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Molecular docking of balanol to dynamics snapshots of protein kinase A

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What this work says

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

inferredcites →https://doi.org/10.1002/(sici)1096-987x(19981115)19:14<1639::aid-jcc10>3.0.co;2-bopenalex-snapshot
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
inferredcites →https://doi.org/10.1002/(sici)1096-987x(199902)20:3<287::aid-jcc1>3.0.co;2-hopenalex-snapshot
Harmonic modes as variables to approximately account for receptor flexibility in ligand-receptor docking simulations: Application to DNA minor groove ligand complex
inferredcites →https://doi.org/10.1002/(sici)1097-0134(19981101)33:2<227::aid-prot7>3.0.co;2-fopenalex-snapshot
Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm
inferredcites →https://doi.org/10.1002/(sici)1097-0134(19990501)35:2<153::aid-prot2>3.0.co;2-eopenalex-snapshot
Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation
inferredcites →https://doi.org/10.1002/(sici)1097-0134(19991101)37:2<228::aid-prot8>3.0.co;2-8openalex-snapshot
Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking
inferredcites →https://doi.org/10.1002/(sici)1099-1352(199601)9:1<1::aid-jmr241>3.0.co;2-6openalex-snapshot
Automated docking of flexible ligands: Applications of autodock
inferredcites →https://doi.org/10.1002/(sici)1099-1352(199905/06)12:3<177::aid-jmr451>3.0.co;2-zopenalex-snapshot
Prediction of the binding energy for small molecules, peptides and proteins
inferredcites →https://doi.org/10.1002/bip.10218openalex-snapshot
The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme
inferredcites →https://doi.org/10.1002/jcc.1031openalex-snapshot
Solvent models for protein–ligand binding: Comparison of implicit solvent poisson and surface generalized born models with explicit solvent simulations
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/10.1006/jmbi.1996.0776openalex-snapshot
Molecular docking to ensembles of protein structures 1 1Edited by B. Honig
inferredcites →https://doi.org/10.1006/jmbi.2001.4551openalex-snapshot
FlexE: efficient molecular docking considering protein structure variations
inferredcites →https://doi.org/10.1016/s0009-2614(97)01074-9openalex-snapshot
Flexible docking of a ligand peptide to a receptor protein by multicanonical molecular dynamics simulation
inferredcites →https://doi.org/10.1016/s0010-4655(00)00065-5openalex-snapshot
High performance computational chemistry: An overview of NWChem a distributed parallel application
inferredcites →https://doi.org/10.1016/s0022-2836(02)01446-8openalex-snapshot
Dynamic Features of cAMP-dependent Protein Kinase Revealed by Apoenzyme Crystal Structure
inferredcites →https://doi.org/10.1016/s0022-2836(05)80038-5openalex-snapshot
Ligand docking to proteins with discrete side-chain flexibility
inferredcites →https://doi.org/10.1016/s0959-440x(00)00197-4openalex-snapshot
Macromolecular electrostatics: continuum models and their growing pains
inferredcites →https://doi.org/10.1021/bi982064gopenalex-snapshot
Determinants of Ligand Binding to cAMP-Dependent Protein Kinase
inferredcites →https://doi.org/10.1021/bi9820659openalex-snapshot
Crystal Structure of the Potent Natural Product Inhibitor Balanol in Complex with the Catalytic Subunit of cAMP-Dependent Protein Kinase
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/ja0160086openalex-snapshot
Fully Flexible Low-Mode Docking: Application to Induced Fit in HIV Integrase
inferredcites →https://doi.org/10.1021/ja0260162openalex-snapshot
Computational Drug Design Accommodating Receptor Flexibility: The Relaxed Complex Scheme
inferredcites →https://doi.org/10.1021/ja0273851openalex-snapshot
All-Atom Structure Prediction and Folding Simulations of a Stable Protein
inferredcites →https://doi.org/10.1021/ja955032eopenalex-snapshot
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J . Am . Chem . Soc . 1995 , 117 , 5179−5197
inferredcites →https://doi.org/10.1021/ja9939385openalex-snapshot
Molecular Dynamics Simulations of Nucleic Acids with a Generalized Born Solvation Model
inferredcites →https://doi.org/10.1063/1.1480013openalex-snapshot
Novel generalized Born methods
inferredcites →https://doi.org/10.1063/1.448118openalex-snapshot
Molecular dynamics with coupling to an external bath
inferredcites →https://doi.org/10.1063/1.464397openalex-snapshot
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
inferredcites →https://doi.org/10.1110/ps.0202302openalex-snapshot
Efficient docking of peptides to proteins without prior knowledge of the binding site
inferredcites →https://doi.org/10.1146/annurev.physchem.51.1.129openalex-snapshot
Generalized Born Models of Macromolecular Solvation Effects

