cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.14272/mztwjeoskwzeiv-ghvjwsgmsa-n/1hnmr
title: 1H NMR (, InChI=1S/C20H13ClN2O4/c21-16-3-1-2-4-17(16)22-23-18-11-14(20(26)27)9-10-15(18)12-5-7-13(8-6-12)19(24)25/h1-11H,(H,24,25)(H,26,27)/b23-22+)

description: dataset for 1H NMR
      
      1H NMR (400 MHz, DMSO-d6, ppm) δ = 7.35 (dd, J = 8.1 Hz, J = 1.5 Hz, 1H, CHAr), 7.42–7.49 (m, 1H, CHAr), 7.57 (td, J = 7.7 Hz, J = 1.6 Hz, 1H, CHAr), 7.65–7.67 (m, 2H, CHAr), 7.74 (dd, J = 8.0 Hz, J = 1.1 Hz, 1H, CHAr), 7.84 (d, J = 8.0 Hz, 1H, CHAr), 8.04–8.06 (m, 2H, CHAr), 8.22 (dd, J = 8.0 Hz, J = 1.7 Hz, 1H, CHAr), 8.28 (d, J = 1.6 Hz, 1H, CHAr), 13.25 (s, 2H, OH). Spectrum contains around 5% impurities due E/Z isomerization at the conditions used for the measurement.
DOI: 10.14272/mztwjeoskwzeiv-ghvjwsgmsa-n/ir
title: IR (, InChI=1S/C20H13ClN2O4/c21-16-3-1-2-4-17(16)22-23-18-11-14(20(26)27)9-10-15(18)12-5-7-13(8-6-12)19(24)25/h1-11H,(H,24,25)(H,26,27)/b23-22+)

description: dataset for IR
      
      IR (ATR, ṽ) = 2835, 2540, 1678, 1601, 1462, 1419, 1286, 1188, 1122, 1057, 1004, 915, 867, 840, 782, 759, 738, 700, 665, 609, 539, 483, 450, 418 cm–1.
DOI: 10.14272/mztwjeoskwzeiv-ghvjwsgmsa-n/mass
title: Mass (, InChI=1S/C20H13ClN2O4/c21-16-3-1-2-4-17(16)22-23-18-11-14(20(26)27)9-10-15(18)12-5-7-13(8-6-12)19(24)25/h1-11H,(H,24,25)(H,26,27)/b23-22+)

description: dataset for Mass
      
      APCI (m/z): 381/383 (100/36) [M+H]+, 255 (12), 254 (13).
DOI: 10.14272/apqlrcletllpan-ghvjwsgmsa-n.1
title: C20H13ClN2O4
title: InChI=1S/C20H13ClN2O4/c21-15-2-1-3-16(11-15)22-23-18-10-14(20(26)27)8-9-17(18)12-4-6-13(7-5-12)19(24)25/h1-11H,(H,24,25)(H,26,27)/b23-22+

description: This dataset contains experimental data from a sample (InChI=1S/C20H13ClN2O4/c21-15-2-1-3-16(11-15)22-23-18-10-14(20(26)27)8-9-17(18)12-4-6-13(7-5-12)19(24)25/h1-11H,(H,24,25)(H,26,27)/b23-22+).
      The datasets from the following experiments are available:
      
      1H NMR
      
      13C NMR
      
      Mass
      
      IR
DOI: 10.5281/zenodo.2485428
title: Restricted access data for the paper Fake News on Twitter During the 2016 U.S. Presidential Election

description: Restricted access data for replicating results in the paper Fake News on Twitter During the 2016 U.S. Presidential Election.
DOI: 10.5281/zenodo.2485429
title: Restricted access data for the paper Fake News on Twitter During the 2016 U.S. Presidential Election

description: Restricted access data for replicating results in the paper Fake News on Twitter During the 2016 U.S. Presidential Election.
DOI: 10.5281/zenodo.2645908
title: Simulations of membrane proteins in a mixture of lipids with varying levels of chain unsaturation

description: Four structurally distinct membrane proteins were simulated in a mixture of phospholipids. The membranes contained one copy of one of the protein types with equimolar concentrations of DPPC, DOPC, DLiPC, SDPC, and cholesterol. The CHARMM36 force field [1] was employed, and the systems were built using the CHARMM-GUI web portal [2]. The 4-microsecond long simulations were performed using GROMACS [3]. Further details on the setup of the systems as well as on the simulation protocol can be found in the related paper at DOI: 10.1371/journal.pcbi.1007033.

