|
View: |
Part 1: Document Description
|
|
Citation |
|
|---|---|
|
Title: |
PDB: 5OCX, Crystal structure of ACPA E4 in complex with CII-C-13-CIT (311K, 38°C, 100 ns): random seed #2 |
|
Identification Number: |
doi:10.7910/DVN/LBPX7T |
|
Distributor: |
Harvard Dataverse |
|
Date of Distribution: |
2023-10-16 |
|
Version: |
4 |
|
Bibliographic Citation: |
Stan, Razvan, 2023, "PDB: 5OCX, Crystal structure of ACPA E4 in complex with CII-C-13-CIT (311K, 38°C, 100 ns): random seed #2", https://doi.org/10.7910/DVN/LBPX7T, Harvard Dataverse, V4, UNF:6:uNGxEceuJxucRCFtVS4ZxA== [fileUNF] |
|
Citation |
|
|
Title: |
PDB: 5OCX, Crystal structure of ACPA E4 in complex with CII-C-13-CIT (311K, 38°C, 100 ns): random seed #2 |
|
Identification Number: |
doi:10.7910/DVN/LBPX7T |
|
Authoring Entity: |
Stan, Razvan (Chonnam National University) |
|
Distributor: |
Harvard Dataverse |
|
Access Authority: |
Stan, Razvan |
|
Depositor: |
Stan, Razvan |
|
Date of Deposit: |
2023-10-16 |
|
Holdings Information: |
https://doi.org/10.7910/DVN/LBPX7T |
|
Study Scope |
|
|
Keywords: |
Computer and Information Science, Medicine, Health and Life Sciences, fever, autoimmune diseases, inflammation, Anti-Citrullinated Protein Antibodies, rheumatoid arthritis, autoantibodies |
|
Abstract: |
Crystal structure of ACPA E4 in complex with CII-C-13-CIT (311K, 38°C, 100 ns): random seed #2. Contains free binding energy calculations. |
|
Methodology and Processing |
|
|
Sources Statement |
|
|
Data Access |
|
|
Notes: |
<a href="http://creativecommons.org/publicdomain/zero/1.0">CC0 1.0</a> |
|
Other Study Description Materials |
|
|
Related Publications |
|
|
Citation |
|
|
Title: |
Singh PK, Stan RC. ThermoPCD: a database of molecular dynamics trajectories of antibody-antigen complexes at physiologic and fever-range temperatures. Database (Oxford). 2024 Mar 19; 2024:baae015. doi: 10.1093/database/baae015 |
|
Bibliographic Citation: |
Singh PK, Stan RC. ThermoPCD: a database of molecular dynamics trajectories of antibody-antigen complexes at physiologic and fever-range temperatures. Database (Oxford). 2024 Mar 19; 2024:baae015. doi: 10.1093/database/baae015 |
|
File Description--f7466517 |
|
|
File: 5ocx-rs2-311k-hbond.tab |
|
|
|
|
Notes: |
UNF:6:f2omz8IIpxO3piipTvlHnA== |
|
File Description--f7466498 |
|
|
File: 5ocx-rs2-311k-rmsd.tab |
|
|
|
|
Notes: |
UNF:6:tHg4HZqsvPgthGfKk3TrRA== |
|
File Description--f7466459 |
|
|
File: 5ocx-rs2-311k-sasa.tab |
|
|
|
|
Notes: |
UNF:6:lBUz563chnv4gCKK76f2wQ== |
|
List of Variables: |
|
|
Variables |
|
|
f7466517 Location: |
Summary Statistics: Max. 100.0; Min. 0.0; Valid 10001.0; Mean 49.99999999999999; StDev 28.871843550421236; Variable Format: numeric Notes: UNF:6:Xd0BNWL8q82nJpopTOPPCw== |
|
