Find research datasets worth reusing

opencc-by-4.0Jul 2020View details →

Associated Data: RASPD+: Fast protein-ligand binding free energy prediction using simplified physicochemical features

Additional digital data to "RASPD+: Fast protein-ligand binding free energy prediction using simplified physicochemical features" (ChemRxiv preprint:<a href="https://doi.org/10.26434/chemrxiv.12636704.v1">https://doi.org/10.26434/chemrxiv.12636704</a>). Associated code can be found at: <a href="https://github.com/HITS-MCM/RASPDplus">https://github.com/HITS-MCM/RASPDplus</a> Files: <ul> <li>weights.tar.gz: contains the model weights of one random dataset split and its associated crossvalidation folds. Used for standard RASPD+ evaluation.</li> <li>additional_model_replicates.tar.gz: contains the remaining models trained on the full set of descriptors.</li> <li>external_test_sets.tar.gz: contains the descriptor tables for all external test sets used</li> <li>dude.tar.gz: contains the descriptor tables for and several identifier lists for evaluation on the Directory of Useful Decoys - Enhanced (DUD-E)</li> <li>run_outputs.tar.gz: Performance metric data and predicted values created during the model training and evaluation runs. Basis for the figures and metrics in the manuscript.</li> </ul>

opencc-by-4.0Jun 2024View details →

Binding Affinity Prediction Workflow - Simulation Input Files and Absolute Binding Free Energies

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. 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. 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/).

opencc-by-4.0Jul 2024View details →

Absolute Binding Free Energies with OneOPES

<h1>Supporting Material: Absolute Binding Free Energies with OneOPES</h1> Further information about the content of the directory can be found in the README file included The Plumed input files can also be found on Plumed-Nest https://www.plumed-nest.org/eggs/24/017/   <h3>Aknowledgements</h3> 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.   <h3>Reference</h3> Absolute Binding Free Energies with OneOPES Maurice Karrenbrock, Alberto Borsatto, Valerio Rizzi, Dominykas Lukauskis, Simone Aureli, and Francesco Luigi Gervasio The Journal of Physical Chemistry Letters 0, 15 DOI: 10.1021/acs.jpclett.4c02352   <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>

opencc-by-4.0Jul 2023View details →

Free energy simulations of receptor-binding domain opening in the SARS-CoV-2 spike indicate a barrierless transition with slow conformational motions

This online data set accompanies the manuscript entitled "Free energy simulations of receptor-binding domain opening in the SARS-CoV-2 spike indicate a barrierless transition with  slow conformational motions." The dataset is composed of the following files: * pmf0-now.dcd -- pmf63-now.dcd : molecular dynamics trajectory frames in each of the 64 umbrella sampling windows, from which water has been removed to save space * s1am_0-now.pdb -- s1am_63-now.pdb : initial coordinates in each of the 64 umbrella sampling windows, from which water has been removed, corresponding to the trajectory data above * view -- Visual Molecular Dynamics command script to load a trajectory,  e.g., in Linux, use "vmd -e view" * s1am_0-cg.dcd -- s1am_63-cg.dcd : molecular dynamics trajectory frames in each of the 64 umbrella sampling windows, coarse-grained to 1 bead per residue. * s1am_0-cg.pdb -- s1am_63-cg.pdb : initial coordinates in each of the 64 umbrella sampling windows, corresponding to the coarse-grained trajectory data above. * viewcg -- Visual Molecular Dynamics command script to load a coarse-grained trajectory,  e.g., in Linux, use "vmd -e viewcg" * 0readme -- brief instructions on how to view the trajectories * colors.vmd -- utility script for VMD * covmacros.vmd -- VMD script to define coronavirus spike subdomains * fe.zip -- ZIP archive that contains data and Matlab analysis files to reproduce the free energy profiles * diff.zip -- ZIP archive that contains data and Matlab analysis files to reproduce the diffusion and mean first passage times calculations * pca-qha.zip -- ZIP archive that contains the data and Matlab analysis files to compute the autocorrelation functions of trajectory displacements along principal/quasiharmonic modes Each ZIP archive contains a "0readme" file with brief instructions, and also the  results of the calculations

opencc-by-4.0Nov 2021View details →

Predictive simulations of core electron binding energies of halogenated species adsorbed on ice surfaces from relativistic quantum embedding calculations

This dataset collects the unprocessed (= outputs from calculations) and processed (= plots, average values for orbital and ionization energies) results discussed in the paper titled "Predictive simulations of core electron binding energies of halogenated species adsorbed on ice surfaces from relativistic quantum embedding calculations" by Richard Asamoah Opoku,  Céline Toubin, and André Severo Pereira Gomes.

opencc-by-4.0Jun 2024View details →

Pose Selector Workflow - Docking Poses, Absolute Binding Free Energy Estimates and Structure Input Files for Machine Learning

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. 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). 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/).

