=========== HEADER =========== Readme.txt for [dataset title]________________________________ Item Handle: [to be added after record is created] Documentation written on 2026-04-23 By Corey Barber, Heather Coates, Updated , by ________________________ =========== SUGGESTED DATA CITATION =========== Please cite this data in the references for any publication which uses it. Kimble-Hill, A. C., Biak, R. C., Zathang, S., Ray, B. D., Petrache, H. I. (2026). Nanopeptide based on Amot80 AEKEYEGSE, KKQVYVDKV, LEGCYEKVA, SSASYQPVP, VSEAYENLV [Data set]. IU Indianapolis University Library. =========== PRIMARY STUDY INFORMATION =========== ACKNOWLEDGEMENTS Project title: Nanopeptide based on Amot80 KKQVYVDKV Funding agency: Award Number: Award Period: Investigator Name: Ann C. Kimble-Hill Investigator Institution: Indiana University Indianapolis Investigator Address: 635 Barnhill Dr, Indianapolis, IN 46202 Investigator Email: ankimble@iu.edu Investigator Role (related to this dataset): PI Investigator ID (ORCID): https://orcid.org/0000-0001-9575-5454 Investigator Name: Roger C. Biak Investigator Institution: Indiana University Indianapolis Investigator Address: 402 N. Blackford St. Indianapolis, IN 46202 Investigator Email: rogerbiak@yahoo.com Investigator Role (related to this dataset): data analysis, data visualization Investigator ID (ORCID): N/A Investigator Name: Suitintial Zathang Investigator Institution: Indiana University Indianapolis Investigator Address: 402 N. Blackford St. Indianapolis, IN 46202 Investigator Email: suitintial2@gmail.com Investigator Role (related to this dataset): data collection, data processing/cleaning, data analysis, data visualization Investigator ID (ORCID): N/A Investigator Name: Bruce D. Ray Investigator Institution: Indiana University Indianapolis Investigator Address: 402 N. Blackford St. Indianapolis, IN 46202 Investigator Email: bray@iu.edu Investigator Role (related to this dataset): supervision, data collection, data processing/cleaning, data analysis, data visualization, & lab manager Investigator ID (ORCID): https://orcid.org/0000-0002-7663-2333 Investigator Name: Horia I. Petrache Investigator Institution: Indiana University Indianapolis Investigator Address: 402 N. Blackford St. Indianapolis, IN 46202 Investigator Email: hpetrach@iu.edu Investigator Role (related to this dataset): Co-PI Investigator ID (ORCID): https://orcid.org/0000-0003-4363-9456 DATE(S) of DATA COLLECTION 20150711 to 20150713 INSTRUMENT INFORMATION Instrument information: Varian Inova 500 NMR spectrometer Instrument affiliation Indiana University Indianapolis Physics Department Instrument location Indianapolis, Indiana FILE INFORMATION *.pdb files can be opened and worked with any of the following applications: PyMOL: Highly recommended for visualization, featuring an open-source version. VMD (Visual Molecular Dynamics): Used for rendering, capable of downloading PDB files directly. Swiss-PDBViewer: A specialized application for analyzing protein structures. UCSF ChimeraX: An advanced, free, and widely used tool for molecular modeling, visualization, and analysis. