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Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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“Scaffold-Hopping” by Topological Pharmacophore Search: A Contribution to Virtual Screening

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Cascade Reactions in Quantitative Solid-State Syntheses

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The Hydrogen Bond in the Solid State

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FDS: Flexible ligand and receptor docking with a continuum solvent model and soft‐core energy function

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ConsDock: A new program for the consensus analysis of protein–ligand interactions

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Improved protein–ligand docking using GOLD

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Comparative evaluation of eight docking tools for docking and virtual screening accuracy

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A Fast Flexible Docking Method using an Incremental Construction Algorithm

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Fragonomics: fragment-based drug discovery

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High-throughput X-ray crystallography for drug discovery

inferredcites →https://doi.org/10.1016/s1074-5521(96)90093-9openalex-snapshot

Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites

inferredcites →https://doi.org/10.1016/s1093-3263(98)00018-7openalex-snapshot

Development of filter functions for protein–ligand docking

inferredcites →https://doi.org/10.1016/s1359-6446(03)02831-9openalex-snapshot

A ‘Rule of Three’ for fragment-based lead discovery?

inferredcites →https://doi.org/10.1016/s1359-6446(04)03069-7openalex-snapshot

Ligand efficiency: a useful metric for lead selection

inferredcites →https://doi.org/10.1016/s1359-6446(04)03087-9openalex-snapshot

Promiscuity: what protects us, perplexes us

inferredcites →https://doi.org/10.1021/ci034231bopenalex-snapshot

Comparison of Fingerprint-Based Methods for Virtual Screening Using Multiple Bioactive Reference Structures

inferredcites →https://doi.org/10.1021/ci034289qopenalex-snapshot

Virtual Screening Using Protein−Ligand Docking: Avoiding Artificial Enrichment

inferredcites →https://doi.org/10.1021/ci040120gopenalex-snapshot

Similarity Search Profiles as a Diagnostic Tool for the Analysis of Virtual Screening Calculations

inferredcites →https://doi.org/10.1021/ci049870gopenalex-snapshot

Expanded Interaction Fingerprint Method for Analyzing Ligand Binding Modes in Docking and Structure-Based Drug Design

inferredcites →https://doi.org/10.1021/ci049970mopenalex-snapshot

Assessment of Docking Poses: Interactions-Based Accuracy Classification (IBAC) versus Crystal Structure Deviations

inferredcites →https://doi.org/10.1021/ci050026fopenalex-snapshot

Improved FlexX Docking Using FlexS-Determined Base Fragment Placement

inferredcites →https://doi.org/10.1021/ci050262qopenalex-snapshot

VISCANA: Visualized Cluster Analysis of Protein−Ligand Interaction Based on the ab Initio Fragment Molecular Orbital Method for Virtual Ligand Screening

inferredcites →https://doi.org/10.1021/ci050276wopenalex-snapshot

Anatomy of Fingerprint Search Calculations on Structurally Diverse Sets of Active Compounds

inferredcites →https://doi.org/10.1021/ci0503255openalex-snapshot

On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors

inferredcites →https://doi.org/10.1021/ci050348jopenalex-snapshot

New Methods for Ligand-Based Virtual Screening: Use of Data Fusion and Machine Learning to Enhance the Effectiveness of Similarity Searching

inferredcites →https://doi.org/10.1021/ci050352vopenalex-snapshot

Assessing the Scaffold Diversity of Screening Libraries

inferredcites →https://doi.org/10.1021/ci050372xopenalex-snapshot

sc-PDB: an Annotated Database of Druggable Binding Sites from the Protein Data Bank

inferredcites →https://doi.org/10.1021/ci050420dopenalex-snapshot

Knowledge-Based Interaction Fingerprint Scoring: A Simple Method for Improving the Effectiveness of Fast Scoring Functions

inferredcites →https://doi.org/10.1021/ci050510iopenalex-snapshot

A Distance Function for Retrieval of Active Molecules from Complex Chemical Space Representations

inferredcites →https://doi.org/10.1021/jm001044lopenalex-snapshot

Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations

inferredcites →https://doi.org/10.1021/jm020406hopenalex-snapshot

Surflex: Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search Engine

inferredcites →https://doi.org/10.1021/jm020472jopenalex-snapshot

Informative Library Design as an Efficient Strategy to Identify and Optimize Leads: Application to Cyclin-Dependent Kinase 2 Antagonists

