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How Good Are State-of-the-Art Docking Tools in Predicting Ligand Binding Modes in Protein–Protein Interfaces?
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
inferredcites →https://doi.org/10.1002/0471250953.bi0814s24openalex-snapshot
Using AutoDock for Ligand‐Receptor Docking
inferredcites →https://doi.org/10.1002/1521-3773(20020802)41:15<2644::aid-anie2644>3.0.co;2-oopenalex-snapshot
Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors
inferredcites →https://doi.org/10.1002/cmdc.200900146openalex-snapshot
Elastic Potential Grids: Accurate and Efficient Representation of Intermolecular Interactions for Fully Flexible Docking
inferredcites →https://doi.org/10.1002/cmdc.200900314openalex-snapshot
Comparison of Structure‐ and Ligand‐Based Virtual Screening Protocols Considering Hit List Complementarity and Enrichment Factors
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/10.1002/prot.10232openalex-snapshot
A new test set for validating predictions of protein–ligand interaction
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The atomic structure of protein-protein recognition sites 1 1Edited by A. R. Fersht
inferredcites →https://doi.org/10.1006/jmbi.1999.3371openalex-snapshot
Knowledge-based scoring function to predict protein-ligand interactions
inferredcites →https://doi.org/10.1016/j.cbpa.2011.05.024openalex-snapshot
Chemical and structural lessons from recent successes in protein–protein interaction inhibition (2P2I)
inferredcites →https://doi.org/10.1016/j.drudis.2008.10.009openalex-snapshot
Predicting druggable binding sites at the protein–protein interface
inferredcites →https://doi.org/10.1016/s1359-6446(05)03386-6openalex-snapshot
Ligand efficiency indices as guideposts for drug discovery
inferredcites →https://doi.org/10.1021/ci200322sopenalex-snapshot
Hot Spots and Transient Pockets: Predicting the Determinants of Small-Molecule Binding to a Protein–Protein Interface
inferredcites →https://doi.org/10.1021/ci700470copenalex-snapshot
Investigation of MM-PBSA Rescoring of Docking Poses
inferredcites →https://doi.org/10.1021/ci800298zopenalex-snapshot
Empirical Scoring Functions for Advanced Protein−Ligand Docking with PLANTS
inferredcites →https://doi.org/10.1021/ci900056copenalex-snapshot
Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy
inferredcites →https://doi.org/10.1021/jm025507uopenalex-snapshot
Docking into Knowledge-Based Potential Fields: A Comparative Evaluation of DrugScore
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/10.1038/nature06526openalex-snapshot
Reaching for high-hanging fruit in drug discovery at protein–protein interfaces
inferredcites →https://doi.org/10.1073/pnas.93.1.13openalex-snapshot
Principles of protein-protein interactions.
inferredcites →https://doi.org/10.1093/nar/gkq471openalex-snapshot
DrugScorePPI webserver: fast and accurate in silico alanine scanning for scoring protein–protein interactions
inferredcites →https://doi.org/10.1101/pdb.prot5200openalex-snapshot
Computational Docking of Biomolecular Complexes with AutoDock
inferredcites →https://doi.org/10.1126/science.1096361openalex-snapshot
The Many Roles of Computation in Drug Discovery
inferredcites →https://doi.org/10.2174/092986706778201530openalex-snapshot
Targeting Protein-Protein Interactions with Small Molecules: Challenges and Perspectives for omputational Binding Epitope Detection and Ligand Finding
inferredcites →https://doi.org/10.2174/138161212802651553openalex-snapshot
Modulating Protein-Protein Interactions: From Structural Determinants of Binding to Druggability Prediction to Application
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/cbdv.202200933openalex-snapshot
Identification of Four New Chemical Series of Small Drug‐Like Natural Products as Potential Neuropilin‐1 Inhibitors by Structure‐Based Virtual Screening: Pharmacophore‐Based Molecular Docking and Dynamics Simulation
inferred← citeshttps://doi.org/10.1002/cbic.202300812openalex-snapshot
Identification, characterization and application of M16AT, a new organic solvent–tolerant (R)–enantio–selective type IV amine transaminase from Mycobacterium sp. ACS1612
inferred← citeshttps://doi.org/10.1002/jcc.24259openalex-snapshot
Flexible CDOCKER : Development and application of a pseudo‐explicit structure‐based docking method within CHARMM
