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Knowledge-Based Scoring Functions in Drug Design: 2. Can the Knowledge Base Be Enriched?
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/(sici)1096-987x(19981115)19:14<1639::aid-jcc10>3.0.co;2-bopenalex-snapshot
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
inferredcites →https://doi.org/10.1002/(sici)1096-987x(199908)20:11<1165::aid-jcc7>3.0.co;2-aopenalex-snapshot
BLEEP?potential of mean force describing protein-ligand interactions: I. Generating potential
inferredcites →https://doi.org/10.1002/1096-987x(200103)22:4<418::aid-jcc1012>3.0.co;2-3openalex-snapshot
Effect of ligand volume correction on PMF scoring
inferredcites →https://doi.org/10.1002/jcc.20504openalex-snapshot
An iterative knowledge‐based scoring function to predict protein–ligand interactions: I. Derivation of interaction potentials
inferredcites →https://doi.org/10.1002/jcc.20634openalex-snapshot
A semiempirical free energy force field with charge‐based desolvation
inferredcites →https://doi.org/10.1002/jcc.21334openalex-snapshot
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
inferredcites →https://doi.org/10.1006/jmbi.1999.3371openalex-snapshot
Knowledge-based scoring function to predict protein-ligand interactions
inferredcites →https://doi.org/10.1007/bf00126743openalex-snapshot
The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
inferredcites →https://doi.org/10.1016/1074-5521(95)90050-0openalex-snapshot
Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming
inferredcites →https://doi.org/10.1016/s1359-6446(02)02556-4openalex-snapshot
Chris Lipinski discusses life and chemistry after the Rule of Five
inferredcites →https://doi.org/10.1021/ci049733jopenalex-snapshot
An Extensive Test of 14 Scoring Functions Using the PDBbind Refined Set of 800 Protein−Ligand Complexes
inferredcites →https://doi.org/10.1021/ci050400bopenalex-snapshot
The Blue Obelisk—Interoperability in Chemical Informatics
inferredcites →https://doi.org/10.1021/ci100182copenalex-snapshot
Knowledge-Based Scoring Functions in Drug Design. 1. Developing a Target-Specific Method for Kinase−Ligand Interactions
inferredcites →https://doi.org/10.1021/ci7004719openalex-snapshot
An Improved PMF Scoring Function for Universally Predicting the Interactions of a Ligand with Protein, DNA, and RNA
inferredcites →https://doi.org/10.1021/ci800023xopenalex-snapshot
Ranking Targets in Structure-Based Virtual Screening of Three-Dimensional Protein Libraries: Methods and Problems
inferredcites →https://doi.org/10.1021/ci9000053openalex-snapshot
Comparative Assessment of Scoring Functions on a Diverse Test Set
inferredcites →https://doi.org/10.1021/ci9002987openalex-snapshot
Inclusion of Solvation and Entropy in the Knowledge-Based Scoring Function for Protein−Ligand Interactions
inferredcites →https://doi.org/10.1021/ct100215copenalex-snapshot
A Displaced-Solvent Functional Analysis of Model Hydrophobic Enclosures
inferredcites →https://doi.org/10.1021/ja960751uopenalex-snapshot
SMoG: de Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates. 1. Methodology and Supporting Evidence
inferredcites →https://doi.org/10.1021/jm0105833openalex-snapshot
SMall Molecule Growth 2001 (SMoG2001): An Improved Knowledge-Based Scoring Function for Protein−Ligand Interactions
inferredcites →https://doi.org/10.1021/jm0203783openalex-snapshot
Comparative Evaluation of 11 Scoring Functions for Molecular Docking
inferredcites →https://doi.org/10.1021/jm030489hopenalex-snapshot
Assessing Scoring Functions for Protein−Ligand Interactions
inferredcites →https://doi.org/10.1021/jm0306430openalex-snapshot