inferredcites →https://doi.org/10.1021/jm030161oopenalex-snapshot

Multiple Active Site Corrections for Docking and Virtual Screening

inferredcites →https://doi.org/10.1021/jm0302997openalex-snapshot

Evaluation of Docking Performance: Comparative Data on Docking Algorithms

inferredcites →https://doi.org/10.1021/jm0303195openalex-snapshot

Classification of Kinase Inhibitors Using a Bayesian Model

inferredcites →https://doi.org/10.1021/jm030331xopenalex-snapshot

Structural Interaction Fingerprint (SIFt): A Novel Method for Analyzing Three-Dimensional Protein−Ligand Binding Interactions

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/jm030827eopenalex-snapshot

Discovery of a Potent and Selective Protein Kinase CK2 Inhibitor by High-Throughput Docking

inferredcites →https://doi.org/10.1021/jm049081qopenalex-snapshot

Validation and Use of the MM-PBSA Approach for Drug Discovery

inferredcites →https://doi.org/10.1021/jm049092jopenalex-snapshot

Virtual Screening Workflow Development Guided by the “Receiver Operating Characteristic” Curve Approach. Application to High-Throughput Docking on Metabotropic Glutamate Receptor Subtype 4

inferredcites →https://doi.org/10.1021/jm049312topenalex-snapshot

Interaction Profiles of Protein Kinase−Inhibitor Complexes and Their Application to Virtual Screening

inferredcites →https://doi.org/10.1021/jm0493360openalex-snapshot

PostDOCK: A Structural, Empirical Approach to Scoring Protein Ligand Complexes

inferredcites →https://doi.org/10.1021/jm049970dopenalex-snapshot

Combination of a Naive Bayes Classifier with Consensus Scoring Improves Enrichment of High-Throughput Docking Results

inferredcites →https://doi.org/10.1021/jm050381xopenalex-snapshot

Knowledge-Based Design of Target-Focused Libraries Using Protein−Ligand Interaction Constraints

inferredcites →https://doi.org/10.1021/jm050554iopenalex-snapshot

Protein Structures in Virtual Screening: A Case Study with CDK2

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Application of Fragment Screening and Fragment Linking to the Discovery of Novel Thrombin Inhibitors

inferredcites →https://doi.org/10.1021/jm990352kopenalex-snapshot

Consensus Scoring: A Method for Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures into Proteins

inferredcites →https://doi.org/10.1023/a:1016399411208openalex-snapshot

Flexible docking under pharmacophore type constraints

inferredcites →https://doi.org/10.1038/nrd1549openalex-snapshot

Docking and scoring in virtual screening for drug discovery: methods and applications

inferredcites →https://doi.org/10.1039/b409813gopenalex-snapshot

Molecular similarity: a key technique in molecular informatics

inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot

The Protein Data Bank

inferredcites →https://doi.org/10.1111/j.1747-0285.2005.00323.xopenalex-snapshot

Structural Interaction Fingerprints: A New Approach to Organizing, Mining, Analyzing, and Designing Protein–Small Molecule Complexes

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Development of CYP3A4 Inhibition Models: Comparisons of Machine-Learning Techniques and Molecular Descriptors

inferredcites →https://doi.org/10.2174/1568026054637700openalex-snapshot

Library Design for Fragment Based Screening

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inferred← citeshttps://doi.org/10.1016/j.ejmech.2018.10.060openalex-snapshot

Structure-based exploration and pharmacological evaluation of N-substituted piperidin-4-yl-methanamine CXCR4 chemokine receptor antagonists

inferred← citeshttps://doi.org/10.1016/j.ejmech.2026.118872openalex-snapshot

Deciphering covalent kinase inhibitor binding landscape through structural kinome profiling

inferred← citeshttps://doi.org/10.1016/j.ejphar.2011.05.071openalex-snapshot

Agonist-dependent effects of mutations in the sphingosine-1-phosphate type 1 receptor

inferred← citeshttps://doi.org/10.1016/j.febslet.2011.10.027openalex-snapshot

The structure of active opsin as a basis for identification of GPCR agonists by dynamic homology modelling and virtual screening assays