The files are named based on the PDB codes of the proteins (1AFO, 2M0B, 3EML, and 3EMN). For each system, the original simulation run input file (tpr) and the corresponding outputs (xtc, edr) are provided. Additionally, the simulations can be extended using the continue point (cpt) file. For each system the files required to generate the run input file are also provided: the topology file (top), index file (ndx), and a common run parameter file (mdp). The CHARMM36 force field can be downloaded from http://mackerell.umaryland.edu/charmm_ff.shtml

Notably, the protein definition files (itp) were re-generated. After performing these simulations, the atom ordering of cholesterol in the CHARMM36 force field was changed. The provided gro files, as well as the lipid definition files (itp) correspond to this new atom order. While they can be used to generate a run input file, yet this run input file will not be identical to the one provided. Therefore: 1) for analysis, the provided xtc+tpr files are fine; 2) for extending the simulation, the tpr+cpt files are fine; 3) for new simulations, the tpr file can be generated based on the provided files, yet it cannot be used together with the provided xtc file.

[1] <strong>DOI: </strong>10.1021/jp101759q

[2] <strong>DOI: </strong>10.1021/acs.jctc.5b00935

[3] <strong>DOI: </strong>10.1016/j.softx.2015.06.001
DOI: 10.5281/zenodo.2645909
title: Simulations of membrane proteins in a mixture of lipids with varying levels of chain unsaturation

description: Four structurally distinct membrane proteins were simulated in a mixture of phospholipids. The membranes contained one copy of one of the protein types with equimolar concentrations of DPPC, DOPC, DLiPC, SDPC, and cholesterol. The CHARMM36 force field [1] was employed, and the systems were built using the CHARMM-GUI web portal [2]. The 4-microsecond long simulations were performed using GROMACS [3]. Further details on the setup of the systems as well as on the simulation protocol can be found in the related paper at DOI: 10.1371/journal.pcbi.1007033.

The files are named based on the PDB codes of the proteins (1AFO, 2M0B, 3EML, and 3EMN). For each system, the original simulation run input file (tpr) and the corresponding outputs (xtc, edr) are provided. Additionally, the simulations can be extended using the continue point (cpt) file. For each system the files required to generate the run input file are also provided: the topology file (top), index file (ndx), and a common run parameter file (mdp). The CHARMM36 force field can be downloaded from http://mackerell.umaryland.edu/charmm_ff.shtml

Notably, the protein definition files (itp) were re-generated. After performing these simulations, the atom ordering of cholesterol in the CHARMM36 force field was changed. The provided gro files, as well as the lipid definition files (itp) correspond to this new atom order. While they can be used to generate a run input file, yet this run input file will not be identical to the one provided. Therefore: 1) for analysis, the provided xtc+tpr files are fine; 2) for extending the simulation, the tpr+cpt files are fine; 3) for new simulations, the tpr file can be generated based on the provided files, yet it cannot be used together with the provided xtc file.

[1] <strong>DOI: </strong>10.1021/jp101759q

[2] <strong>DOI: </strong>10.1021/acs.jctc.5b00935

[3] <strong>DOI: </strong>10.1016/j.softx.2015.06.001
DOI: 10.14272/apqlrcletllpan-ghvjwsgmsa-n/13cnmr
title: 13C NMR (, InChI=1S/C20H13ClN2O4/c21-15-2-1-3-16(11-15)22-23-18-10-14(20(26)27)8-9-17(18)12-4-6-13(7-5-12)19(24)25/h1-11H,(H,24,25)(H,26,27)/b23-22+)

