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6 results for “absolute binding free energy”
Binding Affinity Prediction Workflow - Simulation Input Files and Absolute Binding Free Energies
<p>The Binding Affinity Prediction (BAP) workflow calculates absolute binding free energies for protein-ligand complexes by taking their crystal structures, converting them into input files for molecular dynamics (MD) simulations with GROMACS after they have passed extensive quality checks, and analysing the resulting trajectories with the Generalised Born model of implicit solvation as implemented in gmx_MMPBSA to obtain the free-energy estimates. The workflow was designed for soluble proteins without post-translational modifications, co-factors and non-standard amino acids, and it has limited support for coordinated ions.</p> <p>For the dataset published here, the BAP workflow was run on the PDBbind 2020 (http://www.pdbbind.org.cn/index.php) refined set. This entry contains the MD simulation input files (BAPSimulationInputFiles.tar.gz) and the ABFE estimates (BAPBindingFreeEnergyEstimates.csv) obtained from four 250 ns trajectories for each complex. The MD simulations for more than 4000 complexes were run on the Leonardo supercomputer while the implicit-solvent calculations were carried out on Galileo, both operated by Cineca (Italy). The MD trajectories will be stored at Cineca for approx. 1 year after publication of this entry; contact Cineca's user support if you are interested in the trajectories.</p> <p>The README file describes how to reproduce the MD trajectories and the subsequent implicit-solvent calculations yielding the free-energy estimates. The workflow scripts can be downloaded from GitHub (https://github.com/LigateProject/Binding-Affinity-Prediction-workflow). The MD simulations were run with GROMACS 2023.2 (https://manual.gromacs.org/2023.2/index.html), and the implicit-solvent calculations were carried out with gmx_MMPBSA 1.6.1 (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/v1.6.1/).</p>
Absolute Binding Free Energies with OneOPES
<h1>Supporting Material: Absolute Binding Free Energies with OneOPES</h1> <p>Further information about the content of the directory can be found in the README file included</p> <p>The Plumed input files can also be found on Plumed-Nest https://www.plumed-nest.org/eggs/24/017/</p> <p> </p> <h3>Aknowledgements</h3> <p>The authors acknowledge PRACE and the Swiss National Supercomputing Centre (CSCS) for large supercomputer time allocations on Piz Daint, project IDs: pr126, s1107, s1169, s1228. FLG acknowledges the Swiss National Science Foundation and Bridge for financial support (projects number: 200021_204795, CRSII5_216587 and 40B2-0_203628). The authors are grateful to Nicola Piasentin for helping in devising the error-informed stopping strategy and for carefully reading the manuscript.</p> <p> </p> <h3>Reference</h3> <p>Absolute Binding Free Energies with OneOPES<br>Maurice Karrenbrock, Alberto Borsatto, Valerio Rizzi, Dominykas Lukauskis, Simone Aureli, and Francesco Luigi Gervasio<br>The Journal of Physical Chemistry Letters 0, <em> 15<br>DOI: 10.1021/acs.jpclett.4c02352 </em></p> <p> </p> <h3>Versions :</h3> <ul> <li>1.0.0 First version</li> <li>1.0.1 Bugfix: added the missing topology files (top.top)</li> <li>1.1.0 Bugfix: added missing index files (index.ndx) and missing Slurm files (run.slr). New: added a directory with what is needed to equilibrate the systems</li> </ul>
Pose Selector Workflow - Docking Poses, Absolute Binding Free Energy Estimates and Structure Input Files for Machine Learning
<p>The Pose Selector (PS) workflow calculates absolute binding free energies (ABFEs) for binding poses of protein-ligand complexes. First, it converts the binding poses (both docking poses as well as experimentally observed ligand binding poses), which are provided as a combination of protein PDB file and ligand MOL2 file, into input files for molecular dynamics (MD) simulations with GROMACS after they have passed extensive quality checks and repair steps. Next, the PS workflow post-processes and analyses the last frame of the resulting eight 100 ps trajectories per binding pose with the Generalised Born model of implicit solvation as implemented in gmx_MMPBSA to obtain the ABFE estimates. The workflow was designed for soluble proteins without post-translational modifications, co-factors and non-standard amino acids, and it has limited support for coordinated ions.</p> <p>For the dataset published here, the PS workflow was run on docking poses generated for the PDBbind 2020 dataset (http://www.pdbbind.org.cn/index.php), shared in dockingPosesPDBBind2020.tar.gz. This entry and its partner entry 10.5281/zenodo.11397486 also share the intial coordinates used in the MD simulations of >800,000 docking poses of 4022 protein-ligand complexes (structureFiles_dockingPoses1.tar.gz in this entry and structureFiles_dockingPoses2.tar.gz in 10.5281/zenodo.11397486) and of the experimental ligand binding pose of 4549 complexes (structureFiles_experimentalStructures.tar.gz) as well as the corresponding ABFE estimates (absoluteBindingFreeEnergyEstimates.tar.gz). The MD simulations were run on the LUMI and MeluXina supercomputers while the implicit-solvent calculations were carried out on Galileo (Cineca).</p> <p>The README file describes the structure of the shared data in more detail and points out how to reproduce the MD trajectories and the subsequent implicit-solvent calculations yielding the free-energy estimates as well as how to use the data provided in this entry to train a machine-learning model predicting the ABFE of binding poses of protein-ligand complexes. The workflow scripts can be downloaded from GitHub (https://github.com/LigateProject/Pose-Selector-workflow). The MD simulations were run with GROMACS 2023.2 (https://manual.gromacs.org/2023.2/index.html), and the implicit-solvent calculations were carried out with gmx_MMPBSA 1.6.1 (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/v1.6.1/).</p>
Supporting material of "A nonequilibrium alchemical method for drug-receptor absolute binding free energy calculations: the role of restraints"
<p>Supporting material of the paper "A nonequilibrium alchemical method for drug-receptor absolute binding free energy calculations: the role of restraints".</p> <p>The directory is fully documented with README files.</p> <p>Differences of V2.0 with V1.0:</p> <ul> <li>Due to a software bug we had to re-parametrize the ligands whose torsions were parametized with ANI-2.X (ligand 6 and 7).</li> <li>During the peer reviewing process we also parametrized with ANI-2.X and docked ligand 8.</li> </ul>
Benchmark set inputs for absolute binding free energy calculations of fragment optimisations
<p>Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process"</p> <p>Provided here are the various scripts, input files, and results necessary to reproduce the outcomes of the above mentioned publication. Please see the provided README.md files for further information on the contents of this dataset.</p>
Data for "Absolute binding free energy calculation based on the fragment molecular orbital method and its application in designing novel SHP-2 allosteric inhibitors"
<p>Data for publication "Absolute binding free energy calculation based on the fragment molecular orbital method and its application in designing novel SHP-2 allosteric inhibitors".All structures of complex and input files for FMO , FMO/SMD , FMO/PCM , and COSMO calculation are provided .</p>
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