opencc-by-4.0Dec 2022View details →

Ammonia Binding Energy distribution at Interstellar Icy Grains

Zip file containing all the structures and input obtained in our article ACS Earth Space Chem. 2022, 6, 6, 1514–1526, <a href="https://doi.org/10.1021/acsearthspacechem.2c00040">https://doi.org/10.1021/acsearthspacechem.2c00040</a> To easily handle all these structures an online interactive page is created: <a href="https://tinaccil.github.io/Jmol_BE_NH3_visualization/">https://tinaccil.github.io/Jmol_BE_NH3_visualization/</a>

opencc-by-4.0Feb 2023View details →

Supporting material of "A nonequilibrium alchemical method for drug-receptor absolute binding free energy calculations: the role of restraints"

Supporting material of the paper "A nonequilibrium alchemical method for drug-receptor absolute binding free energy calculations: the role of restraints". The directory is fully documented with README files. Differences of V2.0 with V1.0: <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>

openother-openJan 2022View details →

Benchmark set inputs for absolute binding free energy calculations of fragment optimisations

Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process" 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.

opencc-by-4.0Feb 2022View details →

Relative binding free energy between chemically distant compounds using a bidirectional non-equilibrium approach

Data from "Relative binding free energy between chemically distant compounds using a bidirectional nonequilibrium approach" Submitted to J Chem Theory Comput, February  2022. This archive contains the following directories: traj -> This directory contains trajectory files for SAMPL9:         g??_w.pdb.gz file contains ~ 160 snapshots from the 48 ns HREM sampling         of the target bound state of G1-G13 including water solvent.         g??_1.pdb.gz file contains ~ 3500 snapshots (no solvent included) of the     target bound state of G1-G13 work -> This trajectory contains the work data (in kJ/mol) obtained in         the NE trajectories for SAMPL9:     gxx-gyy_b_TIME.wrk is the work sample obtained for the xx->yy transmutation         in the bound state with a duration time of TIME.     gxx-gyy_u_TIME.wrk is the work sample obtained for the xx->yy transmutation         in the unbound state with a duration time of TIME. pdb -> This directory contains the pdb initial structures of the G1-G18 guests and the WP6 host ff ->  This directory contains the force field specification for SAMPL9:     the PrimaDORAC generated (http://www1.chim.unifi.it/orac/primadorac/)         tpg and prm files for the guests and the host in orac format.  (see         http://ftp.chim.unifi.it/orac/MAN/orac-manual.html) bin -> This directory contains the script files to compute all bidirectional and unidirectional RBFE estimates as reported in Table 2 of the paper.        In order to compute an RBFE using the work data in the work dir, do the following:        1) cd into the bin directory        2) issue the command              source source_this_file.bash       (N.B.: gfortran must be installed)        3) cd ../        4) from the main dir, issue the command:              RBFE.bash -b 720 -u 360 B A           where  B and A are the ghost and physical compound, respectively        Results for DG(A->B) are printed to the standard output        Example:                     RBFE.bash -b 720 -u 360 g01 g03 > g03g01       In the g03g01 file, estimates and properties of the work data are       printed in the format      "g05->g02   DG_bar=   -5.13   0.37  DG_ff_G=   -4.2   0.8  DG_ff_J=   -3.0   0.4  sig_AB_u=  0.90 sig_AB_b=  2.16 ADT_AB_u=  0.26 ADT_AB_b=  0.23 DG_rr_G=  130.5  33.5  DG_rr_J=   -7.2   0.8  sig_BA_u=  1.10 sig_BA_b= 13.61 ADT_BA_u=  0.48 ADT_BA_b=  3.40  DG_fr_G=  -4.27  1.04  DG_fr_J=  -3.23  0.58 bias_fr=  0.2  DG_rf_G= 127.88 30.30  DG_rf_J=  -7.16  0.66 bias_rf=  0.0 DG_BAR=  -5.26 0.0 tb=  720 tu=  360"      To compute all DDG estimates of Table 2 launch the script      "do_all.bash" from the main dir         shift-pot -> This directory contains two gnuplot scripts showing the evolution of the       Beutler LJ and elec soft-core potentials (soft.gplt)  and of the shifted LJ and       elec soft-core potentials used in this work  (shift.gplt)

opencc-by-4.0Jun 2022View details →

Does Hamiltonian Replica Exchange via lambda-hopping enhance the sampling in alchemical binding free energy calculations?

t-REM HREM lamba-hopping/FEP+ tests on the APA molecule with ORAC (www.chim.unifi.it/orac)  The untarred archive contains the following directories:  t-rem -> contains input for gas-phase tests st-hrem ->  contains input for solvated APA with solute tempering lam-hop ->  contains input for solvated APA with lambda-hopping bin -> scripts for REM analysis  lib -> APA starting conf and potential parameters for the runs  see also README files inside each dir for further details

opencc-by-4.0Jul 2022View details →

Binding Energies of Interstellar Relevant S-bearing Species on Water Ice Mantles: A Quantum Mechanical Investigation

