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Pharmacophore-Based Similarity Scoring for DOCK

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What this work says

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

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Über den jetzigen Stand der Chemotherapie

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UCSF Chimera—A visualization system for exploratory research and analysis

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Implementation and evaluation of a docking‐rescoring method using molecular footprint comparisons

inferredcites →https://doi.org/10.1002/jcc.23245openalex-snapshot

Grid‐based molecular footprint comparison method for docking and de novo design: Application to HIVgp41

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Automated docking with grid‐based energy evaluation

inferredcites →https://doi.org/10.1002/prot.10266openalex-snapshot

Pharmacophore‐based molecular docking to account for ligand flexibility

inferredcites →https://doi.org/10.1002/prot.10296openalex-snapshot

Automated generation of MCSS‐derived pharmacophoric DOCK site points for searching multiconformation databases

inferredcites →https://doi.org/10.1007/978-1-4614-7951-2_2openalex-snapshot

Glossary of Terms Used

inferredcites →https://doi.org/10.1007/bf00124324openalex-snapshot

A genetic algorithm for flexible molecular overlay and pharmacophore elucidation

inferredcites →https://doi.org/10.1007/s10822-006-9060-4openalex-snapshot

Development and validation of a modular, extensible docking program: DOCK 5

inferredcites →https://doi.org/10.1007/s10822-006-9082-yopenalex-snapshot

GALAHAD: 1. Pharmacophore identification by hypermolecular alignment of ligands in 3D

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PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results

inferredcites →https://doi.org/10.1007/s10822-012-9565-yopenalex-snapshot

Evaluation of DOCK 6 as a pose generation and database enrichment tool

inferredcites →https://doi.org/10.1016/j.bmc.2013.10.022openalex-snapshot

Strategies for lead discovery: Application of footprint similarity targeting HIVgp41

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Footprint-based identification of viral entry inhibitors targeting HIVgp41

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Virtual ligand screening: strategies, perspectives and limitations

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Pharmacophore modeling and applications in drug discovery: challenges and recent advances

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A graph distance metric based on the maximal common subgraph

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Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings 1PII of original article: S0169-409X(96)00423-1. The article was originally published in Advanced Drug Delivery Reviews 23 (1997) 3–25. 1

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ProSep Inc, Canada

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A Water-Based Mechanism of Specificity and Resistance for Lapatinib with ErbB Family Kinases

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Quantitative Prediction of Fold Resistance for Inhibitors of EGFR

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Molecular Similarity Searching Using Atom Environments, Information-Based Feature Selection, and a Naïve Bayesian Classifier

inferredcites →https://doi.org/10.1021/ci049714+openalex-snapshot

ZINC − A Free Database of Commercially Available Compounds for Virtual Screening

inferredcites →https://doi.org/10.1021/ci0498719openalex-snapshot

Similarity Searching of Chemical Databases Using Atom Environment Descriptors (MOLPRINT 2D): Evaluation of Performance

inferredcites →https://doi.org/10.1021/ci049885eopenalex-snapshot

LigandScout: 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters

inferredcites →https://doi.org/10.1021/ci1001982openalex-snapshot

Docking Validation Resources: Protein Family and Ligand Flexibility Experiments

inferredcites →https://doi.org/10.1021/ci2005274openalex-snapshot

Comparative Analysis of Pharmacophore Screening Tools

inferredcites →https://doi.org/10.1021/ci400143ropenalex-snapshot

Exploring the Potential of Protein-Based Pharmacophore Models in Ligand Pose Prediction and Ranking

inferredcites →https://doi.org/10.1021/ci400534hopenalex-snapshot

Implementation of the Hungarian Algorithm to Account for Ligand Symmetry and Similarity in Structure-Based Design

inferredcites →https://doi.org/10.1021/ci5000533openalex-snapshot

Setting the Record Straight: The Origin of the Pharmacophore Concept

inferredcites →https://doi.org/10.1021/ci9002816openalex-snapshot

Multiobjective Optimization of Pharmacophore Hypotheses: Bias Toward Low-Energy Conformations