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
inferredcites →https://doi.org/10.1021/jm048957qopenalex-snapshot
The PDBbind Database: Methodologies and Updates
inferredcites →https://doi.org/10.1021/jm049314dopenalex-snapshot
A Knowledge-Based Energy Function for Protein−Ligand, Protein−Protein, and Protein−DNA Complexes
inferredcites →https://doi.org/10.1021/jm050043wopenalex-snapshot
M-Score: A Knowledge-Based Potential Scoring Function Accounting for Protein Atom Mobility
inferredcites →https://doi.org/10.1021/jm050362nopenalex-snapshot
A Critical Assessment of Docking Programs and Scoring Functions
inferredcites →https://doi.org/10.1021/jm050436vopenalex-snapshot
DrugScore CSD Knowledge-Based Scoring Function Derived from Small Molecule Crystal Data with Superior Recognition Rate of Near-Native Ligand Poses and Better Affinity Prediction
inferredcites →https://doi.org/10.1021/jm0606589openalex-snapshot
In Silico-Guided Target Identification of a Scaffold-Focused Library: 1,3,5-Triazepan-2,6-diones as Novel Phospholipase A2 Inhibitors
inferredcites →https://doi.org/10.1021/jm060999mopenalex-snapshot
Prediction of Protein−Ligand Interactions. Docking and Scoring: Successes and Gaps
inferredcites →https://doi.org/10.1021/jm100112jopenalex-snapshot
A Medicinal Chemist’s Guide to Molecular Interactions
inferredcites →https://doi.org/10.1021/jm980536jopenalex-snapshot
A General and Fast Scoring Function for Protein−Ligand Interactions: A Simplified Potential Approach
inferredcites →https://doi.org/10.1023/a:1008729005958openalex-snapshot
A knowledge-based scoring function for protein-ligand interactions: Probing the reference state
inferredcites →https://doi.org/10.1038/nrd1549openalex-snapshot
Docking and scoring in virtual screening for drug discovery: methods and applications
inferredcites →https://doi.org/10.1038/sj.bjp.0707515openalex-snapshot
Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go
inferredcites →https://doi.org/10.1073/pnas.93.21.11628openalex-snapshot
An iterative method for extracting energy-like quantities from protein structures.
inferredcites →https://doi.org/10.1093/nar/gkl114openalex-snapshot
TarFisDock: a web server for identifying drug targets with docking approach
inferredcites →https://doi.org/10.1103/physreve.68.011202openalex-snapshot
Determination of the interaction potential from the pair distribution function: An inverse Monte Carlo technique
inferredcites →https://doi.org/10.2174/138920306778559395openalex-snapshot
Scoring Functions for Protein-Ligand Docking
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/9783527645947.ch12openalex-snapshot
Scoring Functions for Protein–Ligand Interactions
inferred← citeshttps://doi.org/10.1002/jcc.23170openalex-snapshot
Water PMF for predicting the properties of water molecules in protein binding site
inferred← citeshttps://doi.org/10.1002/jmr.2266openalex-snapshot
Latest developments in molecular docking: 2010–2011 in review
inferred← citeshttps://doi.org/10.1002/med.21483openalex-snapshot
Computational chemical biology and drug design: Facilitating protein structure, function, and modulation studies
inferred← citeshttps://doi.org/10.1002/minf.202200034openalex-snapshot
Towards an Enrichment Optimization Algorithm (EOA)‐based Target Specific Docking Functions for Virtual Screening
inferred← citeshttps://doi.org/10.1007/s10822-016-9897-0openalex-snapshot
Incorporating specificity into optimization: evaluation of SPA using CSAR 2014 and CASF 2013 benchmarks
inferred← citeshttps://doi.org/10.1007/s10822-018-0155-5openalex-snapshot
Rescoring of docking poses under Occam’s Razor: are there simpler solutions?
