Research graph
References from Docking-generated multiple ligand poses for bootstrapping bioactivity classifying Machine Learning: Repurposing covalent inhibitors for COVID-19-related TMPRSS2 as case study. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1093/bib/bbp023
10.1093/bib/bbp023 · External reference
Binding Affinity via Docking: Fact and Fiction
10.3390/molecules23081899 · 2018 · External reference
10.1021/ar800236t
10.1021/ar800236t · External reference
10.3390/ijms20184331
10.3390/ijms20184331 · External reference
Task-Specific Scoring Functions for Predicting Ligand Binding Poses and Affinity and for Screening Enrichment
10.1021/acs.jcim.7b00309 · 2017 · External reference
10.1039/d0ob02273j
10.1039/d0ob02273j · External reference
10.1021/jm001044l
10.1021/jm001044l · External reference
High-Throughput Docking Using Quantum Mechanical Scoring
10.3389/fchem.2020.00246 · 2020 · External reference
Virtual Screening with AutoDock: Theory and Practice
10.1517/17460441.2010.484460 · 2010 · External reference
10.1023/a:1007996124545
10.1023/a:1007996124545 · External reference
10.1023/a:1011115820450
10.1023/a:1011115820450 · External reference
Reduced Dimensionality in Ligand—Protein Structure Prediction: Covalent Inhibitors of Serine Proteases and Design of Site-Directed Combinatorial Libraries
10.1021/bk-1999-0719.ch019 · 1999 · External reference
10.1006/jmbi.1999.3371
10.1006/jmbi.1999.3371 · External reference
10.1021/jm030644s
10.1021/jm030644s · External reference
10.1007/bf00124474
10.1007/bf00124474 · External reference
LigScore: a novel scoring function for predicting binding affinities
10.1016/j.jmgm.2004.11.007 · 2005 · External reference
10.1007/s10822-020-00329-7
10.1007/s10822-020-00329-7 · External reference
An Overview of Scoring Functions Used for Protein-Ligand Interactions in Molecular Docking
2019 · External reference
Prediction of ligand binding mode among multiple cross-docking poses by molecular dynamics simulations
10.1007/s10822-020-00340-y · 2020 · External reference
10.1007/s10822-010-9363-3
10.1007/s10822-010-9363-3 · External reference
10.1007/0-306-46883-2_7
10.1007/0-306-46883-2_7 · External reference
Effect of ligand volume correction on PMF scoring
10.1002/1096-987x(200103)22:4<418::aid-jcc1012>3.0.co;2-3 · 2001 · External reference
PMF Scoring Revisited
10.1021/jm050038s · 2006 · External reference
10.1021/jm980536j
10.1021/jm980536j · External reference
Protein-ligand Docking: A Review of Recent Advances and Future Perspectives
10.2174/157341208783497597 · 2008 · External reference
Validation Studies of the Site-Directed Docking Program LibDock
10.1021/ci6004299 · 2007 · External reference
10.1006/jmbi.1996.0477
10.1006/jmbi.1996.0477 · External reference
10.2142/biophysico.13.0_181
10.2142/biophysico.13.0_181 · External reference
Advances in Docking
10.2174/0929867325666180904115000 · 2020 · External reference
10.1007/s008940050096 · 1998 · Admitted local publication
10.1023/a:1007999920146
10.1023/a:1007999920146 · External reference
Ranking poses in structure-based lead discovery and optimization: current trends in scoring function development
2007 · External reference
Unresolved reference
External reference
Prediction of Protein−Ligand Interactions. Docking and Scoring: Successes and Gaps
10.1021/jm060999m · 2006 · External reference
Impact of Scoring Functions on Enrichment in Docking-Based Virtual Screening: An Application Study on Renin Inhibitors†
10.1021/ci0342728 · 2004 · External reference
10.1016/j.drudis.2006.05.012
10.1016/j.drudis.2006.05.012 · External reference
10.1002/jcc.21303
10.1002/jcc.21303 · External reference
Docking-Based Comparative Intermolecular Contacts Analysis as New 3-D QSAR Concept for Validating Docking Studies and in Silico Screening: NMT and GP Inhibitors as Case Studies
10.1021/ci100368t · 2011 · External reference
Combining docking-based comparative intermolecular contacts analysis and k-nearest neighbor correlation for the discovery of new check point kinase 1 inhibitors
10.1007/s10822-015-9848-1 · 2015 · External reference
The use of docking-based comparative intermolecular contacts analysis to identify optimal docking conditions within glucokinase and to discover of new GK activators
10.1007/s10822-014-9740-4 · 2014 · External reference
Application of docking-based comparative intermolecular contacts analysis to validate Hsp90α docking studies and subsequent in silico screening for inhibitors
10.1007/s00894-012-1479-z · 2012 · External reference
Combining molecular dynamics simulation and ligand-receptor contacts analysis as a new approach for pharmacophore modeling: beta-secretase 1 and check point kinase 1 as case studies
10.1007/s10822-016-9984-2 · 2016 · External reference
Simulated annealing molecular dynamics and ligand–receptor contacts analysis for pharmacophore modeling. Future
2017 · External reference
Combining Stochastic Deformation/Relaxation and Intermolecular Contacts Analysis for Extracting Pharmacophores from Ligand-Receptor Complexes
10.1021/acs.jcim.7b00708 · 2018 · External reference
Does a more precise chemical description of protein-ligand complexes lead to more accurate prediction of binding affinity?