inferredcites →https://doi.org/10.1021/ci950273ropenalex-snapshot

Identification of Common Functional Configurations Among Molecules

inferredcites →https://doi.org/10.1021/jm00399a006openalex-snapshot

Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure

inferredcites →https://doi.org/10.1021/jm0608356openalex-snapshot

Benchmarking Sets for Molecular Docking

inferredcites →https://doi.org/10.1021/jm300687eopenalex-snapshot

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

inferredcites →https://doi.org/10.1021/jm900817uopenalex-snapshot

Three-Dimensional Pharmacophore Methods in Drug Discovery

inferredcites →https://doi.org/10.1038/nature03197openalex-snapshot

Virtual screening of chemical libraries

inferredcites →https://doi.org/10.1055/s-0029-1204471openalex-snapshot

Ueber die Constitution des Diphtheriegiftes

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

The Protein Data Bank

inferredcites →https://doi.org/10.1093/protein/6.7.723openalex-snapshot

Matching chemistry and shape in molecular docking

inferredcites →https://doi.org/10.1126/science.1096361openalex-snapshot

The Many Roles of Computation in Drug Discovery

inferredcites →https://doi.org/10.1126/science.257.5073.1078openalex-snapshot

Structure-Based Strategies for Drug Design and Discovery

inferredcites →https://doi.org/10.1128/jvi.01060-08openalex-snapshot

Conserved Salt Bridge between the N- and C-Terminal Heptad Repeat Regions of the Human Immunodeficiency Virus Type 1 gp41 Core Structure Is Critical for Virus Entry and Inhibition

inferredcites →https://doi.org/10.1261/rna.1563609openalex-snapshot

DOCK 6: Combining techniques to model RNA–small molecule complexes

inferredcites →https://doi.org/10.1351/pac199870051129openalex-snapshot

Glossary of terms used in medicinal chemistry (IUPAC Recommendations 1998)

inferredcites →https://doi.org/10.1371/journal.pone.0050968openalex-snapshot

Targeting Fatty Acid Binding Protein (FABP) Anandamide Transporters – A Novel Strategy for Development of Anti-Inflammatory and Anti-Nociceptive Drugs

inferredcites →https://doi.org/10.3390/biology1020311openalex-snapshot

Computer-Aided Approaches for Targeting HIVgp41

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/9783527806539.ch6fopenalex-snapshot

Pharmacophore Perception and Applications

inferred← citeshttps://doi.org/10.1002/jcc.23905openalex-snapshot

DOCK 6: Impact of new features and current docking performance

inferred← citeshttps://doi.org/10.1002/jcc.24667openalex-snapshot

Improving scoring-docking-screening powers of protein-ligand scoring functions using random forest

inferred← citeshttps://doi.org/10.1002/jcc.25052openalex-snapshot

Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets

inferred← citeshttps://doi.org/10.1002/jcc.26993openalex-snapshot

A molecular evolution algorithm for ligand design in DOCK

inferred← citeshttps://doi.org/10.1002/jcc.27218openalex-snapshot

DOCK 6: Incorporating hierarchical traversal through precomputed ligand conformations to enable large‐scale docking

inferred← citeshttps://doi.org/10.1002/jcc.27508openalex-snapshot

Fragment and torsion biasing algorithms for construction of small organic molecules in proteins using DOCK

inferred← citeshttps://doi.org/10.1002/slct.202505619openalex-snapshot

Targeting Catalytic Residues of TKTL1: A Multi‐Approach Study With Thiamine Analogs Combining QSAR, Pharmacophore Modeling, DFT, and Molecular Dynamics

inferred← citeshttps://doi.org/10.1007/7653_2015_46openalex-snapshot

Pharmacophore Modeling: Methods and Applications

inferred← citeshttps://doi.org/10.1007/s00894-018-3791-8openalex-snapshot

Virtual screening to identify Leishmania braziliensis N-myristoyltransferase inhibitors: pharmacophore models, docking, and molecular dynamics

inferred← citeshttps://doi.org/10.1007/s00894-018-3838-xopenalex-snapshot

Pharmacophore modeling, docking and molecular dynamics to identify Leishmania major farnesyl pyrophosphate synthase inhibitors

