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| { | ||
| "accessibility": "Open access", | ||
| "additionDate": "2023-10-20T11:34:24.816824Z", | ||
| "biotoolsCURIE": "biotools:ammpdb", | ||
| "biotoolsID": "ammpdb", | ||
| "confidence_flag": "tool", | ||
| "cost": "Free of charge", | ||
| "credit": [ | ||
| { | ||
| "email": "[email protected]", | ||
| "name": "Usha Mina", | ||
| "typeEntity": "Person" | ||
| } | ||
| ], | ||
| "description": "Curated database of Indian anti-tubercular medicinal plants.", | ||
| "editPermission": { | ||
| "type": "private" | ||
| }, | ||
| "function": [ | ||
| { | ||
| "operation": [ | ||
| { | ||
| "term": "Database search", | ||
| "uri": "http://edamontology.org/operation_2421" | ||
| }, | ||
| { | ||
| "term": "Small molecule design", | ||
| "uri": "http://edamontology.org/operation_4009" | ||
| }, | ||
| { | ||
| "term": "Text mining", | ||
| "uri": "http://edamontology.org/operation_0306" | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "homepage": "https://www.ammpdb.com/", | ||
| "lastUpdate": "2023-10-20T11:34:24.819433Z", | ||
| "name": "AMMPDB", | ||
| "operatingSystem": [ | ||
| "Linux", | ||
| "Mac", | ||
| "Windows" | ||
| ], | ||
| "owner": "Pub2Tools", | ||
| "publication": [ | ||
| { | ||
| "doi": "10.1016/J.JAIM.2023.100712", | ||
| "metadata": { | ||
| "abstract": "The utilization of medicinal plants for their therapeutic properties has long been a key component of Indian culture. Unique medicinal characteristics can be found in the phytochemicals that are extracted from these plants. Globally, tuberculosis (TB) burden and management are challenged due to the emergence of new resistant strains of Mycobacterium tuberculosis (Mtb). This highlights the importance of new drug molecules from diverse sources as well as their innovative management options. In this context, the present study formulated an Anti Mtb medicinal plant database (AMMPDB Ver. 1.1), a manually curated database of native Indian medicinal plants that reported anti-tubercular (anti-TB) activities and their potential therapeutic phytochemicals. This is the first-ever freely accessible digital repository. The current version of the database provides users, with information regarding 118 native Indian anti-tubercular medicinal plants and their 3374 phytochemicals. The database provides the following information: Taxonomical ID, botanical description, vernacular names, conservation status, geographical distribution maps, IC-50 value, phytochemical details which include - name, Compound ID, Synonyms, location in plant part, 2D, 3D structures (as per the availability), and their medicinal uses reported in the literature. The tools section of the database is equipped with sequentially catalogued and hyperlinked open-access tools utilized for computational drug designing. A case study has been incorporated under the contributors section to validate the tools section and the phytochemicals of the database. AMMPDB Ver 1.1 will be serviceable to research in computational drug designing and discovery with effectiveness and ease. Database URL: https://www.ammpdb.com/", | ||
| "authors": [ | ||
| { | ||
| "name": "Gautam A." | ||
| }, | ||
| { | ||
| "name": "Kanneganti J." | ||
| }, | ||
| { | ||
| "name": "Mina U." | ||
| }, | ||
| { | ||
| "name": "Singh A." | ||
| }, | ||
| { | ||
| "name": "Somvanshi P." | ||
| } | ||
| ], | ||
| "date": "2023-03-01T00:00:00Z", | ||
| "journal": "Journal of Ayurveda and Integrative Medicine", | ||
| "title": "Anti Mtb Medicinal Plants Database (AMMPDB): A curated database of Indian anti-tubercular medicinal plants" | ||
| }, | ||
| "pmcid": "PMC10172712", | ||
| "pmid": "37120901", | ||
| "type": [ | ||
| "Primary" | ||
| ] | ||
| } | ||
| ], | ||
| "toolType": [ | ||
| "Database portal" | ||
| ], | ||
| "topic": [ | ||
| { | ||
| "term": "Data submission, annotation and curation", | ||
| "uri": "http://edamontology.org/topic_0219" | ||
| }, | ||
| { | ||
| "term": "Drug metabolism", | ||
| "uri": "http://edamontology.org/topic_3375" | ||
| }, | ||
| { | ||
| "term": "Medicinal chemistry", | ||
| "uri": "http://edamontology.org/topic_0209" | ||
| }, | ||
| { | ||
| "term": "Medicine", | ||
| "uri": "http://edamontology.org/topic_3303" | ||
| }, | ||
| { | ||
| "term": "Plant biology", | ||
| "uri": "http://edamontology.org/topic_0780" | ||
| } | ||
| ] | ||
| } |
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|---|---|---|
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| { | ||
| "accessibility": "Open access", | ||
| "additionDate": "2023-10-20T11:11:34.753463Z", | ||
| "biotoolsCURIE": "biotools:aodb", | ||
| "biotoolsID": "aodb", | ||
| "confidence_flag": "tool", | ||
| "cost": "Free of charge", | ||
| "credit": [ | ||
| { | ||
| "email": "[email protected]", | ||
| "name": "Ling Wang" | ||
| } | ||
| ], | ||
| "description": "A comprehensive database for antioxidants including small molecules, peptides and proteins.", | ||