inferred← citeshttps://doi.org/10.1016/j.jmb.2016.12.004openalex-snapshot

Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures

inferred← citeshttps://doi.org/10.1016/j.jmgm.2013.08.009openalex-snapshot

Design of e-pharmacophore models using compound fragments for the trans-sialidase of Trypanosoma cruzi: Screening for novel inhibitor scaffolds

inferred← citeshttps://doi.org/10.1016/j.jmgm.2017.10.021openalex-snapshot

FLIP: An assisting software in structure based drug design using fingerprint of protein-ligand interaction profiles

inferred← citeshttps://doi.org/10.1016/j.mencom.2009.09.001openalex-snapshot

Molecular docking: theoretical background, practical applications and perspectives

inferred← citeshttps://doi.org/10.1016/j.mencom.2022.11.009openalex-snapshot

Reducing false-positive rates in virtual screening via cancellation of systematic errors in the scoring function

inferred← citeshttps://doi.org/10.1016/j.molliq.2025.127050openalex-snapshot

Design, synthesis, bioassay, and in silico studies of thiazolidinedione–morpholine hybrid ionic liquids as new antidiabetic agents

inferred← citeshttps://doi.org/10.1016/j.molstruc.2023.136839openalex-snapshot

Synthesis, Anti-microbial, Antifungal and In Silico Assessment of Some 2,4,5-Trisubstituted Imidazole Analogues

inferred← citeshttps://doi.org/10.1016/j.molstruc.2025.143759openalex-snapshot

Design, synthesis, antidiabetic, and in silico studies of 5-arylidene thiazolidinedione acetic acid 1,2-diol monoesters as new antidiabetic agents

inferred← citeshttps://doi.org/10.1016/j.pbiomolbio.2014.05.006openalex-snapshot

Polypharmacology rescored: Protein–ligand interaction profiles for remote binding site similarity assessment

inferred← citeshttps://doi.org/10.1016/j.pharmthera.2017.02.034openalex-snapshot

The impact of in silico screening in the discovery of novel and safer drug candidates

inferred← citeshttps://doi.org/10.1016/j.tips.2015.08.006openalex-snapshot

Advances in Computational Techniques to Study GPCR–Ligand Recognition

inferred← citeshttps://doi.org/10.1016/j.tox.2025.154362openalex-snapshot

Interaction-profile cheminformatic read-across identifies the UV filter benzophenone-4 as a PPARγ agonist and potential obesogen

inferred← citeshttps://doi.org/10.1016/j.ymeth.2014.08.001openalex-snapshot

Virtual screening: An in silico tool for interlacing the chemical universe with the proteome

inferred← citeshttps://doi.org/10.1016/j.ymeth.2022.05.006openalex-snapshot

Multi-level analysis of intrinsically disordered protein docking methods

inferred← citeshttps://doi.org/10.1021/acs.chemrev.5c01081openalex-snapshot

Organic Chemistry as a Catalyst for AI Innovation: Challenges, Methods, and Emerging Paradigms

inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00305openalex-snapshot

PyPLIF HIPPOS: A Molecular Interaction Fingerprinting Tool for Docking Results of AutoDock Vina and PLANTS

inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00556openalex-snapshot

Assessment of the Fragment Docking Program SEED

inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00693openalex-snapshot

LEADS-FRAG: A Benchmark Data Set for Assessment of Fragment Docking Performance

inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00292openalex-snapshot

True Accuracy of Fast Scoring Functions to Predict High-Throughput Screening Data from Docking Poses: The Simpler the Better

inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00746openalex-snapshot

Navigating Chemical Space by Interfacing Generative Artificial Intelligence and Molecular Docking

inferred← citeshttps://doi.org/10.1021/acs.jcim.1c01537openalex-snapshot

AA-Score: a New Scoring Function Based on Amino Acid-Specific Interaction for Molecular Docking

inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00050openalex-snapshot

KiSSim: Predicting Off-Targets from Structural Similarities in the Kinome

inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00485openalex-snapshot

Delta Machine Learning to Improve Scoring-Ranking-Screening Performances of Protein–Ligand Scoring Functions

inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00695openalex-snapshot

Prioritizing Virtual Screening with Interpretable Interaction Fingerprints

inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00275openalex-snapshot

Predicting Regioselectivity of Cytosolic Sulfotransferase Metabolism for Drugs

inferred← citeshttps://doi.org/10.1021/acs.jcim.4c00842openalex-snapshot

IEV2Mol: Molecular Generative Model Considering Protein–Ligand Interaction Energy Vectors

inferred← citeshttps://doi.org/10.1021/acs.jcim.4c01196openalex-snapshot

Elucidating the Selective Mechanism of Drugs Targeting Cyclin-Dependent Kinases with Integrated MetaD-US Simulation

inferred← citeshttps://doi.org/10.1021/acs.jcim.4c01902openalex-snapshot

GRADE and X-GRADE: Unveiling Novel Protein–Ligand Interaction Fingerprints Based on GRAIL Scores

inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00066openalex-snapshot

Structure-Based Prediction of G-Protein-Coupled Receptor Ligand Function: A β-Adrenoceptor Case Study

inferred← citeshttps://doi.org/10.1021/acs.jcim.5c00730openalex-snapshot

On the Difficulty to Rescore Hits from Ultralarge Docking Screens

inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00314openalex-snapshot

Interacting with GPCRs: Using Interaction Fingerprints for Virtual Screening

inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00686openalex-snapshot

3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine

inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00769openalex-snapshot

Do Fragments and Crystallization Additives Bind Similarly to Drug-like Ligands?

inferred← citeshttps://doi.org/10.1021/acs.jcim.6c01658openalex-snapshot

Diversity-Seeking Docking-Guided Molecular Design Discovers Broader Predicted Interaction Profiles across Protein Families

inferred← citeshttps://doi.org/10.1021/acs.jcim.6c02252openalex-snapshot

Performances and Critical Limitations of Docking and Protein–Ligand Interactions for Efficacy-Driven Virtual Screening Targeting Class A GPCRs

inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00017openalex-snapshot

Protein–Ligand Empirical Interaction Components for Virtual Screening

inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00458openalex-snapshot

Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants

inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00779openalex-snapshot

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

inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00652openalex-snapshot

AlphaSpace 2.0: Representing Concave Biomolecular Surfaces Using β-Clusters

inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00699openalex-snapshot

Fragment-Based Computational Method for Designing GPCR Ligands

inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00821openalex-snapshot

Identification of Target Associations for Polypharmacology from Analysis of Crystallographic Ligands of the Protein Data Bank

inferred← citeshttps://doi.org/10.1021/acs.jcim.9b01202openalex-snapshot

Emulating Docking Results Using a Deep Neural Network: A New Perspective for Virtual Screening

inferred← citeshttps://doi.org/10.1021/acs.jctc.4c01024openalex-snapshot

Nonspecific Yet Selective Interactions Contribute to Small Molecule Condensate Binding

inferred← citeshttps://doi.org/10.1021/acs.jctc.6b00449openalex-snapshot

Calculating Partition Coefficients of Small Molecules in Octanol/Water and Cyclohexane/Water

inferred← citeshttps://doi.org/10.1021/acs.jctc.8b00821openalex-snapshot

Toward Learned Chemical Perception of Force Field Typing Rules

inferred← citeshttps://doi.org/10.1021/acs.jctc.9b01134openalex-snapshot

Revealing Acquired Resistance Mechanisms of Kinase-Targeted Drugs Using an on-the-Fly, Function-Site Interaction Fingerprint Approach

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.0c00422openalex-snapshot

A Computer Vision Approach to Align and Compare Protein Cavities: Application to Fragment-Based Drug Design

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.2c00487openalex-snapshot

On the Frustration to Predict Binding Affinities from Protein–Ligand Structures with Deep Neural Networks

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.2c00931openalex-snapshot

Target-Focused Library Design by Pocket-Applied Computer Vision and Fragment Deep Generative Linking

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.2c01303openalex-snapshot

Predicting Regioselectivity of AO, CYP, FMO, and UGT Metabolism Using Quantum Mechanical Simulations and Machine Learning