description: dataset for 13C NMR
      
      13C NMR (100 MHz, DMSO-d6, ppm) δ = 116.6 (CHAr), 122.0 (CHAr), 122.3 (CHAr), 128.8 (2C, CHAr), 130.3 (Cquart.), 131.0 (2C, CHAr), 131.4 (Cquart.), 131.4 (2C, CHAr), 131.5 (CHAr), 132.0 (CHAr), 134.2 (Cquart.), 141.5 (Cquart.), 143.7 (Cquart.), 148.4 (Cquart.), 153.0 (Cquart.), 166.5 (Cquart., COOH), 137.1 (Cquart., COOH).
DOI: 10.14272/apqlrcletllpan-ghvjwsgmsa-n/1hnmr
title: 1H NMR (, InChI=1S/C20H13ClN2O4/c21-15-2-1-3-16(11-15)22-23-18-10-14(20(26)27)8-9-17(18)12-4-6-13(7-5-12)19(24)25/h1-11H,(H,24,25)(H,26,27)/b23-22+)

description: dataset for 1H NMR
      
      1H NMR (400 MHz, DMSO-d6, ppm) δ = 7.68–7.62 (m, 4H, CHAr), 7.74 (s, 1H, CHAr), 7.80−7.76 (m, 1H, CHAr), 7.85 (d, J = 8.0 Hz, 1H, CHAr), 8.03–8.05 (m, 2H, CHAr), 8.22 (dd, J = 8.0 Hz, J = 1.8 Hz, 1H, CHAr), 8.28 (d, J = 1.7 Hz, 1H, CHAr), 13.23 (s, 2H, OH).
DOI: 10.14272/apqlrcletllpan-ghvjwsgmsa-n/ir
title: IR (, InChI=1S/C20H13ClN2O4/c21-15-2-1-3-16(11-15)22-23-18-10-14(20(26)27)8-9-17(18)12-4-6-13(7-5-12)19(24)25/h1-11H,(H,24,25)(H,26,27)/b23-22+)

description: dataset for IR
      
      IR (ATR, ṽ) = 2536, 1677, 1601, 1418, 1286, 1188, 1125, 1067, 1005, 869, 839, 784, 758, 737, 699, 671, 607, 539, 475, 399 cm–1.
DOI: 10.14272/apqlrcletllpan-ghvjwsgmsa-n/mass
title: Mass (, InChI=1S/C20H13ClN2O4/c21-15-2-1-3-16(11-15)22-23-18-10-14(20(26)27)8-9-17(18)12-4-6-13(7-5-12)19(24)25/h1-11H,(H,24,25)(H,26,27)/b23-22+)

description: dataset for Mass
      
      APCI (m/z): 381/383 (100/35) [M+H]+, 255 (14), 254 (13).
DOI: 10.14272/beblrqmatvbyrz-qurgraslsa-n.1
title: C20H13N3O6
title: InChI=1S/C20H13N3O6/c24-19(25)13-7-5-12(6-8-13)15-10-9-14(20(26)27)11-17(15)22-21-16-3-1-2-4-18(16)23(28)29/h1-11H,(H,24,25)(H,26,27)/b22-21+

description: This dataset contains experimental data from a sample (InChI=1S/C20H13N3O6/c24-19(25)13-7-5-12(6-8-13)15-10-9-14(20(26)27)11-17(15)22-21-16-3-1-2-4-18(16)23(28)29/h1-11H,(H,24,25)(H,26,27)/b22-21+).
      The datasets from the following experiments are available:
      
      1H NMR
      
      13C NMR
      
      IR
      
      Mass
DOI: 10.14272/beblrqmatvbyrz-qurgraslsa-n/13cnmr
title: 13C NMR (, InChI=1S/C20H13N3O6/c24-19(25)13-7-5-12(6-8-13)15-10-9-14(20(26)27)11-17(15)22-21-16-3-1-2-4-18(16)23(28)29/h1-11H,(H,24,25)(H,26,27)/b22-21+)