This Supporting Material contains: <ul> <li>Fractional coordinates of DFT optimized adsorption complexes for crystalline periodic ice models in <a href="https://www.moldraw.unito.it/_sgg/m1m1s43_1.htm">.mol</a> format, editable with <a href="http://www.moldraw.unito.it/">MOLDRAW</a>, using <a href="http://www.crystal.unito.it/">CRYSTAL17</a> computer code;</li> <li>Fractional coordinates of HF-3c optimized adsorption complexes for amorphous periodic ice models in <a href="https://www.moldraw.unito.it/_sgg/m1m1s43_1.htm">.mol</a> format, editable with <a href="http://www.moldraw.unito.it/">MOLDRAW</a>, using <a href="http://www.crystal.unito.it/">CRYSTAL17</a> computer code;</li> <li>Images of the adsorption features at crystalline periodic ice models, in which electrostatic potential maps, spin density maps (when available) and vibrational features are displayed;</li> <li>A pdf file with a thorough guide to the computation of BEs and the basis sets employed for the calculations.</li> </ul>

opencc-by-4.0May 2024View details →

Binding energies of ethanol and ethylamine on interstellar water ices

This Supporting Material contains the fractional coordinates of HF-3c optimized adsorption complexes for crystalline and amorphous periodic ice models in <a href="https://www.moldraw.unito.it/_sgg/m1m1s43_1.htm">.mol</a> format, editable with <a href="http://www.moldraw.unito.it/">MOLDRAW</a>, using <a href="http://www.crystal.unito.it/">CRYSTAL17</a> computer code of: <ul> <li>Ethylamine and ethanol adsorption complexes on crystalline ice (CI);</li> <li>Ethylamine and ethanol adsorption complexes on amorphous ice (ASW);</li> <li>A-layer and B-layer (100) surfaces of EtNH2, plus three adsorption complexes of ethylamine on these surfaces;</li> <li>A-layer and B-layer (010) surfaces of EtOH, plus three adsorption complexes of ethanol on these surfaces.</li> </ul>

opencc-by-4.0Dec 2023View details →

Data from " Allostery can convert binding free energies into concerted domain motions in enzymes"

Data from " Allostery can convert binding free energies into concerted domain motions in enzymes"   Electrophysiology data corresponding to the main text figures and supporting information figures. One representative set was chosen for each triplicate and included in this data set. For details are found in the ‘read me explanation.txt’ PDB used for this paper can be found at; 4ake [http://doi.org/10.2210/pdb4AKE/pdb] and 1ake [http://doi.org/10.2210/pdb1AKE/pdb] Full uncropped scans of any cropped gel/blot images are provided. The zip folder contains the MATLAB code package HMM inference, specifically tailored to nanopore ionic current flow data, as analyzed in the publication and can also be found at: https://github.com/yulanvanoppen/nanopore-HMM <pre> </pre>

opencc-by-4.0Aug 2021View details →

Dataset for "Binding energies of molecular solids from fragment and periodic approaches"

Dataset containing many-body contributions to binding energies of molecular crystals as described in the article <pre>"Binding energies of molecular solids from fragment and periodic approaches"</pre> published in Electronic Structure, doi: 10.1088/2516-1075/ac25d6

opencc-by-4.0Jan 2023View details →

Implications of large binding energies of massive stripped core collapse supernova progenitors on the explosion mechanism

Inlist files (r15140) used for the creation of the core-collapse progenitor models in the paper "The implications of large binding energies of massive, stripped, core-collapse supernova progenitors on the explosion mechanism". Based on the ‘20M pre ms to core collapse’ example from MESA r22.05, adapted for use in r15140, and include several variations as detailed in the paper appendix A. See README.txt for running details and example script. Also included are the full simulation list and the profiles of the 52 simulated cases, including the pre-collapse profiles at the point of termination for the 27 models that reached collapse. Profiles are at central oxygen depletion (5% abundance at center), central silicon depletion (5% abundance at center) and collapse, as defined in the paper.

opencc-by-4.0Apr 2023View details →

Theoretical water binding energy distribution and snowline in protoplanetary disks

Zip file containing all the structures and input obtained in our accepted article for publication in ApJ, 2023 To easily handle all these structures an online interactive page is created: <a href="https://tinaccil.github.io/Jmol_BE_H2O_visualization/">https://tinaccil.github.io/Jmol_BE_H2O_visualization/</a>

opencc-by-4.0Aug 2023View details →

Data Set Accompanying "Free Energy Decompositions Illuminate Synergistic Effects in Interfacial Binding Thermodynamics of Mixed Surfactant Systems"

This data set accompanies "Free Energy Decompositions Illuminate Synergistic Effects in Interfacial Binding Thermodynamics of Mixed Surfactant Systems" by Colin K. Egan and Ali Hassanali.  It includes example GROMACS input files for all simulations analyzed in the paper, as well as example data sets and analysis scripts.  See https://doi.org/10.26434/chemrxiv-2023-h11k5 for the preprint manuscript.

opencc-by-4.0Sep 2023View details →

Data for "Absolute binding free energy calculation based on the fragment molecular orbital method and its application in designing novel SHP-2 allosteric inhibitors"

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 .