inferred← citeshttps://doi.org/10.1002/jmr.2471openalex-snapshot
Improvements, trends, and new ideas in molecular docking: 2012–2013 in review
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Towards the Next Generation of Computational Chemogenomics Tools
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Drug‐Like ProteinProtein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology
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Computational Methods Applicable to the Discovery of Small-Molecule Inhibitors of Protein-Protein Interactions
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/10.1016/j.cbpa.2013.10.011openalex-snapshot
Druggable protein–protein interactions – from hot spots to hot segments
inferred← citeshttps://doi.org/10.1016/j.ejmech.2015.09.024openalex-snapshot
Mutational mapping of the transmembrane binding site of the G-protein coupled receptor TGR5 and binding mode prediction of TGR5 agonists
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Structure-based drug repositioning over the human TMPRSS2 protease domain: search for chemical probes able to repress SARS-CoV-2 Spike protein cleavages
inferred← citeshttps://doi.org/10.1016/j.pbiomolbio.2015.02.006openalex-snapshot
In silico design of low molecular weight protein–protein interaction inhibitors: Overall concept and recent advances
inferred← citeshttps://doi.org/10.1016/j.ymeth.2017.08.006openalex-snapshot
In silico structure-based approaches to discover protein-protein interaction-targeting drugs
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00545openalex-snapshot
Fast Rescoring Protocols to Improve the Performance of Structure-Based Virtual Screening Performed on Protein–Protein Interfaces
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00373openalex-snapshot
Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00582openalex-snapshot
Converging a Knowledge-Based Scoring Function: DrugScore2018
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.7b01221openalex-snapshot
Structure-Based Design of Non-natural Macrocyclic Peptides That Inhibit Protein–Protein Interactions
inferred← citeshttps://doi.org/10.1021/acssensors.0c02480openalex-snapshot
An Approach for the Real-Time Quantification of Cytosolic Protein–Protein Interactions in Living Cells
inferred← citeshttps://doi.org/10.1021/ci300417yopenalex-snapshot
How to Improve Docking Accuracy of AutoDock4.2: A Case Study Using Different Electrostatic Potentials
inferred← citeshttps://doi.org/10.1021/ci4005332openalex-snapshot
HADDOCK2P2I: A Biophysical Model for Predicting the Binding Affinity of Protein–Protein Interaction Inhibitors
inferred← citeshttps://doi.org/10.1039/c4md00328dopenalex-snapshot
Rational design of protein–protein interaction inhibitors
inferred← citeshttps://doi.org/10.1039/c7cp05937jopenalex-snapshot
Formation and structure of the ferryl [FeO] intermediate in the non-haem iron halogenase SyrB2: classical and QM/MM modelling agree
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The metagenome‐derived esterase PET40 is highly promiscuous and hydrolyses polyethylene terephthalate ( PET )
inferred← citeshttps://doi.org/10.1201/b18799-21openalex-snapshot
In Silico Approaches Assisting the Rational Design of Low Molecular Weight Protein–Protein Interaction Modulators
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1004586openalex-snapshot
AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1005937openalex-snapshot
Modeling the assembly order of multimeric heteroprotein complexes
inferred← citeshttps://doi.org/10.1371/journal.pone.0089466openalex-snapshot
DrugScorePPI Knowledge-Based Potentials Used as Scoring and Objective Function in Protein-Protein Docking
inferred← citeshttps://doi.org/10.1371/journal.pone.0158898openalex-snapshot
GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing
inferred← citeshttps://doi.org/10.31390/gradschool_dissertations.4233openalex-snapshot
Scheduling and Tuning Kernels for High-performance on Heterogeneous Processor Systems
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Structure-Based Design of Small-Molecule Protein–Protein Interaction Modulators: The Story so Far
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An Approach for the Real-Time Quantification of Cytosolic Protein-Protein Interactions in Living Cells
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