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121 results for “Allosterism”
GluN2B-specific NMDAR positive allosteric modulation reverses cognitive and behavioral abnormalities in Mecp2 and Disc1 transgenic mice
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Comment on "Ancient origins of allosteric activation in a Ser-Thr kinase"
<p>Hadzipasic <em>et al.</em> used ancestral sequence reconstruction to identify historical sequence substitutions that putatively caused Aurora kinases to evolve allosteric regulation. We show that their results arise from an implausible phylogeny and sparse sequence sampling. Addressing either problem reverses their inferences: allostery and the amino acids that confer it were not gained during the diversification of eukaryotes but were lost in a subgroup of Fungi.</p>
The allosteric landscape of the Src kinase
<p>Fitness scores, MoCHI weights and miscellaneous files required to reproduce the analyses and figures in "The allosteric landscape of Src" (https://github.com/lehner-lab/src_allostery/blob/main/README.md) - Beltran A et al., 2025.</p>
MATLAB results files of MS-based analysis and raw photometer data - Systematic identification of allosteric effectors in Escherichia coli metabolism
<p>MATLAB result tables from progress curve analysis for each of the 19 enzymes tested with 79 potential effectors metabolites in MS-based approach. Excel tables with labelled photometer data.</p>
The pocketome of G-protein-coupled receptors reveals previously untargeted allosteric sites
<p>Supplementary Data 1: list of all analysed structures together with the docking files</p> <p>Supplementary Data 2: grid files, template and README for visualising the class-specific density maps by using Pymol</p>
Raw data for: Structure of the human dopamine transporter and mechanisms of allosteric inhibition
<p>This repository contains raw data related to "Structure of the human dopamine transporter and mechanisms of allosteric inhibition" by Srivastava et al.</p> <p>Included are molecular dynamics input parameter files, amber prmtop, production trajectories and analysis scripts. Trajectories are subsampled with one frame every 10 ns. </p> <p> </p> <p>Contact information:</p> <p>Name: Md Fulbabu Sk</p> <p>Institution: Theoretical and Computational Biophysics Group (TCBG), Beckman Institute, University of Illinois Urbana Champaign</p> <p>Address: 405 N. Mathews Avenue, Urbana, Illinois 61801</p> <p>Email: mfsk@illinois.edu</p>
MD data for Structural basis for allosteric regulation of human phosphofructokinase-1
<p>This dataset contains MD data related to the article "Structural basis for allosteric regulation of human phosphofructokinase-1".</p> <p><strong>MD_files.zip:</strong><br>Initial geometries, input files, and final geometries for MD simulations presented in the article.</p> <p><strong>node_degeneracies.xlsx:<br></strong>Results of network path analysis. The spreadsheet contains normalized node degeneracies for residues along the possible paths connecting the C-terminal tail residues and selected residues from the active site and allosteric sites, as shown in Fig S7.</p> <p> </p>
Reproducibility Package for "Design of an allosterically modulated doxycycline and doxorubicin-binding protein"
<p>Files used for MUMBO calculations depicted in the Supplementary Figure 1 of the manuscript "Design of an allosterically modulated doxycycline and doxorubicin-binding protein"</p>
Computational Data for Identification of an allosteric binding site on the Glycine Transporter, GlyT2
<p>Input structures and gromacs trajectories for Identification of an allosteric binding site on the Glycine Transporter, GlyT2, for bioactive lipid analgensics</p>
Structural Model of OSM-OSMRβ-gp130 Ternary Complex Reveals the Pathways of Allosteric Communication in OSM Signaling
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[PART 3] A twist of fate: the helix-turn-helix motif in Pseudomonas aeruginosa ExsA can allosterically stabilize the ligand-binding domain
<p>1273- ExsA - Dimer1 without DNA - alphaFold compact - 230ns/day 10x500ns<br>*1274- ExsA - Dimer2 without DNA - xtal extended (like 1026) - 10x1µs (not everything is 1 µs)<br>1275- ExsA - Dimer3 without DNA - made by hand / 150ns/day (reps 1-5 broken, reps 6-10 correct)<br>*1276- ExsA- monomer - Site1-PexoT - 240 ns/day - 10x1µs (some replicas have pieces missing)<br>*1277- ExsA- monomer - Site2-PexoT - 10x1µs<br>*1278- ExsA - Dimer2 with broken DNA - xtal extended (like 1026) - 5x200ns?</p>
[PART 2] A twist of fate: the helix-turn-helix motif in Pseudomonas aeruginosa ExsA can allosterically stabilize the ligand-binding domain