What points at this work

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

inferred← citeshttps://doi.org/10.1002/9781118523063.ch8openalex-snapshot
Virtual Ligand Screening Against Comparative Models of Proteins
inferred← citeshttps://doi.org/10.1002/bip.20656openalex-snapshot
In silico profiling of tyrosine kinases binding specificity and drug resistance using Monte Carlo simulations with the ensembles of protein kinase crystal structures
inferred← citeshttps://doi.org/10.1002/chem.200701991openalex-snapshot
Total Synthesis of (−)‐Balanol, All Stereoisomers, Their N‐Tosyl Analogues, and Fully Protected Ophiocordin: An Easy Route to Hexahydroazepine Cores from Garner Aldehydes
inferred← citeshttps://doi.org/10.1002/jcc.20534openalex-snapshot
Can MM‐PBSA calculations predict the specificities of protein kinase inhibitors?
inferred← citeshttps://doi.org/10.1002/jcc.21090openalex-snapshot
Conformational selection of protein kinase A revealed by flexible‐ligand flexible‐protein docking
inferred← citeshttps://doi.org/10.1002/jcc.23026openalex-snapshot
Balancing target flexibility and target denaturation in computational fragment‐based inhibitor discovery
inferred← citeshttps://doi.org/10.1002/jmr.984openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/minf.202300250openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.366openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.4065openalex-snapshot
EDock‐ML: A web server for using ensemble docking with machine learning to aid drug discovery
inferred← citeshttps://doi.org/10.1002/prot.21287openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/prot.21423openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/prot.21666openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/prot.21781openalex-snapshot
Flexible protein–flexible ligand docking with disrupted velocity simulated annealing
inferred← citeshttps://doi.org/10.1002/prot.21977openalex-snapshot
Induced fit in liver X receptor beta: A molecular dynamics‐based investigation
inferred← citeshttps://doi.org/10.1002/prot.22223openalex-snapshot
Selected‐fit versus induced‐fit protein binding: Kinetic differences and mutational analysis
inferred← citeshttps://doi.org/10.1002/prot.22826openalex-snapshot
Flexibility and inhibitor binding in cdc25 phosphatases
inferred← citeshttps://doi.org/10.1002/prot.25899openalex-snapshot
Using machine learning to improve ensemble docking for drug discovery
inferred← citeshttps://doi.org/10.1002/qsar.200910031openalex-snapshot
A Restrained Molecular Dynamics Empirical Approach for Generating a Small Set of Structures Representative of the Internal Flexibility of a Receptor
inferred← citeshttps://doi.org/10.1007/7653_2015_56openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-1-61779-520-6_9openalex-snapshot
Leveraging Structural Information for the Discovery of New Drugs: Computational Methods
inferred← citeshttps://doi.org/10.1007/978-90-481-2368-1_2openalex-snapshot
Complementarity of Hydrophobic/Hydrophilic Properties In Protein—Ligand Complexes: A New Tool to Improve Docking Results
inferred← citeshttps://doi.org/10.1007/s00894-007-0257-9openalex-snapshot
Multiple-step virtual screening using VSM-G: overview and validation of fast geometrical matching enrichment
inferred← citeshttps://doi.org/10.1007/s00894-012-1555-4openalex-snapshot
A flexible-protein molecular docking study of the binding of ruthenium complex compounds to PIM1, GSK-3β, and CDK2/Cyclin A protein kinases
inferred← citeshttps://doi.org/10.1007/s00894-014-2491-2openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s00894-017-3384-yopenalex-snapshot
Ensemble-based virtual screening: identification of a potential allosteric inhibitor of Bcr-Abl
inferred← citeshttps://doi.org/10.1007/s10822-021-00391-9openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/b978-0-12-374145-5.00181-9openalex-snapshot
Inhibitors of Cyclic AMP- and Cyclic GMP-Dependent Protein Kinases
inferred← citeshttps://doi.org/10.1016/j.bbapap.2007.10.005openalex-snapshot
