On the public citation graph

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

https://doi.org/10.1002/prot.10296
0 signed · 69 inferred · view as graph

Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

Is this your work? Sign in with ORCID and put your name on the claims that are yours.
Claim with ORCID
Reference health. See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.
See reference health

What this work says

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

inferredcites →https://doi.org/10.1002/(sici)1097-0134(19990101)34:1<4::aid-prot2>3.0.co;2-6openalex-snapshot
Ligand solvation in molecular docking
inferredcites →https://doi.org/10.1002/jcc.540040211openalex-snapshot
CHARMM : A program for macromolecular energy, minimization, and dynamics calculations
inferredcites →https://doi.org/10.1002/jcc.540130412openalex-snapshot
Automated docking with grid‐based energy evaluation
inferredcites →https://doi.org/10.1002/pro.5560070411openalex-snapshot
Flexible ligand docking using conformational ensembles
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.340110104openalex-snapshot
Functionality maps of binding sites: A multiple copy simultaneous search method
inferredcites →https://doi.org/10.1006/jmbi.1996.0026openalex-snapshot
Inhibition and catalytic mechanism of HIV-1 aspartic protease
inferredcites →https://doi.org/10.1007/bf00123669openalex-snapshot
On the use of LUDI to search the Fine Chemicals Directory for ligands of proteins of known three-dimensional structure
inferredcites →https://doi.org/10.1007/bf00126217openalex-snapshot
LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads
inferredcites →https://doi.org/10.1016/0022-2836(82)90153-xopenalex-snapshot
A geometric approach to macromolecule-ligand interactions
inferredcites →https://doi.org/10.1016/s0021-9258(18)33497-5openalex-snapshot
Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. I. General features and binding of methotrexate.
inferredcites →https://doi.org/10.1016/s0163-7258(99)00031-5openalex-snapshot
Computational approaches to structure-based ligand design
inferredcites →https://doi.org/10.1016/s0958-1669(97)80118-8openalex-snapshot
Bioinformatics: from genome data to biological knowledge
inferredcites →https://doi.org/10.1016/s0958-1669(97)80128-0openalex-snapshot
The chemical-biological interface: developments in automated and miniaturised screening technology
inferredcites →https://doi.org/10.1016/s0958-1669(98)80012-8openalex-snapshot
Protein structure prediction
inferredcites →https://doi.org/10.1016/s0969-2126(00)00178-7openalex-snapshot
Crystal structures of substrate binding to Bacillus subtilis holo-(acyl carrier protein) synthase reveal a novel trimeric arrangement of molecules resulting in three active sites
inferredcites →https://doi.org/10.1016/s0969-2126(98)00029-xopenalex-snapshot
Marrying structure and genomics
inferredcites →https://doi.org/10.1016/s1359-0278(97)00011-4openalex-snapshot
Meeting review: the Second Meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP2), Asilomar, California, December 13–16, 1996
inferredcites →https://doi.org/10.1016/s1359-6446(01)02103-1openalex-snapshot
Combinatorial Library Design and Evaluation: Principles, Software Tools and Applications in Drug Discovery
inferredcites →https://doi.org/10.1016/s1359-6446(97)01163-xopenalex-snapshot
Virtual screening—an overview
inferredcites →https://doi.org/10.1021/bi990306mopenalex-snapshot
Pro-1 of Macrophage Migration Inhibitory Factor Functions as a Catalytic Base in the Phenylpyruvate Tautomerase Activity,
inferredcites →https://doi.org/10.1021/ja00124a002openalex-snapshot
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
inferredcites →https://doi.org/10.1021/jm00145a002openalex-snapshot
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
inferredcites →https://doi.org/10.1021/jp952516oopenalex-snapshot
An Experimental Approach to Mapping the Binding Surfaces of Crystalline Proteins
inferredcites →https://doi.org/10.1021/jp973084fopenalex-snapshot
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
inferredcites →https://doi.org/10.1023/a:1011115820450openalex-snapshot
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
inferredcites →https://doi.org/10.1093/protein/9.9.773openalex-snapshot
Comparison of experimental and computational functional group mapping of an RNase A structure: implications for computer-aided drug design
inferredcites →https://doi.org/10.1126/science.257.5073.1078openalex-snapshot
Structure-Based Strategies for Drug Design and Discovery
inferredcites →https://doi.org/10.1126/science.274.5292.1531openalex-snapshot
Discovering High-Affinity Ligands for Proteins: SAR by NMR
inferredcites →https://doi.org/10.1126/science.8451640openalex-snapshot
Structure-Based Discovery of Inhibitors of Thymidylate Synthase
inferredcites →https://doi.org/10.1146/annurev.physchem.48.1.545openalex-snapshot
THEORY OF PROTEIN FOLDING: The Energy Landscape Perspective