f7466517 Location: |
Summary Statistics: Max. 18.0; Min. 1.0; Mean 7.9945005499450605; StDev 2.190997433367893; Valid 10001.0 Variable Format: numeric Notes: UNF:6:tdNRNpnW4EkH504BBal0eQ== |
|
f7466517 Location: |
Summary Statistics: Min. 0.0; StDev 2.1547968315045987; Valid 10001.0; Mean 5.065193480651929; Max. 18.0 Variable Format: numeric Notes: UNF:6:fsBcjReYVHnMeV85sg3Rlw== |
|
f7466498 Location: |
Summary Statistics: Min. 0.0; StDev 28.87184491731381; Max. 100.0000076; Valid 10001.0; Mean 50.00000236995278; Variable Format: numeric Notes: UNF:6:o8DlsKAspsa1vrbsM5xrhw== |
|
f7466498 Location: |
Summary Statistics: Valid 10001.0; Mean 0.42068995661433856; StDev 0.05685132737222645; Min. 5.029E-4; Max. 0.6959121 Variable Format: numeric Notes: UNF:6:GMrtD0L2QfmfVBhS0sDn8A== |
|
f7466459 Location: |
Summary Statistics: Mean 50000.0; Valid 10001.0; StDev 28871.843550421232; Min. 0.0; Max. 100000.0 Variable Format: numeric Notes: UNF:6:yng+oh+Vq/c2RVgjFBvZ7g== |
|
f7466459 Location: |
Summary Statistics: Mean 216.7796580341966; StDev 3.05563062061626; Min. 204.015; Max. 230.496; Valid 10001.0 Variable Format: numeric Notes: UNF:6:7RjevlTXPQE14ep5fzRMig== |
|
Label: |
5ocx-m.pdb |
|
Notes: |
application/vnd.palm |
|
Label: |
5ocx-rs2-311k-0ns.pdb |
|
Notes: |
application/vnd.palm |
|
Label: |
5ocx-rs2-311k-100ns.pdb |
|
Notes: |
application/vnd.palm |
|
Label: |
5ocx-rs2-311k-50ns.pdb |
|
Notes: |
application/vnd.palm |
|
Label: |
5ocx-rs2-311k-hbond.xvg |
|
Notes: |
application/octet-stream |
|
Label: |
5ocx-rs2-311k-rmsd.xvg |
|
Notes: |
application/octet-stream |
|
Label: |
5ocx-rs2-311k-sasa.xvg |
|
Notes: |
application/octet-stream |
|
Label: |
complex.gro |
|
Notes: |
application/octet-stream |
|
Label: |
COM.prmtop |
|
Notes: |
application/octet-stream |
|
Label: |
em.edr |
|
Notes: |
application/octet-stream |
|
Label: |
em.gro |
|
Notes: |
application/octet-stream |
|
Label: |
em.log |
|
Notes: |
text/plain |
|
Label: |
em.mdp |
|
Notes: |
application/octet-stream |
|
Label: |
em.tpr |
|
Notes: |
application/octet-stream |
|
Label: |
em.trr |
|
Notes: |
application/octet-stream |
|
Label: |
FINAL_DECOMP_MMPBSA.dat |
|
Notes: |
text/x-fixed-field |
|
Label: |
FINAL_RESULTS_MMPBSA.csv |
|
Notes: |
text/csv |
|
Label: |
FINAL_RESULTS_MMPBSA.dat |
|
Notes: |
text/x-fixed-field |
|
Label: |
_GMXMMPBSA_COM_FIXED.pdb |
|
Notes: |
application/vnd.palm |
|
Label: |
_GMXMMPBSA_COM_index.ndx |
|
Notes: |
application/octet-stream |
|
Label: |
_GMXMMPBSA_COM.inpcrd |
|
Notes: |
application/octet-stream |
|
Label: |
_GMXMMPBSA_COM.pdb |
|
Notes: |
application/vnd.palm |
|
Label: |
_GMXMMPBSA_complex_gb.mdout.0 |
|
Notes: |
application/octet-stream |
|
Label: |
_GMXMMPBSA_complex_gb_surf.dat.0 |
|
