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Position Specific Interaction Dependent Scoring Technique for Virtual Screening Based on Weighted Protein−Ligand Interaction Fingerprint Profiles

https://doi.org/10.1021/ci800466n
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What this work says

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

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The Process of Structure-Based Drug Design
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/jm030504iopenalex-snapshot
Identification of Compounds with Nanomolar Binding Affinity for Checkpoint Kinase-1 Using Knowledge-Based Virtual Screening
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/10.1038/44565openalex-snapshot
Learning the parts of objects by non-negative matrix factorization
inferredcites →https://doi.org/10.1038/nsb949openalex-snapshot
Structural basis for p38α MAP kinase quinazolinone and pyridol-pyrimidine inhibitor specificity
inferredcites →https://doi.org/10.1073/pnas.0308531101openalex-snapshot
Metagenes and molecular pattern discovery using matrix factorization
inferredcites →https://doi.org/10.1093/bioinformatics/bti653openalex-snapshot
Improving molecular cancer class discovery through sparse non-negative matrix factorization
inferredcites →https://doi.org/10.1101/gr.903503openalex-snapshot
Subsystem Identification Through Dimensionality Reduction of Large-Scale Gene Expression Data
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
inferredcites →https://doi.org/10.1126/science.220.4598.671openalex-snapshot
Optimization by Simulated Annealing
inferredcites →https://doi.org/10.1371/journal.pcbi.1000029openalex-snapshot
Nonnegative Matrix Factorization: An Analytical and Interpretive Tool in Computational Biology

What points at this work

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

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The Challenge of Affinity Prediction: Scoring Functions for Structure‐Based Virtual Screening
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Scoring Functions for Protein–Ligand Interactions
inferred← citeshttps://doi.org/10.1002/cmdc.201100179openalex-snapshot
From Activity Cliffs to Target‐Specific Scoring Models and Pharmacophore Hypotheses
inferred← citeshttps://doi.org/10.1002/jcc.21814openalex-snapshot
Implementation and evaluation of a docking‐rescoring method using molecular footprint comparisons
inferred← citeshttps://doi.org/10.1002/jmr.1077openalex-snapshot
Challenges and advances in computational docking: 2009 in review
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An Improved Weighted‐Residue Profile Based Method of Using Protein–Ligand Interaction Information in Increasing Hits Selection from Virtual Screening: A Study on Virtual Screening of Human GPCR A2A Receptor Antagonists
inferred← citeshttps://doi.org/10.1002/minf.202400159openalex-snapshot
A Molecular Representation to Identify Isofunctional Molecules
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Outstanding challenges in protein–ligand docking and structure‐based virtual screening
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Quantitative Target-specific Toxicity Prediction Modeling (QTTPM): Coupling Machine Learning with Dynamic Protein–Ligand Interaction Descriptors (DyPLIDs) to Predict Androgen Receptor-mediated Toxicity
inferred← citeshttps://doi.org/10.1007/978-81-322-1780-0_9openalex-snapshot
Integration of Automated Workflow in Chemoinformatics for Drug Discovery
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Improving performance of docking-based virtual screening by structural filtration
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Structure-based protein–ligand interaction fingerprints for binding affinity prediction
inferred← citeshttps://doi.org/10.1016/j.drudis.2022.07.004openalex-snapshot
Harnessing systematic protein–ligand interaction fingerprints for drug discovery
inferred← citeshttps://doi.org/10.1016/j.jmgm.2011.09.006openalex-snapshot
Binding of GSH conjugates to π-GST: A cross-docking approach
inferred← citeshttps://doi.org/10.1016/j.jmgm.2017.12.002openalex-snapshot
PLHINT: A knowledge-driven computational approach based on the intermolecular H bond interactions at the protein-ligand interface from docking solutions
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.pbiomolbio.2014.05.006openalex-snapshot
Polypharmacology rescored: Protein–ligand interaction profiles for remote binding site similarity assessment
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00749openalex-snapshot
The Development of Target-Specific Pose Filter Ensembles To Boost Ligand Enrichment for Structure-Based Virtual Screening
inferred← citeshttps://doi.org/10.1021/ci2002507openalex-snapshot
Cheminformatics Meets Molecular Mechanics: A Combined Application of Knowledge-Based Pose Scoring and Physical Force Field-Based Hit Scoring Functions Improves the Accuracy of Structure-Based Virtual Screening
inferred← citeshttps://doi.org/10.1021/ci900382eopenalex-snapshot
Combining Machine Learning and Pharmacophore-Based Interaction Fingerprint for in Silico Screening
inferred← citeshttps://doi.org/10.1038/nchembio.2266openalex-snapshot
RETRACTED ARTICLE: Orphan receptor ligand discovery by pickpocketing pharmacological neighbors
inferred← citeshttps://doi.org/10.1038/s41589-021-00746-1openalex-snapshot
Retraction Note: Orphan receptor ligand discovery by pickpocketing pharmacological neighbors
inferred← citeshttps://doi.org/10.1080/17460441.2021.1929921openalex-snapshot
Computational representations of protein–ligand interfaces for structure-based virtual screening
inferred← citeshttps://doi.org/10.1111/j.1747-0285.2010.01007.xopenalex-snapshot
Computational Methodologies for Compound Database Searching that Utilize Experimental Protein–Ligand Interaction Information
inferred← citeshttps://doi.org/10.1186/s12859-017-1750-5openalex-snapshot
Enhance the performance of current scoring functions with the aid of 3D protein-ligand interaction fingerprints
inferred← citeshttps://doi.org/10.1186/s13321-018-0264-0openalex-snapshot
A novel interaction fingerprint derived from per atom score contributions: exhaustive evaluation of interaction fingerprint performance in docking based virtual screening
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Nonnegative Matrix Factorization: An Analytical and Interpretive Tool in Computational Biology
inferred← citeshttps://doi.org/10.1371/journal.pone.0069365openalex-snapshot
Re-Docking Scheme for Generating Near-Native Protein Complexes by Assembling Residue Interaction Fingerprints
inferred← citeshttps://doi.org/10.1371/journal.pone.0103902openalex-snapshot
Characterization of the PH1704 Protease from Pyrococcus horikoshii OT3 and the Critical Functions of Tyr120
inferred← citeshttps://doi.org/10.4018/978-1-5225-0115-2.ch005openalex-snapshot
Protein Ligand Interaction Fingerprints
inferred← citeshttps://doi.org/10.4018/978-1-5225-0115-2.ch012openalex-snapshot
Docking Methodologies and Recent Advances
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Docking Methodologies and Recent Advances
inferred← citeshttps://doi.org/10.4018/978-1-5225-1762-7.ch041openalex-snapshot
Protein Ligand Interaction Fingerprints
inferred← citeshttps://doi.org/10.4155/fmc.11.18openalex-snapshot
Integrating Structure-Based and Ligand-Based Approaches for Computational Drug Design
inferred← citeshttps://doi.org/10.4155/fmc.12.126openalex-snapshot
Fingerprint Design And Engineering Strategies: Rationalizing And Improving Similarity Search Performance
inferred← citeshttps://doi.org/10.5772/14457openalex-snapshot
Understanding Protein-Ligand Interactions Using Simulated Annealing in Dimensionally Reduced Fingerprint Representation
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