10.1021/ci500091r · 2014 · External reference
Structural protein-ligand interaction fingerprints (SPLIF) for structure-based virtual screening: method and benchmark study
10.1021/ci500319f · 2014 · External reference
Structural Interaction Fingerprint (SIFt): A Novel Method for Analyzing Three-Dimensional Protein−Ligand Binding Interactions
10.1021/jm030331x · 2004 · External reference
Expanded Interaction Fingerprint Method for Analyzing Ligand Binding Modes in Docking and Structure-Based Drug Design
10.1021/ci049870g · 2004 · External reference
10.1021/acs.jcim.6b00314
10.1021/acs.jcim.6b00314 · External reference
Knowledge-Based Interaction Fingerprint Scoring: A Simple Method for Improving the Effectiveness of Fast Scoring Functions
10.1021/ci050420d · 2006 · External reference
APIF: A New Interaction Fingerprint Based on Atom Pairs and Its Application to Virtual Screening
10.1021/ci900043r · 2009 · External reference
Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints
10.1021/ci600342e · 2006 · External reference
10.1186/s13321-018-0302-y
10.1186/s13321-018-0302-y · External reference
Discovery of Subtype Selective Janus Kinase (JAK) Inhibitors by Structure-Based Virtual Screening
10.1021/acs.jcim.5b00634 · 2015 · External reference
10.1098/rsta.2012.0222
10.1098/rsta.2012.0222 · External reference
Artificial intelligence for decision making in the era of Big Data – evolution, challenges and research agenda
2019 · External reference
10.1016/j.drudis.2019.07.006
10.1016/j.drudis.2019.07.006 · External reference
Deep Learning in Medical Imaging: General Overview
10.3348/kjr.2017.18.4.570 · 2017 · External reference
PanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome
10.1186/s12859-019-2713-9 · 2019 · External reference
10.1093/bioinformatics/btaa119
10.1093/bioinformatics/btaa119 · External reference
10.1038/s41573-019-0024-5
10.1038/s41573-019-0024-5 · External reference
10.1007/s11427-018-9342-2
10.1007/s11427-018-9342-2 · External reference
Deep learning and virtual drug screening
10.4155/fmc-2018-0314 · 2018 · External reference
Unsupervised Spectral-Spatial Feature Learning With Stacked Sparse Autoencoder for Hyperspectral Imagery Classification
10.1109/lgrs.2015.2482520 · 2015 · External reference
10.1016/j.drudis.2008.03.022
10.1016/j.drudis.2008.03.022 · External reference
Feature extraction and I-NB classification of CT images for early lung cancer detection
2020 · External reference
Machine-learning approaches in drug discovery: methods and applications
10.1016/j.drudis.2014.10.012 · 2015 · External reference
Naive Bayes: applications, variations and vulnerabilities: a review of literature with code snippets for implementation
2020 · External reference
Unresolved reference
2017 · External reference
10.1016/b978-0-12-813314-9.00002-5
10.1016/b978-0-12-813314-9.00002-5 · 2018 · External reference
Unresolved reference
External reference
Support vector machines for drug discovery
10.1517/17460441.2014.866943 · 2013 · External reference
Ligand based virtual screening using SVM on GPU
10.1016/j.compbiolchem.2019.107143 · 2019 · External reference
