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8 results for “Protein Structure Refinement”
Benchmark Datasets for: EGR: Equivariant Graph Refinement and Assessment of 3D Protein Complex Structures
<p>This archive contains three benchmark datasets associated with the Equivariant Graph Refiner (EGR), two for protein complex structure refinement (PSR Test and Benchmark 2) and the other for protein complex structure assessment (M4S Test). The refinement datasets contain (1) a `pred` directory that contains decoy structure PDB files and (2) a `true` directory that contains native structure PDB files. The quality assessment dataset contains (1) `target_name` directories that each contain decoy structure PDB files for a given protein target and (2) a `label_info.csv` file listing each decoy structure's DockQ score and CAPRI class label.</p>
Full Datasets for: EGR: Equivariant Graph Refinement and Assessment of 3D Protein Complex Structures
<p>This archive contains three datasets associated with the Equivariant Graph Refiner (EGR), two for protein complex structure refinement (PSR Test and Benchmark 2) and the other for protein complex structure assessment (M4S Test). The refinement datasets contain (1) a `pred` directory that contains decoy structure PDB files and (2) a `true` directory that contains native structure PDB files. The quality assessment dataset contains (1) `target_name` directories that each contain decoy structure PDB files for a given protein target and (2) a `label_info.csv` file listing each decoy structure's DockQ score and CAPRI class label.</p>
X-ray structure ensemble refinement of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) (space group P21212)
<p>X-ray structure ensemble refinement of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) (space group P21212). Raw diffraction images are available on Zenodo: 10.5281/zenodo.4086066. A single conformer model was deposited in the Protein Data Bank under accession code <a href="https://www.ebi.ac.uk/pdbe/entry/pdb/7AV8">7AV8</a>. Refinement was carried out with <a href="https://www.phenix-online.org/documentation/reference/ensemble_refinement.html">phenix.ensemble_refinement</a> and the repository contains all input and output files:</p> <p>Input:</p> <ul> <li>mx8421v63_xPHIPAx1521_free.mtz</li> <li>refine9.pdb</li> </ul> <p>Output:</p> <ul> <li>PHIPA-P21212_ensemble_refinement_ensemble.geo</li> <li>PHIPA-P21212_ensemble_refinement_ensemble.pdb</li> <li>PHIPA-P21212_ensemble_refinement_ensemble.mtz</li> <li>PHIPA-P21212_ensemble_refinement_ensemble.log</li> </ul>
Benchmark Dataset for Structure Refinement Methods of Protein Complex Models
<p>This is the dataset used in our work entitled " Benchmarking of Structure Refinement Methods for Protein Complex Model " by Jacob Verburgt and Daisuke Kihara, which is under review.</p> <p>ZDOCK Derived Benchmark Dataset:</p> <p>The primary benchmark set used in was directly derived from the <a href="https://zlab.umassmed.edu/benchmark/">ZDOCK Benchmark set</a>. The ZDOCK set contains four structures per target: An unbound ligand, an unbound receptor, a bound ligand, and a bound receptor. The benchmark set is available in such a way where the coordinates of the bound subunits are oriented identical to their complex structure, and the unbound subunits are superimposed onto their respective bound subunits. Our dataset creates the optimially oriented "unbound" complexes by combining the superimposed and unbound subunits, along with removal of waters, ligands, and other non-protein atoms. These unbound complexes are saved in the dataset in the form "XXXX_c_u.pdb", where XXXX is the PDB ID.</p> <p>From the complete ZDOCK Benchmark of 230 targets, 18 targets were removed due to containing multiple ligand chains, which is incompatible with the standard ligand to receptor model used within CAPRI. The ZDOCK PDB ID’s of these targets are 1AKJ", "1BJ1", "1DE4", "1EER", "1EXB", "1EZU", "1GP2", "1I9R", "1JMO", "1K74", "1N2C", "1QFW", "2HMI", "3EO1", "3HMX", "4FQI", "4GXU", and "9QFW".