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An analysis toolkit was developed for evaluating molecular dynamics trajectories generated by Tinker v8.1.2 (dasher.wustl.edu/tinker/) for aqueous models of free amino acids and short peptides containing at least two Cysteine residues. Current functionalities include:
\n\nA tutorial style description, Python source code, a worked out example for CIACGAC and CGGCGGC peptides, description of each algorithm, and the sensitivity of each input parameter with respect to the definition of cluster shapes, min/max distances are provided.
\n\nThe plots generated by the programs can be directly visualized in PSI-Plot (Poly Software International, Pearl River, NY).
\n\nVersion 2.0 contains much improvements in torsional angle analysis for wrapped and mirrored Ramachandran plots, and in the efficiency of the crossover analysis. The S...S distance toolking can now recognize deprotonated Cys, homoCys, and thioGly residues. Please see the versions.log file in the "analysis code.zip" file for the modification of each utility.
", "publication_date": "2018-10-02", "publisher": "Zenodo", "resource_type": { "id": "software", "title": { "de": "Software", "en": "Software" } }, "rights": [ { "description": { "en": "The Creative Commons Attribution license allows re-distribution and re-use of a licensed work on the condition that the creator is appropriately credited." }, "icon": "cc-by-icon", "id": "cc-by-4.0", "props": { "scheme": "spdx", "url": "https://creativecommons.org/licenses/by/4.0/legalcode" }, "title": { "en": "Creative Commons Attribution 4.0 International" } } ], "subjects": [ { "subject": "iron-sulfur clusters; molecular dynamics simulations; peptide conformation; [Fe-S] cluster nesting; ferredoxin maquettes; radical SAM maquettes, secondary structure analysis" } ], "title": "Secondary Structure Analysis Toolkit for Evaluating Iron-Sulfur Cluster Nest Formation", "version": "2.0" }, "parent": { "access": { "owned_by": { "user": 38528 } }, "communities": {}, "id": "1257275", "pids": { "doi": { "client": "datacite", "identifier": "10.5281/zenodo.1257275", "provider": "datacite" } } }, "pids": { "doi": { "client": "datacite", "identifier": "10.5281/zenodo.1442864", "provider": "datacite" }, "oai": { "identifier": "oai:zenodo.org:1442864", "provider": "oai" } }, "revision_id": 5, "stats": { "all_versions": { "data_volume": 31358776322.0, "downloads": 207, "unique_downloads": 137, "unique_views": 234, "views": 248 }, "this_version": { "data_volume": 29315222380.0, "downloads": 166, "unique_downloads": 115, "unique_views": 124, "views": 133 } }, "status": "published", "updated": "2020-01-25T07:21:19.485989+00:00", "versions": { "index": 2, "is_latest": true } }