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LIBSA – A Method for the Determination of Ligand-Binding Preference to Allosteric Sites on Receptor Ensembles

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What this work says

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

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AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
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CHARMM general force field: A force field for drug‐like molecules compatible with the CHARMM all‐atom additive biological force fields
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Algorithms for computational solvent mapping of proteins
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Computational detection of the binding‐site hot spot at the remodeled human growth hormone–receptor interface
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An improved relaxed complex scheme for receptor flexibility in computer-aided drug design
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Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges
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Noise suppression by spectral magnitude estimation —mechanism and theoretical limits—
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VMD: Visual molecular dynamics
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Structural resemblances and comparisons of the relative pharmacological properties of imatinib and nilotinib
inferredcites →https://doi.org/10.1016/j.febslet.2006.01.074openalex-snapshot
Blind docking of drug‐sized compounds to proteins with up to a thousand residues
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Crystal structure at 1.9-A resolution of human immunodeficiency virus (HIV) II protease complexed with L-735,524, an orally bioavailable inhibitor of the HIV proteases
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The Structural Basis of Estrogen Receptor/Coactivator Recognition and the Antagonism of This Interaction by Tamoxifen
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How Does Darunavir Prevent HIV-1 Protease Dimerization?
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Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules
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Computational Drug Design Accommodating Receptor Flexibility: The Relaxed Complex Scheme
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Discovery of a Novel Binding Trench in HIV Integrase
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A Critical Assessment of Docking Programs and Scoring Functions
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Automatic and Efficient Decomposition of Two-Dimensional Structures of Small Molecules for Fragment-Based High-Throughput Docking
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From Docking False-Positive to Active Anti-HIV Agent
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All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
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Benzylidene derivatives of andrographolide inhibit growth of breast and colon cancer cells in vitro by inducing G1 arrest and apoptosis
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Crystal structure of the β2 adrenergic receptor–Gs protein complex
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Small-molecule ligands bind to a distinct pocket in Ras and inhibit SOS-mediated nucleotide exchange activity
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In silico discovery of small-molecule Ras inhibitors that display antitumor activity by blocking the Ras–effector interaction
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Andrographolide derivatives inhibit guanine nucleotide exchange and abrogate oncogenic Ras function
inferredcites →https://doi.org/10.1074/jbc.m009870200openalex-snapshot
Crystal Structure of a Mutant hERα Ligand-binding Domain Reveals Key Structural Features for the Mechanism of Partial Agonism
inferredcites →https://doi.org/10.1093/bioinformatics/btm378openalex-snapshot
Wordom: a program for efficient analysis of molecular dynamics simulations
inferredcites →https://doi.org/10.1093/bioinformatics/btp036openalex-snapshot
Fragment-based identification of druggable ‘hot spots’ of proteins using Fourier domain correlation techniques
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The Golden Ratio and Fibonacci Numbers
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CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures
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Algorithm AS 136: A K-Means Clustering Algorithm

What points at this work

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

inferred← citeshttps://doi.org/10.1002/prot.24786openalex-snapshot
Binding hotspots on K-ras: Consensus ligand binding sites and other reactive regions from probe-based molecular dynamics analysis
inferred← citeshttps://doi.org/10.1007/978-1-0716-0270-6_8openalex-snapshot
Systematic Exploration of Binding Modes of Ligands on Drug Targets
inferred← citeshttps://doi.org/10.1016/b978-0-12-409547-2.12324-8openalex-snapshot
Allosteric Modulators
inferred← citeshttps://doi.org/10.1021/acs.jctc.7b00130openalex-snapshot
Mixed-Probe Simulation and Probe-Derived Surface Topography Map Analysis for Ligand Binding Site Identification
inferred← citeshttps://doi.org/10.1021/acsomega.3c04013openalex-snapshot
Small-Molecule Inhibition of KRAS through Conformational Selection
inferred← citeshttps://doi.org/10.1080/07391102.2021.1935320openalex-snapshot
Electronic and structural study of T315I mutated form in DFG-out conformation of BCR-ABL inhibitors
inferred← citeshttps://doi.org/10.1080/21541248.2019.1655883openalex-snapshot
Approaches to inhibiting oncogenic K-Ras
inferred← citeshttps://doi.org/10.1093/abbs/gmv100openalex-snapshot
Computational allosteric ligand binding site identification on Ras proteins
inferred← citeshttps://doi.org/10.1111/cbdd.13519openalex-snapshot
Multi‐target, ensemble‐based virtual screening yields novel allosteric KRAS inhibitors at high success rate
inferred← citeshttps://doi.org/10.1186/s12859-022-04995-2openalex-snapshot
A multilayer dynamic perturbation analysis method for predicting ligand–protein interactions
inferred← citeshttps://doi.org/10.1186/s13321-017-0255-6openalex-snapshot
Systematic exploration of multiple drug binding sites
inferred← citeshttps://doi.org/10.1208/s12248-015-9776-yopenalex-snapshot
Computational Advances for the Development of Allosteric Modulators and Bitopic Ligands in G Protein-Coupled Receptors
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1003872openalex-snapshot
Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein Interfaces
inferred← citeshttps://doi.org/10.1371/journal.pone.0198632openalex-snapshot
Allosteric binding sites in Rab11 for potential drug candidates
inferred← citeshttps://doi.org/10.15476/elte.2018.091openalex-snapshot
Systematic exploration of multiple drug binding sites
inferred← citeshttps://doi.org/10.6084/m9.figshare.21485795openalex-snapshot
Additional file 1 of A multilayer dynamic perturbation analysis method for predicting ligand–protein interactions
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