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.5b00203openalex-snapshot

Discovery of Potent Inhibitors of Schistosoma mansoni NAD+ Catabolizing Enzyme

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.5b01813openalex-snapshot

PDEStrIAn: A Phosphodiesterase Structure and Ligand Interaction Annotated Database As a Tool for Structure-Based Drug Design

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.5b02041openalex-snapshot

Delineation of Polypharmacology across the Human Structural Kinome Using a Functional Site Interaction Fingerprint Approach

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.6b00078openalex-snapshot

Impact of Binding Site Comparisons on Medicinal Chemistry and Rational Molecular Design

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.6b00855openalex-snapshot

Structure–Activity Relationship Studies for Enhancer of Zeste Homologue 2 (EZH2) and Enhancer of Zeste Homologue 1 (EZH1) Inhibitors

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.6b00981openalex-snapshot

Identification of Ligand Binding Hot Spots of the Histamine H 1 Receptor following Structure-Based Fragment Optimization

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.6b01815openalex-snapshot

Determining Cysteines Available for Covalent Inhibition Across the Human Kinome

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.7b00404openalex-snapshot

Fragment-Based Drug Discovery of Phosphodiesterase Inhibitors

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.8b00256openalex-snapshot

Structural Insights on Fragment Binding Mode Conservation

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.8b00836openalex-snapshot

Aminergic GPCR–Ligand Interactions: A Chemical and Structural Map of Receptor Mutation Data

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.9b00279openalex-snapshot

Structure–Activity and Structure–Conformation Relationships of Aryl Propionic Acid Inhibitors of the Kelch-like ECH-Associated Protein 1/Nuclear Factor Erythroid 2-Related Factor 2 (KEAP1/NRF2) Protein–Protein Interaction

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.9b00447openalex-snapshot

Route to Prolonged Residence Time at the Histamine H1 Receptor: Growing from Desloratadine to Rupatadine

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.9b01184openalex-snapshot

Exhaustive Repertoire of Druggable Cavities at Protein–Protein Interfaces of Known Three-Dimensional Structure

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.9b01462openalex-snapshot

4-(3-Aminoazetidin-1-yl)pyrimidin-2-amines as High-Affinity Non-imidazole Histamine H3 Receptor Agonists with in Vivo Central Nervous System Activity

inferred← citeshttps://doi.org/10.1021/acs.jproteome.0c00623openalex-snapshot

Structural Insights into the Binding Modes of Viral RNA-Dependent RNA Polymerases Using a Function-Site Interaction Fingerprint Method for RNA Virus Drug Discovery

inferred← citeshttps://doi.org/10.1021/acs.langmuir.5c01011openalex-snapshot

High-Precision Multistage Molecular Dynamics Simulations and Quantum Mechanics Investigation of Adsorption Mechanisms of Cerium-Based H3BTC MOF (Ce-H3BTC-MOF) on Pristine and Functionalized Carbon Nanotubes

inferred← citeshttps://doi.org/10.1021/acscentsci.3c01521openalex-snapshot

Protein Structure-Based Organic Chemistry-Driven Ligand Design from Ultralarge Chemical Spaces

inferred← citeshttps://doi.org/10.1021/acsmedchemlett.3c00212openalex-snapshot

How Ligands Interact with the Kinase Hinge

inferred← citeshttps://doi.org/10.1021/acsomega.2c03951openalex-snapshot

Molecular Docking, Molecular Dynamics Simulations, and Free Energy Calculation Insights into the Binding Mechanism between VS-4718 and Focal Adhesion Kinase

inferred← citeshttps://doi.org/10.1021/acsomega.3c02411openalex-snapshot

AQDnet: Deep Neural Network for Protein–Ligand Docking Simulation

inferred← citeshttps://doi.org/10.1021/acsomega.5c08775openalex-snapshot

Structure-Guided Discovery of CHI3L1 Inhibitors from Ultralarge Chemical Spaces for Glioblastoma Therapy

inferred← citeshttps://doi.org/10.1021/acsptsci.3c00078openalex-snapshot

Rigid Scaffolds Are Promising for Designing Macrocyclic Kinase Inhibitors

inferred← citeshttps://doi.org/10.1021/acsptsci.8b00051openalex-snapshot

Identification of Key Structural Motifs Involved in 7 Transmembrane Signaling of Adhesion GPCRs