What points at this work

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

inferred← citeshttps://doi.org/10.1002/0471266949.bmc141openalex-snapshot
Recent Trends in Structure‐Based Drug Design and Energetics
inferred← citeshttps://doi.org/10.1002/9780470027318.a9193openalex-snapshot
Protein Dynamics
inferred← citeshttps://doi.org/10.1002/chir.20399openalex-snapshot
Enantiomeric separation and determination of absolute stereochemistry of asymmetric molecules in drug discovery—Building chiral technology toolboxes
inferred← citeshttps://doi.org/10.1002/ddr.20398openalex-snapshot
Pharmacophore inference and its application to computational drug discovery
inferred← citeshttps://doi.org/10.1002/jcc.23214openalex-snapshot
Message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines
inferred← citeshttps://doi.org/10.1002/prot.10266openalex-snapshot
Pharmacophore‐based molecular docking to account for ligand flexibility
inferred← citeshttps://doi.org/10.1007/s10822-006-9057-zopenalex-snapshot
Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors
inferred← citeshttps://doi.org/10.1007/s10822-007-9119-xopenalex-snapshot
Ligand design by a combinatorial approach based on modeling and experiment: application to HLA-DR4
inferred← citeshttps://doi.org/10.1007/s10822-008-9231-6openalex-snapshot
Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design
inferred← citeshttps://doi.org/10.1007/s10822-009-9287-yopenalex-snapshot
The multi-copy simultaneous search methodology: a fundamental tool for structure-based drug design
inferred← citeshttps://doi.org/10.1007/s10822-009-9293-0openalex-snapshot
Challenges of fragment screening
inferred← citeshttps://doi.org/10.1007/s10822-014-9728-0openalex-snapshot
Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling
inferred← citeshttps://doi.org/10.1016/j.bpj.2014.11.095openalex-snapshot
Pharmacophore Modeling using Site-Identification by Ligand Competitive Saturation (SILCS) Method with Multiple Probe Molecules
inferred← citeshttps://doi.org/10.1016/j.cbpa.2004.05.001openalex-snapshot
High-throughput docking as a source of novel drug leads
inferred← citeshttps://doi.org/10.1016/j.ejmech.2008.06.005openalex-snapshot
Structure-based virtual screening for identification of novel 11β-HSD1 inhibitors
inferred← citeshttps://doi.org/10.1016/j.ejmech.2011.04.018openalex-snapshot
Pharmacophore based virtual screening, molecular docking studies to design potent heat shock protein 90 inhibitors
inferred← citeshttps://doi.org/10.1016/j.jmgm.2005.09.014openalex-snapshot
Evaluation of a neural networks QSAR method based on ligand representation using substituent descriptors
inferred← citeshttps://doi.org/10.1016/j.jmgm.2023.108429openalex-snapshot
Structure-based pharmacophore modeling 1. Automated random pharmacophore model generation
inferred← citeshttps://doi.org/10.1016/j.jmgm.2023.108488openalex-snapshot
Structure-based pharmacophore modeling 2. Developing a novel framework for structure-based pharmacophore model generation and selection
inferred← citeshttps://doi.org/10.1016/j.jsbmb.2004.01.007openalex-snapshot
Identification of novel estrogen receptor α antagonists
inferred← citeshttps://doi.org/10.1016/s1574-1400(05)01012-1openalex-snapshot
Chapter 12 Structure-Based Lead Optimization
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00121openalex-snapshot
AutoPH4: An Automated Method for Generating Pharmacophore Models from Protein Binding Pockets
inferred← citeshttps://doi.org/10.1021/ci049814fopenalex-snapshot
SitePrint: Three-Dimensional Pharmacophore Descriptors Derived from Protein Binding Sites for Family Based Active Site Analysis, Classification, and Drug Design
inferred← citeshttps://doi.org/10.1021/ci400731wopenalex-snapshot
Fragment-Based Lead Discovery and Design
inferred← citeshttps://doi.org/10.1021/ci500691popenalex-snapshot
Pharmacophore Modeling Using Site-Identification by Ligand Competitive Saturation (SILCS) with Multiple Probe Molecules
inferred← citeshttps://doi.org/10.1021/ci700470copenalex-snapshot
Investigation of MM-PBSA Rescoring of Docking Poses
inferred← citeshttps://doi.org/10.1021/ci900056copenalex-snapshot
Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy
inferred← citeshttps://doi.org/10.1021/cr040426mopenalex-snapshot
Molecular Dynamics: Survey of Methods for Simulating the Activity of Proteins
inferred← citeshttps://doi.org/10.1021/ja068256dopenalex-snapshot
Protein Flexibility and Species Specificity in Structure-Based Drug Discovery: Dihydrofolate Reductase as a Test System
inferred← citeshttps://doi.org/10.1021/ja0709728openalex-snapshot
Exploring Experimental Sources of Multiple Protein Conformations in Structure-Based Drug Design
inferred← citeshttps://doi.org/10.1021/jm100533popenalex-snapshot
Identification and Characterization of Acidic Mammalian Chitinase Inhibitors
inferred← citeshttps://doi.org/10.1021/jp506555wopenalex-snapshot
Pharmacophore-Based Similarity Scoring for DOCK
inferred← citeshttps://doi.org/10.1023/b:jcam.0000030033.26053.40openalex-snapshot
Gaussian mapping of chemical fragments in ligand binding sites
inferred← citeshttps://doi.org/10.2147/dddt.s126344openalex-snapshot
Quantum mechanics implementation in drug-design workflows: does it really help?
inferred← citeshttps://doi.org/10.21608/japs.2024.253925.1007openalex-snapshot
Molecular docking and pharmacophore modelling; A bridged explanation with emphasis on validation
inferred← citeshttps://doi.org/10.2174/157018009789108321openalex-snapshot
In Silico Screening of Novel Inhibitors for HPV: A Rational Structure Based Approach (Docking Versus Pharmacophore Model Generation)
inferred← citeshttps://doi.org/10.4155/fmc.14.155openalex-snapshot
Computational Solvent Mapping in Structure-Based Drug Design
inferred← citeshttps://doi.org/10.5012/bkcs.2012.33.7.2365openalex-snapshot
Discovery of Novel 11β-HSD1 Inhibitors by Pharmacophore-Based Virtual Screening
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.