inferred← citeshttps://doi.org/10.1007/s13205-023-03608-wopenalex-snapshot
In-silico study: docking simulation and molecular dynamics of peptidomimetic fullerene-based derivatives against SARS-CoV-2 Mpro
inferred← citeshttps://doi.org/10.1016/j.csbj.2022.02.004openalex-snapshot
Protein-ligand binding affinity prediction based on profiles of intermolecular contacts
inferred← citeshttps://doi.org/10.1016/j.ejmech.2021.113705openalex-snapshot
Current trends in computer aided drug design and a highlight of drugs discovered via computational techniques: A review
inferred← citeshttps://doi.org/10.1016/j.jmgm.2014.07.010openalex-snapshot
An electronic environment and contact direction sensitive scoring function for predicting affinities of protein–ligand complexes in Contour®
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Structure-based drug design of novel peptidomimetic cellulose derivatives as HCV-NS3 protease inhibitors
inferred← citeshttps://doi.org/10.1016/j.saa.2014.10.045openalex-snapshot
The QSAR and docking calculations of fullerene derivatives as HIV-1 protease inhibitors
inferred← citeshttps://doi.org/10.1016/j.tips.2013.08.004openalex-snapshot
Computational methods for drug design and discovery: focus on China
inferred← citeshttps://doi.org/10.1016/j.ymeth.2014.10.019openalex-snapshot
Structure based virtual screening to discover putative drug candidates: Necessary considerations and successful case studies
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.6b01785openalex-snapshot
Discovery of Novel Disruptor of Silencing Telomeric 1-Like (DOT1L) Inhibitors using a Target-Specific Scoring Function for the (S)-Adenosyl- l -methionine (SAM)-Dependent Methyltransferase Family
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.9b00510openalex-snapshot
Discovery and Development of a Series of Pyrazolo[3,4-d]pyridazinone Compounds as the Novel Covalent Fibroblast Growth Factor Receptor Inhibitors by the Rational Drug Design
inferred← citeshttps://doi.org/10.1021/ci200274qopenalex-snapshot
DSX: A Knowledge-Based Scoring Function for the Assessment of Protein–Ligand Complexes
inferred← citeshttps://doi.org/10.1021/ci2003939openalex-snapshot
Knowledge-Based Scoring Functions in Drug Design: 3. A Two-Dimensional Knowledge-Based Hydrogen-Bonding Potential for the Prediction of Protein–Ligand Interactions
inferred← citeshttps://doi.org/10.1021/ci3002638openalex-snapshot
Integrating Ligand-Based and Protein-Centric Virtual Screening of Kinase Inhibitors Using Ensembles of Multiple Protein Kinase Genes and Conformations
inferred← citeshttps://doi.org/10.1021/ci500081mopenalex-snapshot
Comparative Assessment of Scoring Functions on an Updated Benchmark: 2. Evaluation Methods and General Results
inferred← citeshttps://doi.org/10.1021/ci500647fopenalex-snapshot
An Accurate Metalloprotein-Specific Scoring Function and Molecular Docking Program Devised by a Dynamic Sampling and Iteration Optimization Strategy
inferred← citeshttps://doi.org/10.1097/js9.0000000000001289openalex-snapshot
Current perspectives and trend of computer-aided drug design: a review and bibliometric analysis
inferred← citeshttps://doi.org/10.1111/cbdd.12470openalex-snapshot
TS ‐Chemscore, a Target‐Specific Scoring Function, Significantly Improves the Performance of Scoring in Virtual Screening
inferred← citeshttps://doi.org/10.11606/d.75.2012.tde-17042012-170802openalex-snapshot
Planejamento de inibidores da enzima gliceraldeído-3-fosfato desidrogenase de Trypanosoma cruzi e avaliação bioquímica por calorimetria de titulação isotérmica
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In silico analysis: Fulleropyrrolidine derivatives against HIV-PR mutants and SARS-CoV-2 Mpro
inferred← citeshttps://doi.org/10.2174/1568026614666140929115506openalex-snapshot
Revisiting De Novo Drug Design: Receptor Based Pharmacophore Screening
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Deep Neural Network Classifier for Virtual Screening Inhibitors of (S)-Adenosyl-L-Methionine (SAM)-Dependent Methyltransferase Family
inferred← citeshttps://doi.org/10.3390/ijms24119226openalex-snapshot
Recent Advances in Computer-Aided Structure-Based Drug Design on Ion Channels
inferred← citeshttps://doi.org/10.3390/molecules20058997openalex-snapshot
S4MPLE—Sampler for Multiple Protein-Ligand Entities: Methodology and Rigid-Site Docking Benchmarking
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Past, Present, and Future Perspectives on Computer-Aided Drug Design Methodologies
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