A probabilistic neural network approach for modeling and classification of bacterial growth/no-growth data
10.1016/s0167-7012(02)00080-5 · 2002 · External reference
Diagnosing Breast Cancer Type by Using Probabilistic Neural Network in Decision Support System
10.18178/ijke.2016.2.1.056 · 2016 · External reference
Application of probabilistic neural networks in modelling structural deterioration of stormwater pipes
10.1080/15730620600961684 · 2006 · External reference
Unresolved reference
2008 · External reference
Data mining applications in healthcare
2005 · External reference
Unresolved reference
External reference
Unresolved reference
2000 · External reference
Unresolved reference
2011 · External reference
Bootstrapping the out-of-sample predictions for efficient and accurate cross-validation
10.1007/s10994-018-5714-4 · 2018 · External reference
Classifier performance estimation under the constraint of a finite sample size: resampling schemes applied to neural network classifiers
10.1016/j.neunet.2007.12.012 · 2008 · External reference
10.1113/jphysiol.2012.239376
10.1113/jphysiol.2012.239376 · External reference
10.1016/j.antiviral.2013.08.015
10.1016/j.antiviral.2013.08.015 · External reference
10.1016/j.cell.2020.02.052
10.1016/j.cell.2020.02.052 · External reference
Targeting Novel Coronavirus 2019: A Systematic Drug Repurposing Approach to Identify Promising Inhibitors Against 3C-like Proteinase and 2'-O-Ribose Methyltransferase
2020 · External reference
10.1016/j.coviro.2017.03.018
10.1016/j.coviro.2017.03.018 · External reference
10.1016/j.csbj.2020.08.016
10.1016/j.csbj.2020.08.016 · External reference
Identification of the first synthetic inhibitors of the type II transmembrane serine protease TMPRSS2 suitable for inhibition of influenza virus activation
10.1042/bj20130101 · 2013 · External reference
PolypharmDB, a deep learning-based resource, quickly identifies repurposed drug candidates for COVID-19
2020 · External reference
Homology Modeling of TMPRSS2 Yields Candidate Drugs That May Inhibit Entry of SARS-CoV-2 into Human Cells
2020 · External reference
10.1136/jclinpath-2020-206987
10.1136/jclinpath-2020-206987 · External reference
Unresolved reference
External reference
Potential Therapeutic Targeting of Coronavirus Spike Glycoprotein Priming
10.3390/molecules25102424 · 2020 · External reference
Recent progress on inhibitors of the type II transmembrane serine proteases, hepsin, matriptase and matriptase-2
10.4155/fmc-2018-0446 · 2019 · External reference
Identification of Nafamostat as a Potent Inhibitor of Middle East Respiratory Syndrome Coronavirus S Protein-Mediated Membrane Fusion Using the Split-Protein-Based Cell-Cell Fusion Assay
10.1128/aac.01043-16 · 2016 · External reference
10.1002/iub.186
10.1002/iub.186 · External reference
Nafamostat Mesylate Blocks Activation of SARS-CoV-2: New Treatment Option for COVID-19
10.1128/aac.00754-20 · 2020 · External reference
Unresolved reference
2020 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
10.1002/anie.201601091
10.1002/anie.201601091 · External reference
Serine proteases: how did chemists tease out their catalytic mechanism?