</p> <p>There are an additional 8 targets where the superimpostion of the ligand and receptor structures onto the complex led to entanglement of the chains and were subsequently removed from the dataset. The ZDOCK PDB IDs for these targets are "1BGX", "1H1V", "1IRA", "1R8S", "1Y64", "2OT3", "3AAD", "4GAM".</p> <p>Note:</p> <p>In the work, we also used CAPRI scoring model dataset derived from CAPRI rounds 38-45. This dataset is unable to be distributed directly by us due to CAPRI guidelines, but can be derived from "Scoring round" models from the <a href="https://www.ebi.ac.uk/pdbe/complex-pred/capri/">CAPRI Website </a>.</p> <p>The targets considered were T122-T125, T131-T133, and T136, as these were targets which contained globular protein ligands and receptors. Please contact us directly if you have any further questions on this dataset.</p>
Data for manuscript "Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting"
<p>The tar file contains the input files for RADICAL augmented MDFF implementation (R-MDFF) for two protein systems, Adenylate Kinase (ADK) and Carbon Monoxide Dehydrogenase (CODH). These examples demonstrate the implementation of R-MDFF using RADICAL-Cybertools to flexibly fit biomolecules in cryo-EM density maps with on-the-fly decision making.</p> <p>All molecular simulations were performed using CUDA enabled NAMD 2.14 installed on OLCF Summit HPC resource. The CHARMM36 force field parameters were used for the proteins. Synthetic density maps were prepared at 1.8, 3 and 5 Å for ADK and 1.8 and 3 Å for CODH using VMD 1.9.3 software installed on OLCF Summit HPC resource. During the analysis stage, the cross correlation coefficients between density maps and atomic model were computed using VMD 1.9.3 on Summit HPC as part of the R-MDFF workflow.</p> <p>The source code is publicly available on GitHub: <a href="https://github.com/radical-collaboration/MDFF-EnTK">https://github.com/radical-collaboration/MDFF-EnTK </a></p> <p>The preprint of this research is submitted on bioRxiv, doi: <a href="https://doi.org/10.1101/2021.12.07.471672">https://doi.org/10.1101/2021.12.07.471672 </a></p> <p>To obtain maximum compression of the data, the tar command used to generate this tarball was:</p> <pre><code class="language-bash">GZIP=-9 tar --exclude='last.pdb' --exclude='*last_from_prev_iter.pdb' --exclude='*old' --exclude='*log' --exclude='*coor' --exclude='*vel' --exclude='*xsc' --exclude='*dcd' --exclude='lastframepdbs_fix' --exclude='*out' --exclude='*sl' --exclude='*rs' --exclude='*prof' --exclude='*err' --exclude='*dx' --exclude='*grid.pdb' --exclude='*txt' -cvzf rmdffv2.tar.gz rmdff-zenodo/</code></pre> <p> </p>
Dataset for Protein Structure Refinement using PCS Restrains of the dArmRP A4M4C
<p>The dataset contains all the experimental data and information used to refine the A4M4C dArmRP in the free and (KR)4 bound state from pseudocontact shifts. Individual modules are restraints during refinement.</p>
Data from: Modelling dynamics in protein crystal structures by ensemble refinement
Single-structure models derived from X-ray data do not adequately account for the inherent, functionally important dynamics of protein molecules. We generated ensembles of structures by time-averaged refinement, where local molecular vibrations were sampled by molecular-dynamics (MD) simulation whilst global disorder was partitioned into an underlying overall translation–libration–screw (TLS) model. Modeling of 20 protein datasets at 1.1–3.1 Å resolution reduced cross-validated R_free values by 0.3–4.9%, indicating that ensemble models fit the X-ray data better than single structures. The ensembles revealed that, while most proteins display a well-ordered core, some proteins exhibit a 'molten core' likely supporting functionally important dynamics in ligand binding, enzyme activity and protomer assembly. Order–disorder changes in HIV protease indicate a mechanism of entropy compensation for ordering the catalytic residues upon ligand binding by disordering specific core residues. Thus, ensemble refinement extracts dynamical details from the X-ray data that allow a more comprehensive understanding of structure–dynamics–function relationships.
Data from: Modelling dynamics in protein crystal structures by ensemble refinement
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