description: dataset for 13C NMR
      
      13C NMR (100 MHz, DMSO-d6, ppm) δ = 116.9 (CHAr), 118.4 (CHAr), 124.4 (CHAr), 128.9 (2C, CHAr), 130.4 (Cquart.), 130.9 (2C, CHAr), 131.5 (Cquart.), 131.7 (CHAr), 132.0 (CHAr), 132.5 (CHAr), 134.0 (CHAr), 141.2 (Cquart.), 144.0 (Cquart.), 144.4 (Cquart.), 147.1 (Cquart.), 148.7 (Cquart.), 166.4 (Cquart., CO2H), 167.1 (Cquart., CO2H).
DOI: 10.14272/beblrqmatvbyrz-qurgraslsa-n/1hnmr
title: 1H NMR (, InChI=1S/C20H13N3O6/c24-19(25)13-7-5-12(6-8-13)15-10-9-14(20(26)27)11-17(15)22-21-16-3-1-2-4-18(16)23(28)29/h1-11H,(H,24,25)(H,26,27)/b22-21+)

description: dataset for 1H NMR
      
      1H NMR (400 MHz, DMSO-d6, ppm) δ = 7.44 (dd, J = 7.9 Hz, J = 1.3 Hz, 1H, CHAr), 7.65–7.67 (m, 2H, CHAr), 7.77 (td, J = 7.8 Hz, J = 1.4 Hz, 1H, CHAr), 7.89–7.82 (m, 2H, CHAr), 8.05–8.07 (m, 2H, CHAr), 8.15 (dd, J = 8.0 Hz, J = 1.3 Hz, 1H, CHAr), 8.17 (d, J = 1.7 Hz, 1H, CHAr), 8.24 (dd, J = 8.0 Hz, J = 1.7 Hz, 1H, CHAr), 13.29 (bs, 2H, COOH).
DOI: 10.14272/beblrqmatvbyrz-qurgraslsa-n/ir
title: IR (, InChI=1S/C20H13N3O6/c24-19(25)13-7-5-12(6-8-13)15-10-9-14(20(26)27)11-17(15)22-21-16-3-1-2-4-18(16)23(28)29/h1-11H,(H,24,25)(H,26,27)/b22-21+)

description: dataset for IR
      
      IR (ATR, ṽ) = 2811, 2530, 1680, 1600, 1524, 1416, 1340, 1283, 1122, 1003, 918, 866, 840, 805, 778, 759, 730, 690, 662, 610, 533, 482, 415 cm–1.
DOI: 10.5281/zenodo.2640439
title: Atomistic simulations of the adenosine A2 receptor in membranes with varying levels of SDPE

description: An adenosine A2 receptor was simulated in membranes consisting of DSPC, cholesterol (20 mol%), and varying levels (0, 4, or 8 mol%) of SDPE with a polyunsaturated chain. Upon increasing SDPE concentration, the concentration of DSPC was correspondingly decreased. The initial structures for these simulations were obtained from the final structures of corresponding coarse-grained simulations, where an SDPE-rich corona formed around the receptor. After fine-graining, the systems were simulated using the CHARMM36 [1] force field for 200 ns using the GROMACS package [2].

These simulations were also repeated in the absence of protein. These systems were set up using the CHARMM-GUI web portal [3]. The corresponding files have the 'NOPROT' suffix, and the simulation parameter file is called md_noprot.mdp.

For details on the fine-graining and the simulation protocol, please see the related paper at DOI: 10.1371/journal.pcbi.1007033.

The files named PUFA_X.* correspond to simulations with X mol% of SDPE with the protein, whereas the files names PUFA_X_NOPROT.* are the corresponding files in the absence of the protein. For each concentration, a run input file (tpr) and the simulation outputs (xtc, edr, log, gro) are provided. Moreover, the simulations can be extended using the provided cpt files.

Moreover, the files required to generate the run input file are also provided. For each system, a topology file (top) and an index file (ndx) are provided. The CHARMM36 force field and the molecule definitions (itp) referenced by the topology are also provided. The used simulation parameters are provided in the md.mdp file. For the fine-graining of SDPE, the mapping file is also provided (sdpe.charmm36.map).