Flexible ligand–flexible protein docking in protein kinase systems
inferred← citeshttps://doi.org/10.1016/j.bpj.2010.01.014openalex-snapshot
Predicting Interaction Sites from the Energetics of Isolated Proteins: A New Approach to Epitope Mapping
inferred← citeshttps://doi.org/10.1016/j.coph.2010.09.001openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.dental.2024.07.035openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.molstruc.2015.05.007openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.partic.2023.03.023openalex-snapshot
Synergistic precipitant powered self-assembly of papain for cross-linked enzyme crystals preparation
inferred← citeshttps://doi.org/10.1016/j.sbi.2008.01.004openalex-snapshot
Flexible ligand docking to multiple receptor conformations: a practical alternative
inferred← citeshttps://doi.org/10.1016/j.str.2009.05.010openalex-snapshot
Improving Structure-Based Function Prediction Using Molecular Dynamics
inferred← citeshttps://doi.org/10.1016/j.str.2014.06.002openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00791openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci2005934openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci300342zopenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci4005767openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci500301sopenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci500414bopenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci9003706openalex-snapshot
Molecular Docking Screens Using Comparative Models of Proteins
inferred← citeshttps://doi.org/10.1021/jp411111gopenalex-snapshot
Molecular Dynamics Simulation Studies on the Positive Cooperativity of the Kemptide Substrate with Protein Kinase A Induced by the ATP Ligand
inferred← citeshttps://doi.org/10.1038/s41420-018-0108-8openalex-snapshot
YL064 directly inhibits STAT3 activity to induce apoptosis of multiple myeloma cells
inferred← citeshttps://doi.org/10.1039/c3mb70620fopenalex-snapshot
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inferred← citeshttps://doi.org/10.1039/c4cp04528aopenalex-snapshot
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inferred← citeshttps://doi.org/10.1063/1.2710270openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/glycob/cwae025openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/cbdd.13764openalex-snapshot
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inferred← citeshttps://doi.org/10.1142/s0219633619200013openalex-snapshot
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inferred← citeshttps://doi.org/10.1146/annurev.biophys.36.040306.132550openalex-snapshot
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inferred← citeshttps://doi.org/10.11606/t.46.2016.tde-03082016-145527openalex-snapshot
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inferred← citeshttps://doi.org/10.11606/t.46.2018.tde-14122017-135400openalex-snapshot
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inferred← citeshttps://doi.org/10.1186/s12859-017-1955-7openalex-snapshot
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inferred← citeshttps://doi.org/10.1371/journal.pcbi.1005039openalex-snapshot
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inferred← citeshttps://doi.org/10.1517/17460441.2015.1078308openalex-snapshot
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inferred← citeshttps://doi.org/10.2172/877558openalex-snapshot
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inferred← citeshttps://doi.org/10.2174/138161211796355056openalex-snapshot
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inferred← citeshttps://doi.org/10.4172/jpb.1000348openalex-snapshot
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inferred← citeshttps://doi.org/10.5012/bkcs.2012.33.3.770openalex-snapshot
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inferred← citeshttps://doi.org/10.6026/97320630003014openalex-snapshot
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