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20 results for “Free energy calculation”
Docked structures from "Optimizing active learning for free energy calculations"
<p>This archive contains the docked TYK2 structures used in the paper "Optimizing active learning for free energy calculations" (<a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.ailsci.2022.100050" target="_blank" rel="noreferrer noopener"><span><span>https://doi.org/10.1016/j.ailsci.2022.100050</span></span></a>). AM1-BCC charges are stored in the field "AM1Cache" in the SD file. The charges can be extracted using the code sample below. </p> <p> </p> <pre><code>from rdkit import Chem import base64 import pickle suppl = Chem.SDMolSupplier("10k_most_similar_tyk2_charged.sdf", removeHs=False) for mol in suppl: am1 = mol.GetProp("AM1Cache") am1_charges = pickle.loads(base64.b64decode(mol.GetProp("AM1Cache"))) assert len(am1_charges) == mol.GetNumAtoms(), "Charge cache has different number of charges than mol atoms"</code></pre>
Minute-timescale free-energy calculations reveal a pseudo-active state in the adenosine A2A receptor activation mechanism
<p>Dataset of the paper "Minute-timescale free-energy calculations reveal a pseudo-active state in the adenosine A2A receptor activation mechanism" accepted for publication on ACS Chem journal.</p>
Aldeghi et al. Files for absolute free energy calculations in gromacs.
<p>These are the files for performing absolute free energy calculations using gromacs as reported in "Accurate calculation of the absolute free energy of binding for drug molecules. Aldeghi M, Heifetz A, Bodkin MJ, Knapp S, Biggin PC.<br /> Chem Sci. 2016 Jan 14;7(1):207-218. DOI: 10.1039/C5SC02678D"</p> <p> </p> <p>The files should prove useful for anyone wishing to try out their own methodology for comparison purposes or even just to repeat the work on a known dataset. The data is presented as a zip archive that should unpack into a directory called "Aldeghi-et-al-chemical-science-2016". There are four sub-directories in there and a README.txt file which should explain the details of the data.</p> <p> </p>
Benchmark set for relative free energy calculations
<p>Created by Christina Schindler and Daniel Kuhn, Merck KGaA, Darmstadt, Germany.</p> <p>December 2018</p> <p>Manuscript in preparation.</p> <p>Previously presented at Alchemical Free Energy Workshop 2019 in Goettingen, Germany.</p> <p>DOI: 10.5281/zenodo.3258925</p> <p> </p> <p>References for datasets used in benchmark</p> <p>CDK8<br> Schiemann, Kai, et al. "Discovery of potent and selective CDK8 inhibitors from an HSP90 pharmacophore." Bioorganic & medicinal chemistry letters 26.5 (2016): 1443-1451.</p> <p>DOI: 10.1016/j.bmcl.2016.01.062</p> <p>c-Met</p> <p>Dorsch, Dieter, et al. "Identification and optimization of pyridazinones as potent and selective c-Met kinase inhibitors." Bioorganic & medicinal chemistry letters 25.7 (2015): 1597-1602.</p> <p>DOI: 10.1016/j.bmcl.2015.02.002<br> Eg5</p> <p>Schiemann, Kai, et al. "The discovery and optimization of hexahydro-2H-pyrano [3, 2-c] quinolines (HHPQs) as potent and selective inhibitors of the mitotic kinesin-5." Bioorganic & medicinal chemistry letters 20.5 (2010): 1491-1495.</p> <p>DOI: 10.1016/j.bmcl.2010.01.110<br> Hif2a</p> <p>Wallace, Eli M., et al. "A small-molecule antagonist of HIF2α is efficacious in preclinical models of renal cell carcinoma." Cancer research 76.18 (2016): 5491-5500.</p> <p>DOI: 10.1158/0008-5472.CAN-16-0473</p> <p>Dixon, Darryl David, et al. "Aryl ethers and uses thereof." U.S. Patent No. 9,908,845. 6 Mar. 2018.</p> <p>URL: Google Patents<br> PFKFB3</p> <p>Boutard, Nicolas, et al. "Discovery and Structure–Activity Relationships of N-Aryl 6-Aminoquinoxalines as Potent PFKFB3 Kinase Inhibitors." ChemMedChem 14.1 (2019): 169-181.</p> <p>DOI: 10.1002/cmdc.201800569<br> SHP2</p> <p>Chen, Ying-Nan P., et al. "Allosteric inhibition of SHP2 phosphatase inhibits cancers driven by receptor tyrosine kinases." Nature 535.7610 (2016): 148.</p> <p>DOI:10.1038/nature18621</p> <p>Garcia Fortanet, Jorge, et al. "Allosteric inhibition of SHP2: identification of a potent, selective, and orally efficacious phosphatase inhibitor." Journal of medicinal chemistry 59.17 (2016): 7773-7782.</p> <p>DOI: 10.1021/acs.jmedchem.6b00680</p> <p>Chen, Christine Hiu-tung, et al. "1-pyridazin-/triazin-3-yl-piper (-azine)/idine/pyrolidine derivatives and compositions thereof for inhibiting the activity of shp2." U.S. Patent Application No. 15/110,498.</p> <p>URL: Google Patents</p> <p> </p> <p>SYK<br> Currie, Kevin S., et al. "Discovery of GS-9973, a selective and orally efficacious inhibitor of spleen tyrosine kinase." Journal of medicinal chemistry 57.9 (2014): 3856-3873.</p> <p>DOI: 10.1021/jm500228a</p> <p>TNKS2<br> Buchstaller, Hans-Peter, et al. "Discovery and Optimization of 2-Arylquinazolin-4-ones into a Potent and Selective Tankyrase Inhibitor Modulating Wnt Pathway Activity." Journal of medicinal chemistry 62.17 (2019): 7897-7909.</p> <p>DOI: 10.1021/acs.jmedchem.9b00656</p>
Supplementary underlying data for "Evaluating parameterization protocols for hydration free energy calculations with the AMOEBA polarizable force field"