[1] <strong>DOI: </strong>10.1021/jp101759q

[2] <strong>DOI: </strong>10.1016/j.softx.2015.06.001

[3] <strong>DOI: </strong>10.1021/acs.jctc.5b00935
DOI: 10.5519/qd.wudbey3d
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.14272/beblrqmatvbyrz-qurgraslsa-n/mass
title: Mass (, InChI=1S/C20H13N3O6/c24-19(25)13-7-5-12(6-8-13)15-10-9-14(20(26)27)11-17(15)22-21-16-3-1-2-4-18(16)23(28)29/h1-11H,(H,24,25)(H,26,27)/b22-21+)

description: dataset for Mass
      
      APCI (m/z): 392 (12) [M+H]+, 374 (100), 328 (20), 271 (10), 254 (82).
DOI: 10.14272/irlrffncejwnjf-ghvjwsgmsa-n.1
title: C20H13ClN2O4
title: InChI=1S/C20H13ClN2O4/c21-15-6-8-16(9-7-15)22-23-18-11-14(20(26)27)5-10-17(18)12-1-3-13(4-2-12)19(24)25/h1-11H,(H,24,25)(H,26,27)/b23-22+

description: This dataset contains experimental data from a sample (InChI=1S/C20H13ClN2O4/c21-15-6-8-16(9-7-15)22-23-18-11-14(20(26)27)5-10-17(18)12-1-3-13(4-2-12)19(24)25/h1-11H,(H,24,25)(H,26,27)/b23-22+).
      The datasets from the following experiments are available:
      
      1H NMR
      
      13C NMR
      
      IR
      
      Mass
DOI: 10.14272/irlrffncejwnjf-ghvjwsgmsa-n/13cnmr
title: 13C NMR (, InChI=1S/C20H13ClN2O4/c21-15-6-8-16(9-7-15)22-23-18-11-14(20(26)27)5-10-17(18)12-1-3-13(4-2-12)19(24)25/h1-11H,(H,24,25)(H,26,27)/b23-22+)

description: dataset for 13C NMR
      
      13C NMR (100 MHz, DMSO-d6, ppm) δ = 116.6 (CHAr), 124.6 (2C, CHAr), 128.9 (2C, CHAr), 129.8 (2C, CHAr), 130.2 (Cquart.), 130.9 (2C, CHAr), 131.4 (Cquart.), 131.5 (CHAr), 131.7 (CHAr), 136.5 (Cquart.), 141.5 (Cquart.), 143.5 (Cquart.), 148.5 (Cquart.), 150.6 (Cquart.), 166.5 (Cquart., COOH), 167.1 (Cquart., COOH). Die spectrum contains up to 20% of the complementary isomer.
DOI: 10.14272/irlrffncejwnjf-ghvjwsgmsa-n/1hnmr
title: 1H NMR (, InChI=1S/C20H13ClN2O4/c21-15-6-8-16(9-7-15)22-23-18-11-14(20(26)27)5-10-17(18)12-1-3-13(4-2-12)19(24)25/h1-11H,(H,24,25)(H,26,27)/b23-22+)

description: dataset for 1H NMR
      
      1H NMR (400 MHz, DMSO-d6, ppm) δ = 7.62−7.70 (m, 4H, CHAr), 7.77–7.81 (m, 2H, CHAr), 7.83 (d, J = 8.0 Hz, 1H, CHAr), 8.05–8.07 (m, 2H, CHAr), 8.21 (dd, J = 8.0 Hz, J = 1.8 Hz, 1H, CHAr), 8.28 (d, J = 1.7 Hz, 1H, CHAr), 13.27 (s, 2H, OH). Die spectrum contains up to 20% of the complementary isomer.
DOI: 10.14272/irlrffncejwnjf-ghvjwsgmsa-n/ir
title: IR (, InChI=1S/C20H13ClN2O4/c21-15-6-8-16(9-7-15)22-23-18-11-14(20(26)27)5-10-17(18)12-1-3-13(4-2-12)19(24)25/h1-11H,(H,24,25)(H,26,27)/b23-22+)