Notes: |
application/octet-stream |
|
Label: |
_GMXMMPBSA_complex.mdcrd.0 |
|
Notes: |
application/octet-stream |
|
Label: |
_GMXMMPBSA_complex_pb.mdout.0 |
|
Notes: |
application/octet-stream |
|
Label: |
_GMXMMPBSA_complex.pdb |
|
Notes: |
application/vnd.palm |
|
Label: |
_GMXMMPBSA_dummycomplex.inpcrd |
|
Notes: |
application/octet-stream |
|
Label: |
_GMXMMPBSA_dummyligand.inpcrd |
|
Notes: |
application/octet-stream |
|
Label: |
_GMXMMPBSA_dummyreceptor.inpcrd |
|
Notes: |
application/octet-stream |
|
Label: |
_GMXMMPBSA_gb_decomp_com.mdin |
|
Notes: |
application/octet-stream |
|
Label: |
_GMXMMPBSA_gb_decomp_lig.mdin |
|
Notes: |
application/octet-stream |
|
Label: |
_GMXMMPBSA_gb_decomp_rec.mdin |
|
Notes: |
application/octet-stream |
|
Label: |
_GMXMMPBSA_info |
|
Notes: |
text/plain; charset=US-ASCII |
|
Label: |
_GMXMMPBSA_ligand_gb.mdout.0 |
|
Notes: |
application/octet-stream |
|
Label: |
_GMXMMPBSA_ligand_gb_surf.dat.0 |
|
Notes: |
application/octet-stream |
|
Label: |
_GMXMMPBSA_ligand.mdcrd.0 |
|
Notes: |
application/octet-stream |
|
Label: |
_GMXMMPBSA_ligand_pb.mdout.0 |
|
Notes: |
application/octet-stream |
|
Label: |
_GMXMMPBSA_ligand.pdb |
|
Notes: |
application/vnd.palm |
|
Label: |
_GMXMMPBSA_LIG.pdb |
|
Notes: |
application/vnd.palm |
|
Label: |
gmx_MMPBSA.log |
|
Notes: |
text/plain |
|
Label: |
_GMXMMPBSA_normal_traj_cpptraj.out |
|
Notes: |
application/octet-stream |
|
Label: |
_GMXMMPBSA_pb_decomp_com.mdin |
|
Notes: |
application/octet-stream |
|
Label: |
_GMXMMPBSA_pb_decomp_lig.mdin |
|
Notes: |
application/octet-stream |
|
Label: |
_GMXMMPBSA_pb_decomp_rec.mdin |
|
Notes: |
application/octet-stream |
|
Label: |
_GMXMMPBSA_receptor_gb.mdout.0 |
|
Notes: |
application/octet-stream |
|
Label: |
_GMXMMPBSA_receptor_gb_surf.dat.0 |
|
Notes: |
application/octet-stream |
|
Label: |
_GMXMMPBSA_receptor.mdcrd.0 |
|
Notes: |
application/octet-stream |
|
Label: |
_GMXMMPBSA_receptor_pb.mdout.0 |
|
Notes: |
application/octet-stream |
|
Label: |
_GMXMMPBSA_receptor.pdb |
|
Notes: |
application/vnd.palm |
|
Label: |
_GMXMMPBSA_REC.pdb |
|
Notes: |
application/vnd.palm |
|
Label: |
_GMXMMPBSA_restrt.0 |
|
Notes: |
application/netcdf |
|
Label: |
index.ndx |
|
Notes: |
application/octet-stream |
|
Label: |
ions.mdp |
|
Notes: |
application/octet-stream |
|
Label: |
ions.tpr |
|
Notes: |
application/octet-stream |
|
Label: |
LIG.prmtop |
|
Notes: |
application/octet-stream |
|
Label: |
md_0_10-1.tpr |
|
Notes: |
application/octet-stream |
|
Label: |
md_0_10.cpt |
|
Notes: |
application/mac-compactpro |
|
Label: |
md_0_10.edr |
|
Notes: |
application/octet-stream |
|
Label: |
md_0_10.gro |
|
Notes: |
application/octet-stream |
|
Label: |
md_0_10.log |
|
Notes: |
text/plain |
|
Label: |
