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DOLINA – Docking Based on a Local Induced-Fit Algorithm: Application toward Small-Molecule Binding to Nuclear Receptors

https://doi.org/10.1021/ci400098y
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What this work says

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

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Side-chain flexibility in proteins upon ligand binding
inferredcites →https://doi.org/10.1002/jcc.22948openalex-snapshot
Flexible protein‐ligand docking using the Fleksy protocol
inferredcites →https://doi.org/10.1002/jcc.23087openalex-snapshot
Modeling loop backbone flexibility in receptor‐ligand docking simulations
inferredcites →https://doi.org/10.1002/prot.21086openalex-snapshot
ROSETTALIGAND: Protein–small molecule docking with full side‐chain flexibility
inferredcites →https://doi.org/10.1007/bf00117280openalex-snapshot
Class IV charge models: A new semiempirical approach in quantum chemistry
inferredcites →https://doi.org/10.1007/s10822-008-9188-5openalex-snapshot
A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)
inferredcites →https://doi.org/10.1007/s10822-012-9611-9openalex-snapshot
Consensus Induced Fit Docking (cIFD): methodology, validation, and application to the discovery of novel Crm1 inhibitors
inferredcites →https://doi.org/10.1016/0022-2836(91)90859-5openalex-snapshot
“Soft docking”: Matching of molecular surface cubes
inferredcites →https://doi.org/10.1016/0022-2860(92)85083-sopenalex-snapshot
CRC Handbook of Chemistry and Physics
inferredcites →https://doi.org/10.1016/j.bmc.2011.09.023openalex-snapshot
A new method for induced fit docking (genius) and its application to virtual screening of novel HCV NS3-4A protease inhibitors
inferredcites →https://doi.org/10.1016/j.coph.2010.09.001openalex-snapshot
Computer-aided drug-discovery techniques that account for receptor flexibility
inferredcites →https://doi.org/10.1016/j.drudis.2009.01.003openalex-snapshot
Managing protein flexibility in docking and its applications
inferredcites →https://doi.org/10.1016/j.ejmech.2011.09.056openalex-snapshot
Molecular mechanism of serotonin transporter inhibition elucidated by a new flexible docking protocol
inferredcites →https://doi.org/10.1016/j.jmb.2008.11.010openalex-snapshot
RosettaLigand Docking with Full Ligand and Receptor Flexibility
inferredcites →https://doi.org/10.1016/j.sbi.2008.01.004openalex-snapshot
Flexible ligand docking to multiple receptor conformations: a practical alternative
inferredcites →https://doi.org/10.1021/bi2004558openalex-snapshot
Efficient Incorporation of Protein Flexibility and Dynamics into Molecular Docking Simulations
inferredcites →https://doi.org/10.1021/ci2005934openalex-snapshot
Potential and Limitations of Ensemble Docking
inferredcites →https://doi.org/10.1021/ci800081sopenalex-snapshot
Fully Automated Molecular Mechanics Based Induced Fit Protein−Ligand Docking Method
inferredcites →https://doi.org/10.1021/ja00065a080openalex-snapshot
Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model. [Erratum to document cited in CA103(2):11627f]
inferredcites →https://doi.org/10.1021/ja00168a021openalex-snapshot
A new force field for modeling metalloproteins
inferredcites →https://doi.org/10.1021/ja00315a051openalex-snapshot
A new force field for molecular mechanical simulation of nucleic acids and proteins
inferredcites →https://doi.org/10.1021/ja202726yopenalex-snapshot
How Does a Drug Molecule Find Its Target Binding Site?
inferredcites →https://doi.org/10.1021/jm049756popenalex-snapshot
Soft Docking and Multiple Receptor Conformations in Virtual Screening
inferredcites →https://doi.org/10.1021/jm800217kopenalex-snapshot
Flexible Side Chain Models Improve Enrichment Rates in In Silico Screening
inferredcites →https://doi.org/10.1021/jm8009958openalex-snapshot
Four-Dimensional Docking: A Fast and Accurate Account of Discrete Receptor Flexibility in Ligand Docking
inferredcites →https://doi.org/10.1021/jp911085dopenalex-snapshot
Dynamic Ligand-Induced-Fit Simulation via Enhanced Conformational Samplings and Ensemble Dockings: A Survivin Example
inferredcites →https://doi.org/10.1021/jp9610776openalex-snapshot
Model for Aqueous Solvation Based on Class IV Atomic Charges and First Solvation Shell Effects
inferredcites →https://doi.org/10.1074/jbc.m705524200openalex-snapshot
Structural Characterization of the Human Androgen Receptor Ligand-binding Domain Complexed with EM5744, a Rationally Designed Steroidal Ligand Bearing a Bulky Chain Directed toward Helix 12
inferredcites →https://doi.org/10.1111/cbdd.12051openalex-snapshot
Accounting for Receptor Flexibility and Enhanced Sampling Methods in Computer‐Aided Drug Design
inferredcites →https://doi.org/10.1186/1471-2105-12-417openalex-snapshot
Predicting protein ligand binding motions with the conformation explorer
inferredcites →https://doi.org/10.1186/1479-7364-5-5-497openalex-snapshot
Survey of public domain software for docking simulations and virtual screening