description: dataset for IR
      
      IR (ATR, ṽ) = 2528, 1680, 1602, 1573, 1480, 1419, 1286, 1126, 1088, 1006, 917, 870, 830, 780, 758, 740, 697, 662, 601, 537, 434, 338 cm–1.
DOI: 10.5281/zenodo.2640438
title: Atomistic simulations of the adenosine A2 receptor in membranes with varying levels of SDPE

description: An adenosine A2 receptor was simulated in membranes consisting of DSPC, cholesterol (20 mol%), and varying levels (0, 4, or 8 mol%) of SDPE with a polyunsaturated chain. Upon increasing SDPE concentration, the concentration of DSPC was correspondingly decreased. The initial structures for these simulations were obtained from the final structures of corresponding coarse-grained simulations, where an SDPE-rich corona formed around the receptor. After fine-graining, the systems were simulated using the CHARMM36 [1] force field for 200 ns using the GROMACS package [2].

These simulations were also repeated in the absence of protein. These systems were set up using the CHARMM-GUI web portal [3]. The corresponding files have the 'NOPROT' suffix, and the simulation parameter file is called md_noprot.mdp.

For details on the fine-graining and the simulation protocol, please see the related paper at DOI: 10.1371/journal.pcbi.1007033.

The files named PUFA_X.* correspond to simulations with X mol% of SDPE with the protein, whereas the files names PUFA_X_NOPROT.* are the corresponding files in the absence of the protein. For each concentration, a run input file (tpr) and the simulation outputs (xtc, edr, log, gro) are provided. Moreover, the simulations can be extended using the provided cpt files.

Moreover, the files required to generate the run input file are also provided. For each system, a topology file (top) and an index file (ndx) are provided. The CHARMM36 force field and the molecule definitions (itp) referenced by the topology are also provided. The used simulation parameters are provided in the md.mdp file. For the fine-graining of SDPE, the mapping file is also provided (sdpe.charmm36.map).

[1] <strong>DOI: </strong>10.1021/jp101759q

[2] <strong>DOI: </strong>10.1016/j.softx.2015.06.001

[3] <strong>DOI: </strong>10.1021/acs.jctc.5b00935
DOI: 10.5281/zenodo.2646048
title: Coarse-grained simulations of protein partitioning in membranes with varying levels of SDPE

description: The free energies of transfer between liquid ordered (Lo) and liquid disordered (Ld) domains was calculated for three proteins (Adenosine A2 receptor, A2AR; dopamine D2 receptor, D2R; and glucose transporter (GLUT)) using coarse-grained molecular dynamics simulations together with free energy perturbation. Each of these proteins was embedded in a Lo membrane consisting of DSPC, cholesterol, and varying levels (0–16 mol%) of SDPE. First, the lipids were allowed to reorganize during a 10 microsecond simulations. Then, for each protein and for each SDPE concentration, the DSPC lipids were mutated into DOPC ones and the free energy of this change was calculated. This process was repeated in the absence of the proteins for each SDPE concentration. By substracting the corresponding values for the protein-containing and protein-free cases, the free energy of transfer between Lo and Ld domains was calculated for each of the proteins as a function of SDPE concentration. All simulations were performed using the Martini force field [1] and the GROMACS simulation package [2]. For more details of the setup and the simulations, please see the related paper at DOI: 10.1371/journal.pcbi.1007033.

The original equilibration simulations (10 microseconds in the presence of the protein and SDPE and shorter in the absence of either SDPE or the protein). The run input files for these simulations are provided as X_PUFAY_EQ.tpr and the trajectories as X_PUFAY_EQ.xtc, where X stands for the protein (or says 'NOPROT' for the case without protein) and Y for the SDPE concentration.

The run input files for the free energy of transfer simulations are provided as the tar files; one tar for each protein and one for the protein-free case. Each of these tars contains a folder for each used SDPE concentration, including the more realistic membrane compositions (with a suffix 'REAL'). For each SDPE concentration, the run input files (tpr) and the simulation input parameter files (mdp) for each window in the free energy perturbation are provided. Here, the windows are numbered from 0 to 26, where 0 corresponds to DSPC and 26 to DOPC. Also, for each SDPE concentration, common topology (top), index (ndx) and start configuration (gro) are provided. The molecule definitions (itp) are provided in the TOP.tar archive.