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems. Mol* (Molstar): The default 3D viewer for the RCSB PDB website, offering fast and interactive visualization directly in the browser. iCn3D: A National Institutes of Health tool that runs in browsers, allowing for specialized viewing of 3D, 2D, and 1D data. Jmol: A free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems. *.nef files can be opened and worked with any of the following applications: CCPN Analysis 3.2.2, open source NMR spectroscopy software that runs on Windows, Mac OS X, and Linux/Unix systems. NMRFAM-SPARKY, open source software from National Magnetic Resonance Facility, University of Wisconsin, Madison that runs on Windows, Mac OS X, and Linux/Unix systems. *.par and *.spc files are linked together and can only be opened with CCPN Analysis 3.2.2, open source NMR spectroscopy software that runs on Windows, Mac OS X, and Linux/Unix systems. When referring to membrane docking results, cite the Orientations of Proteins in Membranes (OPM) database and refer to: Lomize MA, Pogozheva ID, Joo H., Mosberg HI, Lomize AL (2012) OPM database and PPM web server: resources for positioning of proteins in membranes. Nucleic Acids Res. 40 (Database issue), D370-D376. For an explanation of our method please refer to: Lomize AL, Todd SC, Pogozheva ID. (2022) Spatial arrangement of proteins in planar and curved membranes by PPM 3.0. Protein Sci. 31: 930-946. When referring to results from the ROSIE ligand docking, cite the following articles: 1) Deluca, S., Khar, K., Meiler, J. (2015). Fully Flexible Docking of Medium Sized Ligand Libraries with RosettaLigand. PLoS ONE 10(7): e0132508. doi:10.1371/journal.pone.0132508. 2) Combs, S. A., Deluca, S. L., DeLuca, S. H., Lemmon, G. H., Nannemann, D. P., Nguyen, E. D., et al. (2013). Small-molecule ligand docking into comparative models with Rosetta. Nature Protocols, 8(7), 1277–1298. doi:10.1038/nprot.2013.074. 3) BCL conformer generation: Kothiwale, S., Mendenhall, J.L., Meiler, J. (2015) BCL::Conf: small molecule conformational sampling using a knowledge based rotamer library. J. Cheminform., 7, 47. doi:10.1186/s13321-015-0095-1. 4) Lyskov S, Chou FC, Conchúir SÓ, Der BS, Drew K, Kuroda D, Xu J, Weitzner BD, Renfrew PD, Sripakdeevong P, Borgo B, Havranek JJ, Kuhlman B, Kortemme T, Bonneau R, Gray JJ, Das R., "Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE)". PLoS One. 2013 May 22;8(5):e63906. doi: 10.1371/journal.pone.0063906. When referring to results from Alphafold, cite the following paper: Fleming, J., Magana, P., Nair, S., Tsenkov, M., Bertoni, D., Pidruchna, I., Afonso, M.Q.L., Midlik, A., Paramval, U., Žídek, A. and Laydon, A., 2025. AlphaFold protein structure database and 3D-Beacons: new data and capabilities. Journal of Molecular Biology, 437(15), p.168967. dot: 10.1016/j.jmb.2025.168967. Files Included KKQVYVDKV-water.nef KKQVYVDKV_water.pdb Alphafold structure excised from AF-Q4VCS5-F1-model (Protein Angiomotin, Gene AMOT, Source organism Homo sapiens, UniProt Q4VCS5): KKQVYVDKV alphafold model.pdb In KKQVYVDKV_azara spectrum (*.spc) and parameter files (*.par) ass follows: KKQVYVDKV-cosy-07-12-2015.par KKQVYVDKV-cosy-07-12-2015.spc KKQVYVDKV-dqcosy-07-13-2015.par KKQVYVDKV-dqcosy-07-13-2015.spc KKQVYVDKV-roesy-07-11-2015.par KKQVYVDKV-roesy-07-11-2015.spc KKQVYVDKV-tocsy-07-12-2015.par KKQVYVDKV-tocsy-07-12-2015.spc