10.1007/s40828-019-0093-4 · 2019 · External reference
10.1517/17460441.2012.688744
10.1517/17460441.2012.688744 · External reference
10.1021/cr010182v
10.1021/cr010182v · External reference
10.1039/c7sc02941a
10.1039/c7sc02941a · External reference
10.1038/nchembio.1582
10.1038/nchembio.1582 · External reference
10.1016/j.chembiol.2020.07.008
10.1016/j.chembiol.2020.07.008 · External reference
10.1021/jm8002075
10.1021/jm8002075 · External reference
10.1021/jm501371s
10.1021/jm501371s · External reference
10.1038/nrd3620
10.1038/nrd3620 · External reference
Targeting biomolecules with reversible covalent chemistry
10.1016/j.cbpa.2016.08.011 · 2016 · External reference
10.1002/edm2.2
10.1002/edm2.2 · External reference
A comparative study of the binding modes of recently launched dipeptidyl peptidase IV inhibitors in the active site
10.1016/j.bbrc.2013.03.010 · 2013 · External reference
10.1039/c9cs00720b
10.1039/c9cs00720b · External reference
10.1073/pnas.0901982106
10.1073/pnas.0901982106 · External reference
10.1038/nature06782
10.1038/nature06782 · External reference
10.1039/b718357g
10.1039/b718357g · External reference
Microwave-Assisted Metal-Free Decarboxylative Iodination/Bromination of Isoxazole-4-carboxylic Acids
10.1002/ajoc.201900572 · 2019 · External reference
Furazan and furoxan sulfonamides are strong α-carbonic anhydrase inhibitors and potential antiglaucoma agents
10.1016/j.bmc.2014.06.016 · 2014 · External reference
Synthesis and binding affinity of new muscarinic ligands structurally related to oxotremorine
10.1016/s0960-894x(97)00150-9 · 1997 · External reference
Synthesis of 3,4,5-Trisubstituted Isoxazoles from Morita-Baylis-Hillman Acetates by an NaNO2/I2-Mediated Domino Reaction
10.1002/ange.201504529 · 2015 · External reference
10.1016/j.ejmech.2016.07.039
10.1016/j.ejmech.2016.07.039 · External reference
Emerging and Re-Emerging Warheads for Targeted Covalent Inhibitors: Applications in Medicinal Chemistry and Chemical Biology
10.1021/acs.jmedchem.8b01153 · 2018 · External reference
Synthesis, structural characterization and cytotoxic activity of heterocyclic compounds containing the furoxan ring
10.24820/ark.5550190.p010.229 · 2017 · External reference
Nitro-Group-Containing Drugs
10.1021/acs.jmedchem.8b00147 · 2018 · External reference
Multidirectional Efficacy of Biologically Active Nitro Compounds Included in Medicines
10.3390/ph11020054 · 2018 · External reference
The Nitro Group as a Masked Electrophile in Covalent Enzyme Inhibition
10.1021/acschembio.8b00225 · 2018 · External reference
10.1021/acs.biochem.9b00293
10.1021/acs.biochem.9b00293 · External reference
Studies on furan derivatives.XIV. Nucleophilic substitution of methyl 5-nitro-2-furancarboxylate and 5-Nitrofuran-2-nitrile
10.1002/jhet.5570230443 · 1986 · External reference
A new general synthesis of functionally substituted pyrazolo[1,5-a]pyrimidines
10.1016/j.mencom.2019.07.025 · 2019 · External reference
10.1021/ja5112964
10.1021/ja5112964 · External reference
10.1074/jbc.m805262200
10.1074/jbc.m805262200 · External reference
Active site conformational changes of prostasin provide a new mechanism of protease regulation by divalent cations
10.1002/pro.118 · 2009 · External reference
Synthesis and structure-activity relationships of small-molecular di-basic esters, amides and carbamates as flaviviral protease inhibitors
10.1016/j.ejmech.2019.05.025 · 2019 · External reference
10.1016/s0969-2126(03)00148-5
10.1016/s0969-2126(03)00148-5 · External reference
Molecular mechanism of inhibiting the SARS-CoV-2 cell entry facilitator TMPRSS2 with camostat and nafamostat
10.1039/d0sc05064d · 2021 · External reference
The Kinetic and Structural Characterization of the Reaction of Nafamostat with Bovine Pancreatic Trypsin
10.1016/s0049-3848(00)00206-1 · 2000 · External reference
Crystal Structure of Serine protease Hepsin in complex with Inhibitor
10.2210/pdb5ce1/pdb · 2016 · External reference
BLAST+: architecture and applications
2009 · External reference
10.1038/nmeth.1818
10.1038/nmeth.1818 · External reference
10.1093/nar/gky427
10.1093/nar/gky427 · External reference
10.1002/elps.200900140
10.1002/elps.200900140 · External reference
10.1002/pro.3330
