learn from earlier mistakes?
- (2008) Johannes Kirchmair et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Community benchmarks for virtual screening
- (2008) John J. Irwin JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go
- (2007) N Moitessier et al. BRITISH JOURNAL OF PHARMACOLOGY
- On Evaluating Molecular-Docking Methods for Pose Prediction andEnrichment Factors. [J. Chem. Inf. Model.46, 401−415 (2006)] by
- (2007) Timothy Lovell et al. Journal of Chemical Information and Modeling
Find the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
SearchAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now