inferred← citeshttps://doi.org/10.1007/s00894-020-04470-wopenalex-snapshot

A computational strategy to understand structure-activity relationship of 1,3-disubstituted imidazole [1,5-α] pyrazine derivatives described as ATP competitive inhibitors of the IGF-1 receptor related to Ewing sarcoma

inferred← citeshttps://doi.org/10.1007/s10822-026-00855-wopenalex-snapshot

DOCKweb: a web-based GUI platform for molecular modeling with DOCK6

inferred← citeshttps://doi.org/10.1007/s40203-026-00668-7openalex-snapshot

IGF-1 receptor ATP-competitive inhibitors for the treatment of Ewing sarcoma: a comprehensive virtual screening analysis for a dataset of molecules showing a wide range of chemical structures

inferred← citeshttps://doi.org/10.1016/b978-0-12-822312-3.00024-2openalex-snapshot

Biomolecular Talks—Part 2: Applications and Challenges of Molecular Docking Approaches

inferred← citeshttps://doi.org/10.1016/j.advmem.2024.100103openalex-snapshot

Universal solution to the membrane selectivity challenge: Separation merit and efficiency

inferred← citeshttps://doi.org/10.1016/j.bmc.2016.07.031openalex-snapshot

Identification of small molecule inhibitors of botulinum neurotoxin serotype E via footprint similarity

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Structure-based identification of inhibitors targeting obstruction of the HIVgp41 N-heptad repeat trimer

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Structural insights into NS5B protein of novel equine hepaciviruses and pegiviruses complexed with polymerase inhibitors

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Identification of Zika Virus Inhibitors Using Homology Modeling and Similarity-Based Screening to Target Glycoprotein E

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Identification of a Water-Coordinating HER2 Inhibitor by Virtual Screening Using Similarity-Based Scoring

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Identification of Fatty Acid Binding Protein 5 Inhibitors Through Similarity-Based Screening

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

inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00745openalex-snapshot

Three-Dimensional Similarity in Molecular Docking: Prioritizing Ligand Poses on the Basis of Experimental Binding Modes

inferred← citeshttps://doi.org/10.1021/acs.jcim.6c00082openalex-snapshot

Best Practices in Mixed-Solvent Molecular Dynamics and Solvent-Site-Biased Docking

inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00645openalex-snapshot

Incorporating Explicit Water Molecules and Ligand Conformation Stability in Machine-Learning Scoring Functions

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Virtual Screening for Chemists

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Structure-based discovery of potentially active semiochemicals for Cydia pomonella (L.)

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Divide-and-link peptide docking: a fragment-based peptide docking protocol

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Consensus screening for a challenging target: the quest for P-glycoprotein inhibitors

inferred← citeshttps://doi.org/10.1073/pnas.2112621118openalex-snapshot

Leveraging nonstructural data to predict structures and affinities of protein–ligand complexes

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Discover natural compounds as potential phosphodiesterase-4B inhibitors via computational approaches

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Identification of novel acetylcholinesterase inhibitors through e-pharmacophore-based virtual screening and molecular dynamics simulations

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Identification potential inhibitors against the Streptococcus quorum-sensing signal pathway

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Computer-aided screening for suppressor of variegation 4-20 homolog 1 inhibitors and their preliminary activity validation in human osteosarcoma

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Exploring the chemical space for potential inhibitors against cell surface binding protein of Mpox virus using molecular fingerprint based screening approach

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Reliability analysis and optimization of the consensus docking approach for the development of virtual screening studies

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Identification of Ebola Virus Inhibitors Targeting GP2 Using Principles of Molecular Mimicry

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DLIGAND2: an improved knowledge-based energy function for protein–ligand interactions using the distance-scaled, finite, ideal-gas reference state

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Pharmacophore Modeling for Anti-Chagas Drug Design Using the Fragment Molecular Orbital Method

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Benchmarking AlphaFold‐enabled molecular docking predictions for antibiotic discovery

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Identification of Anticancer and Anti-inflammatory Drugs from Drugtarget Interaction Descriptors by Machine Learning

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DockingApp RF: A State-of-the-Art Novel Scoring Function for Molecular Docking in a User-Friendly Interface to AutoDock Vina

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