<p>1273- ExsA - Dimer1 without DNA - alphaFold compact <br>1274- ExsA - Dimer2 without DNA - xtal extended <br>1275- ExsA - Dimer3 without DNA - made by hand (reps 1-5 broken, reps 6-10 correct)<br>1276- ExsA- monomer - Site1-PexoT <br>1277- ExsA- monomer - Site2-PexoT<br>1278- ExsA - Dimer2 with broken DNA</p>
Gliflozins, sucrose and flavonoids are allosteric activators of lecithin-cholesterol acyltransferase
<p>Computational data of publication "Gliflozins, sucrose and flavonoids are allosteric activators of lecithin-cholesterol acyltransferase" by Akseli Niemelä, Laura Giorgi, Sirine Nouri, Betül Yurttaş, Khushbu Rauniyar, Michael Jeltsch and Artturi Koivuniemi.</p>
Additional data "Client binding shifts the populations of dynamic Hsp90 conformations through an allosteric network"
<p>Additional data containing chemical shift perturbations and intensity changes of Hsp90 upon client binding, intermolecular PREs, and raw scattering data of Hsp90-client complexes.</p>
Allosteric modulation of the adenosine A2A receptor by cholesterol
<p>Cholesterol is a major component of the cell membrane and commonly regulates membrane protein function. Here, we investigate how cholesterol modulates the conformational equilibria and signaling of the adenosine A2A receptor (A2AR) in reconstituted phospholipid nanodiscs. This model system conveniently excludes possible effects arising from cholesterol-induced phase separation or receptor oligomerization and focuses on the question of allostery. GTP hydrolysis assays show that cholesterol weakly enhances the basal signaling of A2AR while decreasing the agonist EC50. Fluorine nuclear magnetic resonance (19F NMR) spectroscopy shows that this enhancement arises from an increase in the receptor's active state population and a G-protein-bound precoupled state. 19F NMR of fluorinated cholesterol analogs reveals transient interactions with A2AR, indicating a lack of high-affinity binding or direct allosteric modulation. The combined results suggest that the observed allosteric effects are largely indirect and originate from cholesterol-mediated changes in membrane properties, as shown by membrane fluidity measurements and high-pressure NMR.</p>
Dataset for modeling of binding modes of xanthine derivatives as allosteric inhibitors of MTHFD2
<p>Dataset with structures from docking and MD simulation trajectories, and exploration of selectivity, of xanthine derived compounds targeting the allosteric site of MTHFD2 versus the isoform MTHFD1. </p>
Receptor cavity-based screening reveals potential allosteric modulators of gonadotropin receptors in carp (Cyprinus carpio)
<p>The dataset include phase database consisting of prepared ligand used in screening of potential allosteric modulators for carp FSHR and LHR. the original dataset were sourced from The compound libraries from <a href="https://enamine.net/compound-libraries">https://enamine.net/compound-libraries</a> and are free to access and downloaded and used as per the mentioned sites terms and conditions the Datasets given here are processed databases constructed using the Phase module (Phase, Schrödinger, LLC, New York, NY, 2021.).</p>
Dataset for: Modeling Allosteric Mechanisms of Eukaryotic Type II Topoisomerases
<p>The set of molecular dynamics trajectories generated and analyzed in the paper "Modeling Allosteric Mechanisms of Eukaryotic Type II Topoisomerases." <strong>Citations should refer directly to the manuscript. </strong> </p> <p>The uploaded zip file "trajectory_data.zip" contains trajectories for the (1) ATP (2) ADP (3) Apo (4) D26N (5) R1128G and (6) D26N/R1128G h3k9ac systems. In each directory is 5 XTC files, which correspond to the trajectories for the 5 different simulations performed for each system, along with an AMBER-formated PRMTOP file. Solvent molecules were removed from each file, and trajectories were strided such that there is one frame per 100 ps. </p>
MD data for "Xanomeline displays concomitant orthosteric and allosteric binding modes at the M4 mAChR".
<p>MD simulations for "W.A. Burger, V. Pham, Z. Vuckovic, A.S. Powers, J.I. Mobbs, Y. Laloudakis, A. Glukhova, D. Wootten, A.B. Tobin, P.M. Sexton, S.M. Paul, C.C. Felder, R. Radostin, R.O. Dror, A. Christopoulos, C. Valant, and D.M. Thal. Xanomeline displays concomitant orthosteric and allosteric binding modes at the M4 mAChR. Nature Communications, 14(1): 5440 (2023)."</p> <p> </p>
A Study of BDTX-189, an Orally Available Allosteric ErbB Inhibitor, in Patients With Advanced Solid Tumors.
ClinicalTrials.gov study NCT04209465. IPD Sharing: NO. Countries: 4. Publications: 0.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.