<p>This dataset includes additional underlying data for the publication "Evaluating parameterization protocols for hydration free energy calculations with the AMOEBA polarizable force field"</p> <p>Contents:</p> <p>Tukey Honest Significant Difference (HSD) results for solutes 1-47 across all seven parameter sets, as *.txt. These are pairwise comparisons of results between all possible parameter sets. Significant differences are treated as p < 0.05.</p>
Thermodynamic database and calculator of free energies and potentials for redox reactions involving iron minerals in aqueous media (IMTD)
<p>Database of free energies of formation for iron minerals and associated aqueous species, which are used in a tableu style spreadsheet to calculate free energies of redox reactions involving iron minerals, which in turn are used to calculate free energies and formal potentials for these reactions, under specified environmental conditions.</p> <p>The database and calculators were assembled by students and postdocs (Jeff Hudson, Ania Pavitt, Ying Lan, and Miranda Bradley) working under direction of Professor Paul G. Tratnyek at the Oregon Health & Science University, Portland, Oregon, USA. Drew Latta, Thomas Robinson, and Michelle Scherer contributed to the database and extended the calculations.</p> <p>Early versions of this tool were used in several publications, including (i) Fan, D., Y. Lan, P. G. Tratnyek, R. L. Johnson, J. Filip, D. M. O'Carroll, A. N. Garcia, and A. Agrawal. 2017. <em>Environ. Sci. Technol.</em> 51(22): 13070–13085. [DOI: 10.1021/acs.est.7b04177] and (ii) Bradley, M. J., and P. G. Tratnyek. 2019. <em>ACS Earth & Space Chemistry</em> 3(3): 688-699. [DOI: 10.1021/acsearthspacechem.8b00200].</p> <p>This tool is provided as a spreadsheet in .xlsx format. The file includes six sheets. The first contains background, constants, and calculations that apply throughout the remaining tabs. The second contains free energies of formation from various authoritative sources, and a mechanism for designating “recommend values”. The third contains a tableu that calculates free energies of redox reactions using the recommended free energy of formation and user-specified stoichiometries. The fourth calculates free energies and formal potentials of the redox reactions using the standard potentials, and specific solution conditions. The last tab summarizes previous published formal potentials from a variety of sources. </p> <p>While the database was checked thoroughly, it still is unlikely to be completely accurate. For critical applications, we recommend that you track-down the primary sources (listed on the first tab of the spreadsheet) and use them for data, conditions, and other caveats. Obviously, we do not accept any responsibility for what anyone does with information obtained from this document.</p> <p>In the future, if significantly corrections or additions are made to this document, we may publish it here as new versions. If the contributions of others result in major improvements, we are open to adding new authors to those versions. Feel free to contact us with corrections, suggests, or offers to help.</p> <p>The development of this version of the tool was funded through grants from the Strategic Environmental Research and Development Program (SERDP) and the U.S. Department of Energy.</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>
Input files for the MD simulations and free energy calculations for the article "Water Dissolved in a Variety of Polymers Studied by Molecular Dynamics Simulation and a Theory of Solutions"
<p>Article:<em> </em><a href="https://pubs.acs.org/doi/10.1021/acs.jpcb.1c04818">J. Phys. Chem. B. 125, 9357–9371 (2021) [DOI: 10.1021/acs.jpcb.1c04818]</a></p> <p>The structures of the homopolymers and copolymers simulated are shown in Figures 1 and S1 and Tables 2 and 3. All-atom MD simulation was carried out using GROMACS, and this repository provides the input files with the GAFF/RESP force and initial coordinate files. The free energy of water dissolution was obtained with <a href="https://sourceforge.net/projects/ermod/">ERmod</a>, and the input files for the free-energy calculations are also contained. See the README files for details.</p>
Underlying data for "Evaluating parameterization protocols for hydration free energy calculations with the AMOEBA polarizable force field"
<p>This dataset includes underlying data for the publication "Evaluating<br /> parameterization protocols for hydration free energy calculations with the<br /> AMOEBA polarizable force field"</p> <p>Contents:<br /> Modified valence parameters for the Poltype software (valence.py). This can be<br /> substituted for the existing valence.py module packaged with Poltype to make the<br /> parameter assignment changes detailed in the article supplementary information. </p> <p>Results files for each parameter set (*.txt). Each consists of a 4 x 47 array of<br /> numbers. Rows correspond to entries for each sequential ligand. The first column<br /> in each row is the experimental hydration free energy. The following three rows<br /> are computational hydration free energy predictions from three independent<br /> repeat simulations.</p> <p>Script for analysis of results files (analyse_hfe.py). Short script to produce<br /> descriptive statistics for packaged datasets. Expects input files in the syntax<br /> of *.txt (i.e. 4 x 47 arrays)</p>
