The specific applications of the TSR-based method in identifying Zn2+ binding sites of proteases and ACE/ACE2
We have developed an alignment-free TSR (Triangular Spatial Relationship)-based computational method for protein structural comparison and motif identification and discovery. To demonstrate the potential applications of the method, we have generated two datasets. One dataset contains five classes: A...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-12-01
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| Series: | Data in Brief |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352340922008356 |
| _version_ | 1811206161314086912 |
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| author | Titli Sarkar Camille R. Reaux Jianxiong Li Vijay V. Raghavan Wu Xu |
| author_facet | Titli Sarkar Camille R. Reaux Jianxiong Li Vijay V. Raghavan Wu Xu |
| author_sort | Titli Sarkar |
| collection | DOAJ |
| description | We have developed an alignment-free TSR (Triangular Spatial Relationship)-based computational method for protein structural comparison and motif identification and discovery. To demonstrate the potential applications of the method, we have generated two datasets. One dataset contains five classes: Actin/Hsp70, serine protease (chymotrypsin/trypsin/elastase), ArsC/Prdx2, PKA/PKB/PKC, and AChE/BChE at the hierarchical level 1 and twelve groups at the level 2. The other dataset includes representative proteases and ACE/ACE2. The x,y, z coordinates of the structures were obtained from PDB. We calculated the keys (or features) that represent each structure using the TSR-based method. The dataset and data presented here include additional information that help the readers become aware of specific applications of the TSR-based method in protein clustering, identification and discovery of metal ion binding sites as well as to understand the effect of amino acid grouping on protein 3D structural relationships at both global and local levels. |
| first_indexed | 2024-04-12T03:43:14Z |
| format | Article |
| id | doaj.art-72530f67cded49c8b58d677e2d8cf66d |
| institution | Directory Open Access Journal |
| issn | 2352-3409 |
| language | English |
| last_indexed | 2024-04-12T03:43:14Z |
| publishDate | 2022-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Data in Brief |
| spelling | doaj.art-72530f67cded49c8b58d677e2d8cf66d2022-12-22T03:49:13ZengElsevierData in Brief2352-34092022-12-0145108629The specific applications of the TSR-based method in identifying Zn2+ binding sites of proteases and ACE/ACE2Titli Sarkar0Camille R. Reaux1Jianxiong Li2Vijay V. Raghavan3Wu Xu4The Center for Advanced Computer Studies, University of Louisiana at Lafayette, Lafayette, LA 70504, USA; Department of Chemistry, University of Louisiana at Lafayette, PO Box 44370, Lafayette, LA 70504, USADepartment of Chemistry, University of Louisiana at Lafayette, PO Box 44370, Lafayette, LA 70504, USAHigh Performance Computing, Frey Computing Services Center, Louisiana State University, Baton Rouge, LA 70803, USAThe Center for Advanced Computer Studies, University of Louisiana at Lafayette, Lafayette, LA 70504, USADepartment of Chemistry, University of Louisiana at Lafayette, PO Box 44370, Lafayette, LA 70504, USA; Corresponding author at: Department of Chemistry, University of Louisiana at Lafayette, Lafayette, LA 70504, USAWe have developed an alignment-free TSR (Triangular Spatial Relationship)-based computational method for protein structural comparison and motif identification and discovery. To demonstrate the potential applications of the method, we have generated two datasets. One dataset contains five classes: Actin/Hsp70, serine protease (chymotrypsin/trypsin/elastase), ArsC/Prdx2, PKA/PKB/PKC, and AChE/BChE at the hierarchical level 1 and twelve groups at the level 2. The other dataset includes representative proteases and ACE/ACE2. The x,y, z coordinates of the structures were obtained from PDB. We calculated the keys (or features) that represent each structure using the TSR-based method. The dataset and data presented here include additional information that help the readers become aware of specific applications of the TSR-based method in protein clustering, identification and discovery of metal ion binding sites as well as to understand the effect of amino acid grouping on protein 3D structural relationships at both global and local levels.http://www.sciencedirect.com/science/article/pii/S2352340922008356TSRMetal ion binding siteProtein similarity3D structureAlignment-freeStructural motif |
| spellingShingle | Titli Sarkar Camille R. Reaux Jianxiong Li Vijay V. Raghavan Wu Xu The specific applications of the TSR-based method in identifying Zn2+ binding sites of proteases and ACE/ACE2 Data in Brief TSR Metal ion binding site Protein similarity 3D structure Alignment-free Structural motif |
| title | The specific applications of the TSR-based method in identifying Zn2+ binding sites of proteases and ACE/ACE2 |
| title_full | The specific applications of the TSR-based method in identifying Zn2+ binding sites of proteases and ACE/ACE2 |
| title_fullStr | The specific applications of the TSR-based method in identifying Zn2+ binding sites of proteases and ACE/ACE2 |
| title_full_unstemmed | The specific applications of the TSR-based method in identifying Zn2+ binding sites of proteases and ACE/ACE2 |
| title_short | The specific applications of the TSR-based method in identifying Zn2+ binding sites of proteases and ACE/ACE2 |
| title_sort | specific applications of the tsr based method in identifying zn2 binding sites of proteases and ace ace2 |
| topic | TSR Metal ion binding site Protein similarity 3D structure Alignment-free Structural motif |
| url | http://www.sciencedirect.com/science/article/pii/S2352340922008356 |
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