inferred← citeshttps://doi.org/10.1021/bk-2011-1076.ch001openalex-snapshot

Overview: Fragment-Based Drug Design

inferred← citeshttps://doi.org/10.1021/cb5001636openalex-snapshot

Increasing Chemical Space Coverage by Combining Empirical and Computational Fragment Screens

inferred← citeshttps://doi.org/10.1021/ci1000407openalex-snapshot

Virtual Fragment Docking by Glide: a Validation Study on 190 Protein−Fragment Complexes

inferred← citeshttps://doi.org/10.1021/ci100050topenalex-snapshot

Extended-Connectivity Fingerprints

inferred← citeshttps://doi.org/10.1021/ci1002608openalex-snapshot

Electron Density Fingerprints (EDprints): Virtual Screening Using Assembled Information of Electron Density

inferred← citeshttps://doi.org/10.1021/ci2003363openalex-snapshot

SERAPhiC: A Benchmark for in Silico Fragment-Based Drug Design

inferred← citeshttps://doi.org/10.1021/ci300073mopenalex-snapshot

Virtual Target Screening: Validation Using Kinase Inhibitors

inferred← citeshttps://doi.org/10.1021/ci300083ropenalex-snapshot

Protein–Ligand-Based Pharmacophores: Generation and Utility Assessment in Computational Ligand Profiling

inferred← citeshttps://doi.org/10.1021/ci300184xopenalex-snapshot

Comparison and Druggability Prediction of Protein–Ligand Binding Sites from Pharmacophore-Annotated Cavity Shapes

inferred← citeshttps://doi.org/10.1021/ci300196gopenalex-snapshot

Structural Insights into the Molecular Basis of the Ligand Promiscuity

inferred← citeshttps://doi.org/10.1021/ci300200ropenalex-snapshot

Predicting Ligand Binding Modes from Neural Networks Trained on Protein–Ligand Interaction Fingerprints

inferred← citeshttps://doi.org/10.1021/ci300355popenalex-snapshot

In Silico Deconstruction of ATP-Competitive Inhibitors of Glycogen Synthase Kinase-3β

inferred← citeshttps://doi.org/10.1021/ci3004094openalex-snapshot

Virtual Fragment Screening: Discovery of Histamine H3 Receptor Ligands Using Ligand-Based and Protein-Based Molecular Fingerprints

inferred← citeshttps://doi.org/10.1021/ci300495ropenalex-snapshot

S4MPLE – Sampler For Multiple Protein–Ligand Entities: Simultaneous Docking of Several Entities

inferred← citeshttps://doi.org/10.1021/ci300508mopenalex-snapshot

Characterization of Small Molecule Binding. I. Accurate Identification of Strong Inhibitors in Virtual Screening

inferred← citeshttps://doi.org/10.1021/ci300566nopenalex-snapshot

Encoding Protein–Ligand Interaction Patterns in Fingerprints and Graphs

inferred← citeshttps://doi.org/10.1021/ci4000163openalex-snapshot

In Silico Fragment-Based Drug Discovery: Setup and Validation of a Fragment-to-Lead Computational Protocol Using S4MPLE

inferred← citeshttps://doi.org/10.1021/ci400025fopenalex-snapshot

CSAR Benchmark Exercise 2011–2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series

inferred← citeshttps://doi.org/10.1021/ci400303nopenalex-snapshot

Computational Profiling of Bioactive Compounds Using a Target-Dependent Composite Workflow

inferred← citeshttps://doi.org/10.1021/ci500319fopenalex-snapshot

Structural Protein?Ligand Interaction Fingerprints (SPLIF) for Structure-Based Virtual Screening: Method and Benchmark Study

inferred← citeshttps://doi.org/10.1021/ci500519wopenalex-snapshot

Target-Specific Native/Decoy Pose Classifier Improves the Accuracy of Ligand Ranking in the CSAR 2013 Benchmark

inferred← citeshttps://doi.org/10.1021/ci500721xopenalex-snapshot

Analyzing Multitarget Activity Landscapes Using Protein–Ligand Interaction Fingerprints: Interaction Cliffs

inferred← citeshttps://doi.org/10.1021/ci700124ropenalex-snapshot

Similarity Based Docking

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