Data for: Alchemical free-energy calculations at quantum-chemical precision
<p><span><span>In the last decade, machine-learned potentials (MLP) have </span><span>demonstrated</span><span> the capability to predict vario</span><span>us</span><span> QM properties learned from </span><span>a set of reference</span><span> QM calculations. </span><span>Accordingly</span><span>,</span><span> hybrid QM/MM simulation</span><span>s </span><span>can be accelerated</span><span> by replacement of </span><span>expensive</span><span> QM calculation</span><span>s</span><span> with </span><span>efficient </span><span>MLP </span><span>energy prediction</span><span>s</span><span>.</span> <span>At the same time</span><span>, alchemical free energy </span><span>perturbation</span><span>s</span><span> (FEP) </span><span>remain</span> <span>un</span><span>ach</span><span>ie</span><span>vable</span><span> at the QM level of theory.</span> <span>In this work</span><span>,</span><span> we extend the capabilities of the Buffer Region Neural Network </span><span>(</span><span>BuRNN</span><span>) </span><span>QM</span><span>/MM</span><span> scheme towards </span><span>FEP</span><span>.</span> <span>BuRNN</span> <span>introduces a buffer region that experiences full electronic polarization by the QM region to minimize artifacts</span> <span>at </span><span>the </span><span>QM/MM interface</span><span>. </span><span>A </span><span>MLP</span> <span>is </span><span>used to </span><span>predict the energies for the QM </span><span>region</span><span> and its interactions with the buffer region</span><span>. Furthermore, </span><span>BuRNN</span> <span>allow</span><span>s</span><span> us to implement </span><span>FEP </span><span>directly into</span> <span>the </span><span>MLP </span><span>H</span><span>amiltonian</span><span>. </span><span>Here</span><span>, </span><span>we describe the alchemical change </span><span>from methanol to methane in water </span><span>at</span><span> the </span><span>MLP</span><span>/MM level as a proof of concept.</span></span><span> </span></p>
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>
Does Hamiltonian Replica Exchange via lambda-hopping enhance the sampling in alchemical binding free energy calculations?
<p>t-REM HREM lamba-hopping/FEP+ tests on the APA molecule with ORAC<br> (www.chim.unifi.it/orac) </p> <p>The untarred archive contains the following directories: </p> <p>t-rem -> contains input for gas-phase tests<br> st-hrem -> contains input for solvated APA with solute tempering<br> lam-hop -> contains input for solvated APA with lambda-hopping<br> bin -> scripts for REM analysis <br> lib -> APA starting conf and potential parameters for the runs </p> <p>see also README files inside each dir for further details </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>
Multiple Parameter Replica Exchange Gaussian Accelerated Molecular Dynamics for Enhanced Sampling and Free Energy Calculation of Biomolecular Systems
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Supplementary Data for "Comprehensive Phase Diagrams of MoS2 Edge Sites Using Dispersion-Corrected DFT Free Energy Calculations"
<p>MoS2 Phase Diagrams to accompany DOI: 10.1021/acs.jpcc.8b02524</p>
Supporting Information for "Broadening the scope of binding free energy calculations using a Separated Topologies approach"
<p>Supporting Information for the publication "Broadening the scope of binding free energy calculations using a Separated Topologies approach" including input files for the datasets used in that study.</p>
Input files for T4 lysozyme free energy calculations with DMBIS non-bonded force field parameters
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Data for "Influence of Wobbling Tryptophan and Mutations on PET Degradation Explored by QM/MM Free Energy Calculations" paper
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Inputs to calculate the solvation free energies of ECC ions in SPCE water
<p>Scripts and input files for the calculation of the solvation free energies of selected cations with the ECC model. The simulation box contains one cation and 800 water molecules. The ion topologies are from https://bitbucket.org/hseara/ions. Notably, before comparison with experimental values, the electronic solvation free energy contribution must be added to the result [1], as well as the correction due to the use of neutralizing charge density [2].</p> <p>In each folder, ./run.sh creates the folders representing different lambda values in the free energy perturbation approach and performs the respective calculation in each folder. There are a total of 31 windows (11 for electrostatics and 20 for Lennard-Jones). After running the script, the free energy can be extracted by</p> <p>gmx bar -f ?/md.xvg ??/md.xvg -temp 298 -o -b 100</p> <p>The results are reported in DOI: [ADD]</p> <p>[1] DOI: 10.1021/ct9005807</p> <p>[2] DOI: 10.1080/08927022.2015.1121544</p>
A new predictive group-contribution ideal-heat-capacity model, and its influence on second-derivative properties calculated using a free-energy equation of state
<p>Calculated data for figures 4-8 presented in publication.</p>
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