md_0_10_prev.cpt |
|
Notes: |
application/mac-compactpro |
|
Label: |
md_0_10.tpr |
|
Notes: |
application/octet-stream |
|
Label: |
md.mdp |
|
Notes: |
application/octet-stream |
|
Label: |
mdout.mdp |
|
Notes: |
application/octet-stream |
|
Label: |
mmpbsa.in |
|
Notes: |
text/plain |
|
Label: |
newbox.gro |
|
Notes: |
application/octet-stream |
|
Label: |
npt.cpt |
|
Notes: |
application/mac-compactpro |
|
Label: |
npt.edr |
|
Notes: |
application/octet-stream |
|
Label: |
npt.gro |
|
Notes: |
application/octet-stream |
|
Label: |
npt.log |
|
Notes: |
text/plain |
|
Label: |
npt.mdp |
|
Notes: |
application/octet-stream |
|
Label: |
npt.tpr |
|
Notes: |
application/octet-stream |
|
Label: |
npt.trr |
|
Notes: |
application/octet-stream |
|
Label: |
nvt.cpt |
|
Notes: |
application/mac-compactpro |
|
Label: |
nvt.edr |
|
Text: | |
|
Notes: |
application/octet-stream |
|
Label: |
nvt.gro |
|
Notes: |
application/octet-stream |
|
Label: |
nvt.log |
|
Notes: |
text/plain |
|
Label: |
nvt.mdp |
|
Notes: |
application/octet-stream |
|
Label: |
nvt.tpr |
|
Notes: |
application/octet-stream |
|
Label: |
nvt.trr |
|
Notes: |
application/octet-stream |
|
Label: |
posre_Protein_chain_A.itp |
|
Notes: |
application/vnd.shana.informed.formtemplate |
|
Label: |
posre_Protein_chain_B.itp |
|
Notes: |
application/vnd.shana.informed.formtemplate |
|
Label: |
posre_Protein_chain_C.itp |
|
Notes: |
application/vnd.shana.informed.formtemplate |
|
Label: |
REC.prmtop |
|
Notes: |
application/octet-stream |
|
Label: |
RESULTS_gmx_MMPBSA.h5 |
|
Notes: |
application/x-hdf5 |
|
Label: |
solv.gro |
|
Notes: |
application/octet-stream |
|
Label: |
solv_ions.gro |
|
Notes: |
application/octet-stream |
|
Label: |
topol-1.top |
|
Notes: |
application/octet-stream |
|
Label: |
topol_Protein_chain_A-1.itp |
|
Notes: |
application/vnd.shana.informed.formtemplate |
|
Label: |
topol_Protein_chain_A.itp |
|
Notes: |
application/vnd.shana.informed.formtemplate |
|
Label: |
topol_Protein_chain_B-1.itp |
|
Notes: |
application/vnd.shana.informed.formtemplate |
|
Label: |
topol_Protein_chain_B.itp |
|
Notes: |
application/vnd.shana.informed.formtemplate |
|
Label: |
topol_Protein_chain_C-1.itp |
|
Notes: |
application/vnd.shana.informed.formtemplate |
|
Label: |
topol_Protein_chain_C.itp |
|
Notes: |
application/vnd.shana.informed.formtemplate |
|
Label: |
topol.top |
|
Notes: |
application/octet-stream |
|
Label: |
_topol.top.1_ |
|
Text: | |
|
Notes: |
application/octet-stream |
|
Label: |
topol.top.1 |
|
Notes: |
application/octet-stream |
|
Label: |
_topol.top.2_ |
|
Text: | |
|
Notes: |
application/octet-stream |
|
Label: |
topol.top.2 |
|
Notes: |
application/octet-stream |
|
Label: |
xvg2csv.py |
|
Notes: |
text/x-python |