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Sitemap program

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SiteMap' is a software program designed to visualize and analyze complex data sets. The core function of SiteMap' is to generate interactive maps that represent the structure and relationships within large, interconnected data sources. The program utilizes advanced algorithms to identify patterns, clusters, and hierarchies within the data, providing users with a comprehensive overview of the data landscape.

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Lab products found in correlation

Prime protein structure prediction program, by Schrödinger (2 mentions) Glidescore, by Schrödinger (2 mentions) Glide 5, by Schrödinger (2 mentions) Protein preparation wizard, by Schrödinger (1 mentions) Glide docking, by Schrödinger (1 mentions)

5 protocols using sitemap program

1

Structural Modeling and Ligand Docking of T. cruzi Proteasome

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The homology model of T. cruzi 20S proteasome was built using ‘Prime’ protein structure prediction program (Schrödinger) and X-ray structure of bovine 20S proteasome (pdb accession code 1IRU)39 (link) as the template. The model was subjected to restrained minimization to relieve inter-chain clashes. ‘SiteMap’ program (Schrödinger) was used to identify pockets on a protein surface suitable for small molecule binding. Flexible ligand docking was performed using ‘Glide 5.8’ (Schrödinger). The grid box was centered in a middle of the identified pocket and extended by 10 Å, with outer box extending additional 20Å. The ligand was docked using the standard precision (SP) algorithm and scored using ‘GlideScore’ (Schrödinger). The GNF6702 GlideScore is equal to −8.5.
Khare S., Nagle A.S., Biggart A., Lai Y.H., Liang F., Davis L.C., Barnes S.W., Mathison C.J., Myburgh E., Gao M.Y., Gillespie J.R., Liu X., Tan J.L., Stinson M., Rivera I.C., Ballard J., Yeh V., Groessl T., Federe G., Koh H.X., Venable J.D., Bursulaya B., Shapiro M., Mishra P.K., Spraggon G., Brock A., Mottram J.C., Buckner F.S., Rao S.P., Wen B.G., Walker J.R., Tuntland T., Molteni V., Glynne R.J, & Supek F. (2016). Proteasome inhibition for treatment of leishmaniasis, Chagas disease and sleeping sickness. Nature, 537(7619), 229-233.
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2

Structural Analysis of Myc-MAX Complex

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The crystal structure with high resolution, that is, 1.80 Å of Myc–MAX heterodimer bound to the enhancer sequence, was downloaded from the PDB (PDB ID: 1NKP (26 (link))). By utilizing the Protein Preparation Wizard utility of Schrödinger Release 2018-4: Maestro, Schrödinger, L.L.C., New York, NY, 2018, we prepared the structure of Myc by adding missing hydrogens, determining correct ionization and protonation states and then optimized its hydrogen bond network. After that, the restrained minimization was performed to minimize the hydrogen atoms, to relax the steric clashes and strained bonds using OPLS 2005 forcefield. To identify a potential druggable site on the flat and large interface, only the crystal structure of Myc (chain A, without MAX and DNA) was subjected to the Sitemap program (27 (link)) of Schrodinger. With a remarkable prediction of balanced as well as standalone hydrophobic and hydrophilic site points, hydrogen bond donor/acceptors properties, it predicted five active sites. These sites were ranked based on the draggability score, site score, and hydrophobicity/hydrophilicity scores.
Singh A., Kumar A., Kumar P., Nayak N., Bhardwaj T., Giri R, & Garg N. (2021). A novel inhibitor L755507 efficiently blocks c-Myc–MAX heterodimerization and induces apoptosis in cancer cells. The Journal of Biological Chemistry, 297(1), 100903.
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3

Identifying Binding Sites of Protein ZO-1

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The binding pockets of the target protein ZO-1 are not clear yet. The Sitemap pro-gram in the Schrödinger software suite was performed to search for potential active sites since it has become an effective means to identify and characterize binding sites with high accuracy (>96%) [34 (link),35 (link)]. The possibility of site determination depended on the site’s proximity to the protein and the degree of solvent protection, and those sites leading to the tightest ligand–protein or protein–protein complex were selected.
Liu J., Gao R., Gu X., Yu B., Wu Y., Li Q., Xiang P, & Xu H. (2022). A New Insight into Toxicity of Colchicine Analogues by Molecular Docking Analysis Based on Intestinal Tight Junction Protein ZO-1. Molecules, 27(6), 1797.
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4

Structural Modeling and Ligand Docking of T. cruzi Proteasome

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The homology model of T. cruzi 20S proteasome was built using ‘Prime’ protein structure prediction program (Schrödinger) and X-ray structure of bovine 20S proteasome (pdb accession code 1IRU)39 (link) as the template. The model was subjected to restrained minimization to relieve inter-chain clashes. ‘SiteMap’ program (Schrödinger) was used to identify pockets on a protein surface suitable for small molecule binding. Flexible ligand docking was performed using ‘Glide 5.8’ (Schrödinger). The grid box was centered in a middle of the identified pocket and extended by 10 Å, with outer box extending additional 20Å. The ligand was docked using the standard precision (SP) algorithm and scored using ‘GlideScore’ (Schrödinger). The GNF6702 GlideScore is equal to −8.5.
Khare S., Nagle A.S., Biggart A., Lai Y.H., Liang F., Davis L.C., Barnes S.W., Mathison C.J., Myburgh E., Gao M.Y., Gillespie J.R., Liu X., Tan J.L., Stinson M., Rivera I.C., Ballard J., Yeh V., Groessl T., Federe G., Koh H.X., Venable J.D., Bursulaya B., Shapiro M., Mishra P.K., Spraggon G., Brock A., Mottram J.C., Buckner F.S., Rao S.P., Wen B.G., Walker J.R., Tuntland T., Molteni V., Glynne R.J, & Supek F. (2016). Proteasome inhibition for treatment of leishmaniasis, Chagas disease and sleeping sickness. Nature, 537(7619), 229-233.
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5

Ligand Binding Site Identification for Mouse-Type T1R1

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The SiteMap program (Schrödinger, LLC) was used to initially identify two potential ligand binding sites for the mouse-type human T1R1; one was near the three mutated residues at the bottom of the binding site, and the other was in the upper region of the allosteric pocket. Glide docking (Schrödinger, LLC) was then performed to allow methional to explore both of these potential binding sites. Standard precision (SP) mode and the OPLS3 force field were used during docking.
Toda Y., Nakagita T., Hirokawa T., Yamashita Y., Nakajima A., Narukawa M., Ishimaru Y., Uchida R, & Misaka T. (2018). Positive/Negative Allosteric Modulation Switching in an Umami Taste Receptor (T1R1/T1R3) by a Natural Flavor Compound, Methional. Scientific Reports, 8, 11796.
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