[1] <strong>DOI: </strong>10.1021/jp071097f ; <strong>DOI: </strong>10.1021/ct700324x ; <strong>DOI: </strong>10.1021/ct300646g

[2] <strong>DOI: </strong>10.1016/j.softx.2015.06.001
DOI: 10.5281/zenodo.2646049
title: Coarse-grained simulations of protein partitioning in membranes with varying levels of SDPE

description: The free energies of transfer between liquid ordered (Lo) and liquid disordered (Ld) domains was calculated for three proteins (Adenosine A2 receptor, A2AR; dopamine D2 receptor, D2R; and glucose transporter (GLUT)) using coarse-grained molecular dynamics simulations together with free energy perturbation. Each of these proteins was embedded in a Lo membrane consisting of DSPC, cholesterol, and varying levels (0–16 mol%) of SDPE. First, the lipids were allowed to reorganize during a 10 microsecond simulations. Then, for each protein and for each SDPE concentration, the DSPC lipids were mutated into DOPC ones and the free energy of this change was calculated. This process was repeated in the absence of the proteins for each SDPE concentration. By substracting the corresponding values for the protein-containing and protein-free cases, the free energy of transfer between Lo and Ld domains was calculated for each of the proteins as a function of SDPE concentration. All simulations were performed using the Martini force field [1] and the GROMACS simulation package [2]. For more details of the setup and the simulations, please see the related paper at DOI: 10.1371/journal.pcbi.1007033.

The original equilibration simulations (10 microseconds in the presence of the protein and SDPE and shorter in the absence of either SDPE or the protein). The run input files for these simulations are provided as X_PUFAY_EQ.tpr and the trajectories as X_PUFAY_EQ.xtc, where X stands for the protein (or says 'NOPROT' for the case without protein) and Y for the SDPE concentration.

The run input files for the free energy of transfer simulations are provided as the tar files; one tar for each protein and one for the protein-free case. Each of these tars contains a folder for each used SDPE concentration, including the more realistic membrane compositions (with a suffix 'REAL'). For each SDPE concentration, the run input files (tpr) and the simulation input parameter files (mdp) for each window in the free energy perturbation are provided. Here, the windows are numbered from 0 to 26, where 0 corresponds to DSPC and 26 to DOPC. Also, for each SDPE concentration, common topology (top), index (ndx) and start configuration (gro) are provided. The molecule definitions (itp) are provided in the TOP.tar archive.

[1] <strong>DOI: </strong>10.1021/jp071097f ; <strong>DOI: </strong>10.1021/ct700324x ; <strong>DOI: </strong>10.1021/ct300646g

[2] <strong>DOI: </strong>10.1016/j.softx.2015.06.001
DOI: 10.5519/qd.j2tjntrp
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.14272/irlrffncejwnjf-ghvjwsgmsa-n/mass
title: Mass (, InChI=1S/C20H13ClN2O4/c21-15-6-8-16(9-7-15)22-23-18-11-14(20(26)27)5-10-17(18)12-1-3-13(4-2-12)19(24)25/h1-11H,(H,24,25)(H,26,27)/b23-22+)

description: dataset for Mass
      
      APCI (m/z): 381/383 (100/47) [M+H]+.
DOI: 10.5517/ccdc.csd.cc200wyw
title: CCDC 1847908: Experimental Crystal Structure Determination

description: Related Article: Yingxia Wang, Andreas Eichhöfer, Florian Weigend, Dieter Fenske, Olaf Fuhr|2019|Dalton Trans.|48|6863|doi:10.1039/C8DT05003A
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc200x32
title: CCDC 1847913: Experimental Crystal Structure Determination

description: Related Article: Yingxia Wang, Andreas Eichhöfer, Florian Weigend, Dieter Fenske, Olaf Fuhr|2019|Dalton Trans.|48|6863|doi:10.1039/C8DT05003A
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.