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44 results for “AlphaFold2”
A computational study of the structure and function of human Zrt and Irt-like proteins metal transporters: An elevator-type transport mechanism predicted by AlphaFold2
<p>Data produced and analyzed in the manuscript "A computational study of the structure and function of human Zrt and Irt-like proteins metal transporters: An elevator-type transport mechanism predicted by AlphaFold2" by Pasquadibisceglie et al.</p> <p><br> If you include these data in your manuscript, please cite: Pasquadibisceglie A, Leccese A and Polticelli F (2022) A computational study of the structure and function of human Zrt and Irt-like proteins metal transporters: An elevator-type transport mechanism predicted by AlphaFold2. <em>Front. Chem.</em> 10:1004815. doi: 10.3389/fchem.2022.1004815</p>
The docked poses from the docking screens against the AlphaFold2 models of the σ2 and 5HT2A receptors
<p>Though AlphaFold2 (AF2) models have had wide impact, they have had mixed success in retrospective ligand recognition. Here, we prospectively docked large libraries against unrefined AF2 models of the σ2 and 5-HT2A receptors, testing hundreds of new molecules and comparing results to docking against the experimental structures. Hit rates were high and similar for the experimental and the AF2 structures, as were affinities. The success of docking against the AF2 models was achieved despite differences in orthosteric residue conformations versus the experimental structures. Determination of the cryoEM structure for one of the more potent 5HT2A ligands from the AF2 docking revealed residue accommodations that resembled the AF2 prediction. AF2 models may sample conformations that differ from experimental structures but remain low energy and relevant for ligand discovery, extending the domain of structure-based ligand discovery. This repository contains docked poses shown in this study.</p> <p>The data contain:</p> <p>1) AlphaFold2 models of the σ2 and 5HT2A receptors used to generate these two docked poses:</p> <ul> <li>AF-Q5BJF2-F1-model_v1_prep.pdb is the AlphaFold2 model used for docking against the σ2 receptor.</li> <li>AF-P28223-F1-model_v1_prep.pdb is the AlphaFold2 model used for docking against the 5HT2A receptor.</li> </ul> <p>2) Docked poses of ZINC866533340 in the σ2 model and Z7757 (ZINClB000002x4yW) in the 5HT2A model:</p> <ul> <li>ZINC000866533340_af.mol2 is the docked pose of ZINC866533340 in the σ2 model.</li> <li>7757_af.mol2 is the docked pose of Z7757 (ZINClB000002x4yW) in the 5HT2A model.</li> </ul>
Modeling flexible protein structure with AlphaFold2 and cross-linking mass spectrometry
<p>Ensembles of models predicted by AlphaFold for the proteins C3 (Complement component 3), luciferase and QBP (glutamine-binding periplasmic protein). Models interpolated between two conformations of C3, and luciferase are also included. This dataset is cited in the following paper: https://www.biorxiv.org/content/10.1101/2023.09.11.557128v1</p>
Alphafold2 modeling of KCTD10 interactions with RNAPII machinery
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Exploring voltage-gated sodium channel conformations and protein-protein interactions using AlphaFold2
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The docked poses from the docking screens against the AlphaFold2 models of the σ2 and 5HT2A receptors
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Structural modeling of ion channels using AlphaFold2, RoseTTAFold2, and ESMFold
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Highly significant improvement of protein sequence alignments with AlphaFold2
<p>Data, figures and tables from the manuscript "Highly significant improvement of protein sequence alignments with AlphaFold2" (https://doi.org/10.1093/bioinformatics/btac625).</p> <p>The repository containing all the steps to replicate the analysis is available at GitHub (https://github.com/cbcrg/msa-af2-nf).</p> <p>*The authors Athanasios Baltzis and Leila Mansouri contributed equally.</p>
AlphaFold2 predicted structures of ThsA and ThsB proteins
<p>This Zenodo record contains the AlphaFold2 models described in the manuscript: Structural characterization of macro domain-containing Thoeris antiphage defense systems</p>
Dataset for "Advances in Docking Protocols for PPIs: Insights from AlphaFold2 and Molecular Dynamics Refinement"
<p>Dataset files used in 'Advances in Docking Protocols for PPIs: Insights from AlphaFold2 and Molecular Dynamics Refinement' (https://github.com/SysBioUAB/docking_benchmark)</p>
Alphafold2_ab_initio iterative predictions for folding intermediate identification
<p>Iterative structure predictions for protein PDB ids starts from 6.</p>
Alphafold2_ab_initio iterative predictions for folding intermediate identification
<div>PDB ids start from 5 and 7.</div> <div> <div> <p> </p> </div> </div>
Alphafold2_ab_initio iterative predictions for folding intermediate identification
<p><span>Iterative structure predictions for protein PDB ids starts from 2.</span></p>
ActTemp+sMSA dataset of "Biasing AlphaFold2 to predict GPCRs and Kinases with user-defined functional or structural properties"
<p>PDB models generated with the protocol described in "Biasing AlphaFold2 to predict GPCRs and Kinases with user-defined functional or structural properties"</p>
MSAs generated for RoseTTAFold and AlphaFold2
<p>The attached zip files contain MSAs generated for protein structures predicted by RoseTTAFold and AlphaFold2 for a study on the 15th iteration of the Critical Assessment for Structure Prediction (CASP15) available targets. Predicted structures as well as results can be found at https://github.com/Bhattacharya-Lab/CASP15</p>
Alphafold2 models of CD8a and CD28 based constructions
<p>Alphafold2 predictions of CD8a and CD28-based dimer constructions are deposited.</p>
DNA_test_129_Preprocessing_using_AlphaFold2
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Exploring Conformational Landscapes and Binding Mechanisms of Convergent Evolition for the SARS-CoV-2 Spike Omicron Variant Complexes with the ACE2 Receptor Using AlphaFold2-Based Structural Ensembles and Molecular Dynamics Simulations
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Atomistic Predictions and Network-Based Allosteric Analysis of Conformational Ensembles for the State-Switching ABL Kinase Mutants Using Combination of Alanine Sequence Scanning and Shallow Subsampling in AlphaFold2
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AlphaFold2 Modeling and Molecular Dynamics Simulations of the Conformational Ensembles for the SARS-CoV-2 Spike Omicron JN.1, KP.2 and KP.3 Variants : Mutational Profiling of Binding Energetics Reveals Epistatic Drivers of the ACE2 Affinity and Escape Hotspots of Antibody Resistance
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Allen Brain Atlas
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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.