PDB files from OPM PPM 3.0 modeling as follows where lipid membrane included 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), lysosome, Endoplasmic reticulum membrane (ER), Golgi apparatus (Golgi), Mitochondrial outer membrane (OuterMito), Eukaryotic plasma membranes (PM): KKQVYVDKV_DMPC docked PPM report.PDF KKQVYVDKV_DMPC docked.pdb KKQVYVDKV_DOPC docked PPM report.pdf KKQVYVDKV_DOPC docked.pdb KKQVYVDKV_Endosome docked PPM report.pdf KKQVYVDKV_Endosome docked.pdb KKQVYVDKV_ER docked PPM report.pdf KKQVYVDKV_ER docked.pdb KKQVYVDKV_Golgi docked PPM report.pdf KKQVYVDKV_Golgi docked.pdb KKQVYVDKV_Lysosome docked PPM report.pdf KKQVYVDKV_Lysosome docked.pdb KKQVYVDKV_OuterMito docking PPM report.pdf KKQVYVDKV_OuterMito docking.pdb KKQVYVDKV_PM docking PPM report.pdf KKQVYVDKV_PM docking.pdb OPM PPM membrane compositions.pdf Top 5 PDB files from Rosie Ligand Dock modeling of lipid head groups as follows including Phosphatidylinositol 3-phosphate (PI3P), Phosphatidylinositol 4-phosphate (PI4P), Phosphatidylinositol (3,4)-bisphosphate (PI3_4P2), Phosphatidylinositol (3,5)-bisphosphate (PI3_5P2), Phosphatidylinositol (4,5)-bisphosphate (PI4_5P2), and Phosphatidylinositol (3,4,5)-trisphosphate (PIP3): KKQVYVDKV ethanolamine Rosie Ligand Dock 0007.pdb.bz2 KKQVYVDKV ethanolamine Rosie Ligand Dock 0020.pdb.bz2 KKQVYVDKV ethanolamine Rosie Ligand Dock 0034.pdb.bz2 KKQVYVDKV ethanolamine Rosie Ligand Dock 0036.pdb.bz2 KKQVYVDKV ethanolamine Rosie Ligand Dock 0046.pdb.bz2 KKQVYVDKV inositol Rosie Ligand Dock 0048.pdb.bz2 KKQVYVDKV inositol Rosie Ligand Dock 0050.pdb.bz2 KKQVYVDKV inositol Rosie Ligand Dock 0086.pdb.bz2 KKQVYVDKV inositol Rosie Ligand Dock 0088.pdb.bz2 KKQVYVDKV inositol Rosie Ligand Dock 00881.pdb.bz2 KKQVYVDKV PI3_4P2 Rosie Ligand Dock 0001.pdb.bz2 KKQVYVDKV PI3_4P2 Rosie Ligand Dock 0003.pdb.bz2 KKQVYVDKV PI3_4P2 Rosie Ligand Dock 00031.pdb.bz2 KKQVYVDKV PI3_4P2 Rosie Ligand Dock 0004.pdb.bz2 KKQVYVDKV PI3_4P2 Rosie Ligand Dock 0007.pdb.bz2 KKQVYVDKV PI3_4P2 Rosie Ligand Dock 0050.pdb.bz2 KKQVYVDKV PI3_5P2 Rosie Ligand Dock 0048.pdb.bz2 KKQVYVDKV PI3_5P2 Rosie Ligand Dock 0049.pdb.bz2 KKQVYVDKV PI3_5P2 Rosie Ligand Dock 0051.pdb.bz2 KKQVYVDKV PI3_5P2 Rosie Ligand Dock 0065.pdb.bz2 KKQVYVDKV PI3P Rosie Ligand Dock 0047.pdb.bz2 KKQVYVDKV PI3P Rosie Ligand Dock 0055.pdb.bz2 KKQVYVDKV PI3P Rosie Ligand Dock 0056.pdb.bz2 KKQVYVDKV PI3P Rosie Ligand Dock 0063.pdb.bz2 KKQVYVDKV PI3P Rosie Ligand Dock 0065.pdb.bz2 KKQVYVDKV PI4P Rosie Ligand Dock 0037.pdb.bz2 KKQVYVDKV PI4P Rosie Ligand Dock 0051.pdb.bz2 KKQVYVDKV PI4P Rosie Ligand Dock 0052.pdb.bz2 KKQVYVDKV PI4P Rosie Ligand Dock 0060.pdb.bz2 KKQVYVDKV PI4P Rosie Ligand Dock 0063.pdb.bz2 KKQVYVDKV PIP3 Rosie Ligand Dock 0039.pdb.bz2 KKQVYVDKV PIP3 Rosie Ligand Dock 0046.pdb.bz2 KKQVYVDKV PIP3 Rosie Ligand Dock 0050.pdb.bz2 KKQVYVDKV PIP3 Rosie Ligand Dock 0077.pdb.bz2 KKQVYVDKV PIP3 Rosie Ligand Dock 0083.pdb.bz2 ACCESS & SHARING Links to thesis, dissertation, reports, or publications that cite or use the data (include DOI): Links/relationships to other data files/sets: =========== CREDITS =========== Template provided by Indiana University UITS Research Storage, Indiana University Bloomington Libraries, IUPUI University Library