What points at this work

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

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Improvements, trends, and new ideas in molecular docking: 2012–2013 in review
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Protein Ligand Docking in Drug Discovery
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Molecular Docking—A Solved Problem?
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Molecular docking—A solved problem?
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Evaluation of the novel algorithm of flexible ligand docking with moveable target-protein atoms
inferred← citeshttps://doi.org/10.1016/j.taap.2023.116638openalex-snapshot
Virtual screening and biological evaluation to identify pharmaceuticals potentially causing hypertension and hypokalemia by inhibiting steroid 11β-hydroxylase
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Bisphenol TMC exhibits greater estrogenic activity than Bisphenol A and three other structural analogues exemplified by higher estrogen receptor α-mediated gene expression and breast cancer cell proliferation
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Molecular mechanisms of endocrine and metabolic disruption: An in silico study on antitrypanosomal natural products and some derivatives
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P12-08 Biological evaluation of pharmaceuticals inhibiting 11β-hydroxylase identified by virtual screening
inferred← citeshttps://doi.org/10.1016/s0378-4274(23)00715-4openalex-snapshot
P16-24: In silico and in vitro workflow to identify pharmaceuticals inhibiting CYP17A1 and CYP11B1
inferred← citeshttps://doi.org/10.1021/acs.chemrestox.7b00070openalex-snapshot
In Silico Prediction of the Toxic Potential of Lupeol
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c01194openalex-snapshot
Computational Assessment of Combination Therapy of Androgen Receptor-Targeting Compounds
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c01403openalex-snapshot
Conformational Changes of Thyroid Receptors in Response to Antagonists
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00744openalex-snapshot
Binding Mode and Induced Fit Predictions for Prospective Computational Drug Design
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.0c02227openalex-snapshot
Decision Making in Structure-Based Drug Discovery: Visual Inspection of Docking Results
inferred← citeshttps://doi.org/10.1101/2023.11.13.566916openalex-snapshot
Quality Matters: Deep Learning-Based Analysis of Protein-Ligand Interactions with Focus on Avoiding Bias
inferred← citeshttps://doi.org/10.1101/2023.11.16.567496openalex-snapshot
PanScreen: A Comprehensive Approach to Off-Target Liability Assessment
inferred← citeshttps://doi.org/10.1186/s13321-017-0216-0openalex-snapshot
Searching for bioactive conformations of drug-like ligands with current force fields: how good are we?
inferred← citeshttps://doi.org/10.1371/journal.pone.0202534openalex-snapshot
Microsecond MD simulations of human CYP2D6 wild-type and five allelic variants reveal mechanistic insights on the function
inferred← citeshttps://doi.org/10.1517/17460441.2015.1094458openalex-snapshot
Understanding the challenges of protein flexibility in drug design
inferred← citeshttps://doi.org/10.18632/oncotarget.10037openalex-snapshot
Discovery and characterization of a novel potent type II native and mutant BCR-ABL inhibitor (CHMFL-074) for Chronic Myeloid Leukemia (CML)
inferred← citeshttps://doi.org/10.3390/ijms19061784openalex-snapshot
Endocrine Disruption at the Androgen Receptor: Employing Molecular Dynamics and Docking for Improved Virtual Screening and Toxicity Prediction
inferred← citeshttps://doi.org/10.35652/igjps.2022.12006openalex-snapshot
A Review on Computational Software Tools for Drug Design and Discovery
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