10.1002/pro.3330 · External reference
Structure validation by Cα geometry: ϕ, ψ and Cβ deviation
10.1002/prot.10286 · 2003 · External reference
10.1002/1097-0134(20010501)43:2<113::aid-prot1023>3.0.co;2-t
10.1002/1097-0134(20010501)43:2<113::aid-prot1023>3.0.co;2-t · External reference
LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites
10.1016/s1093-3263(02)00164-x · 2003 · External reference
Detailed analysis of grid-based molecular docking: A case study of CDOCKER?A CHARMm-based MD docking algorithm
10.1002/jcc.10306 · 2003 · External reference
Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm
10.1002/jcc.10306 · 2003 · External reference
Reduced Dimensionality in Ligand—Protein Structure Prediction: Covalent Inhibitors of Serine Proteases and Design of Site-Directed Combinatorial
1999 · External reference
10.1021/jm980536j
10.1021/jm980536j · External reference
10.1007/0-306-46883-2_7
10.1007/0-306-46883-2_7 · 2002 · External reference
10.1016/s1093-3263(01)00125-5
10.1016/s1093-3263(01)00125-5 · External reference
10.1016/j.drudis.2006.03.009
10.1016/j.drudis.2006.03.009 · External reference
10.1093/nar/gkw1132
10.1093/nar/gkw1132 · External reference
10.1093/bioinformatics/btz828
10.1093/bioinformatics/btz828 · External reference
10.1038/s41598-017-09654-8
10.1038/s41598-017-09654-8 · External reference
Bioactive Molecule Prediction Using Extreme Gradient Boosting
10.3390/molecules21080983 · 2016 · External reference
Unresolved reference
External reference
Probabilistic neural network for evaluating seismic liquefaction potential
10.1139/t01-073 · 2002 · External reference
10.1016/j.compbiomed.2009.11.014
10.1016/j.compbiomed.2009.11.014 · External reference
Development of novel in silico prediction model for drug-induced ototoxicity by using naive Bayes classifier approach
10.1016/j.tiv.2020.104812 · 2020 · External reference
Machine-learning approaches in drug discovery: methods and applications
10.1016/j.drudis.2014.10.012 · 2015 · External reference
Naive Bayes: applications, variations and vulnerabilities: a review of literature with code snippets for implementation
2020 · External reference
Feature extraction and I-NB classification of CT images for early lung cancer detection
2020 · External reference
Unresolved reference
External reference
Support vector machines for drug discovery
10.1517/17460441.2014.866943 · 2013 · External reference
10.1021/jm049092j
10.1021/jm049092j · External reference
Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection–what can we learn from earlier mistakes?
10.1007/s10822-007-9163-6 · 2008 · External reference
Pharmacophore features for machine learning in pharmaceutical virtual screening
10.1007/s11030-019-09961-4 · 2020 · External reference
Interrater reliability: the kappa statistic
10.11613/bm.2012.031 · 2012 · External reference
Applications of machine learning techniques to predict filariasis using socio-economic factors
10.1017/s0950268819001481 · 2019 · External reference
10.1007/s11222-016-9696-4
10.1007/s11222-016-9696-4 · External reference
10.1021/ci500118s
10.1021/ci500118s · External reference
10.2307/2529310
10.2307/2529310 · External reference
10.1016/j.cbi.2019.06.028
10.1016/j.cbi.2019.06.028 · External reference
10.1039/d0ob02273j
10.1039/d0ob02273j · External reference
4D- quantitative structure–activity relationship modeling: making a comeback
10.1080/17460441.2019.1664467 · 2019 · External reference
SCRAMBLE 'N' GAMBLE: a tool for fast and facile generation of random data for statistical evaluation of QSAR models
10.1007/s11696-017-0215-7 · 2017 · External reference
Applicability Domain: A Step Toward Confident Predictions and Decidability for QSAR Modeling
10.1007/978-1-4939-7899-1_6 · 2018 · External reference
Validation of Molecular Docking Programs for Virtual Screening against Dihydropteroate Synthase
10.1021/ci800293n · 2009 · External reference
Effects of Variable Docking Conditions and Scoring Functions on Corresponding Protein-Aligned Comparative Molecular Field Analysis Models Constructed from Diverse Human Protein Tyrosine Phosphatase 1B Inhibitors
10.1021/jm058047o · 2005 · External reference
10.1007/s12551-016-0247-1
10.1007/s12551-016-0247-1 · External reference