| "editPermission": { | ||
| "type": "public" | ||
| }, | ||
| "function": [ | ||
| { | ||
| "operation": [ | ||
| { | ||
| "term": "Data retrieval", | ||
| "uri": "http://edamontology.org/operation_2422" | ||
| }, | ||
| { | ||
| "term": "Database search", | ||
| "uri": "http://edamontology.org/operation_2421" | ||
| }, | ||
| { | ||
| "term": "Protein signal peptide detection", | ||
| "uri": "http://edamontology.org/operation_0418" | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "homepage": "https://aodb.idruglab.cn/", | ||
| "lastUpdate": "2023-10-20T11:11:34.768498Z", | ||
| "name": "AODB", | ||
| "operatingSystem": [ | ||
| "Linux", | ||
| "Mac", | ||
| "Windows" | ||
| ], | ||
| "owner": "Pub2Tools", | ||
| "publication": [ | ||
| { | ||
| "doi": "10.1016/J.FOODCHEM.2023.135992", | ||
| "metadata": { | ||
| "abstract": "Antioxidants are widely used in the fields of food, medicine, nutraceuticals, and cosmetics. Given their important roles in promoting and maintaining human health, a large number of antioxidants have been reported. Some antioxidant-related databases have been developed; however, the annotation of antioxidants and related information stored in existing databases is incomplete and requires more efficient retrieval methods. This study aimed to develop a manually curated comprehensive antioxidant database (AODB). Currently, it stores 56,666 small molecules tested for antioxidant activity, 1480 antioxidant peptides, and 998 antioxidant proteins, including their structures, names, antioxidant assay records, computable physicochemical and ADMET properties, and sources. AODB supports text search and mining, 2D and 3D chemical structure search, and BLAST-based protein sequence search, enabling users to retrieve antioxidant data quickly and easily. AODB, as a one-stop antioxidant database, can facilitate the exploration of antioxidants and potential applications. AODB is publicly available and updated annually at https://aodb.idruglab.cn/.", | ||
| "authors": [ | ||
| { | ||
| "name": "Chen Y." | ||
| }, | ||
| { | ||
| "name": "Deng W." | ||
| }, | ||
| { | ||
| "name": "Sun X." | ||
| }, | ||
| { | ||
| "name": "Wang L." | ||
| } | ||
| ], | ||
| "citationCount": 3, | ||
| "date": "2023-08-30T00:00:00Z", | ||
| "journal": "Food Chemistry", | ||
| "title": "AODB: A comprehensive database for antioxidants including small molecules, peptides and proteins" | ||
| }, | ||
| "pmid": "37001349", | ||
| "type": [ | ||
| "Primary" | ||
| ] | ||
| } | ||
| ], | ||
| "toolType": [ | ||
| "Database portal" | ||
| ], | ||
| "topic": [ | ||
| { | ||
| "term": "Cardiology", | ||
| "uri": "http://edamontology.org/topic_3335" | ||
| }, | ||
| { | ||
| "term": "Molecular biology", | ||
| "uri": "http://edamontology.org/topic_3047" | ||
| }, | ||
| { | ||
| "term": "Nutritional science", | ||
| "uri": "http://edamontology.org/topic_3390" | ||
| }, | ||
| { | ||
| "term": "Pharmacology", | ||
| "uri": "http://edamontology.org/topic_0202" | ||
| }, | ||
| { | ||
| "term": "Small molecules", | ||
| "uri": "http://edamontology.org/topic_0154" | ||
| } | ||
| ] | ||
| } |
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|---|---|---|
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| { | ||
| "accessibility": "Open access", | ||
| "additionDate": "2023-10-17T12:28:18.018465Z", | ||
| "biotoolsCURIE": "biotools:atlasxploretm", | ||
| "biotoolsID": "atlasxploretm", | ||
| "confidence_flag": "tool", | ||
| "cost": "Free of charge", | ||
| "credit": [ | ||
| { | ||
| "email": "[email protected]", | ||
| "name": "Liya Wang", | ||
| "orcidid": "https://orcid.org/0000-0001-6810-1332", | ||
| "typeEntity": "Person" | ||
| } | ||
| ], | ||
| "description": "Web platform for visualizing and sharing spatial epigenome data.", | ||
| "documentation": [ | ||
| { | ||
| "type": [ | ||
| "User manual" | ||
| ], | ||
| "url": "https://docs.atlasxomics.com/projects/AtlasXplore/en/latest/index.html" | ||
| } | ||
| ], | ||
| "editPermission": { | ||
| "type": "public" | ||
| }, | ||
| "function": [ | ||
| { | ||
| "operation": [ | ||
| { | ||
| "term": "Visualisation", | ||
| "uri": "http://edamontology.org/operation_0337" | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "homepage": "https://web.atlasxomics.com", | ||
| "language": [ | ||
| "Python", | ||
| "R" | ||
| ], | ||
| "lastUpdate": "2023-10-17T12:28:18.021169Z", | ||
| "license": "MIT", | ||
| "link": [ | ||
| { | ||
| "type": [ | ||
| "Repository" | ||
| ], | ||
| "url": "https://github.com/atlasxomics" | ||
| } | ||
| ], | ||
| "name": "AtlasXploreTM", | ||
| "operatingSystem": [ | ||
| "Linux", | ||
| "Mac", | ||
| "Windows" | ||
| ], | ||
| "owner": "Pub2Tools", | ||
| "publication": [ | ||
| { | ||
| "doi": "10.1093/bioinformatics/btad447", | ||
| "metadata": { | ||
| "abstract": "Motivation: In recent years, a growing number of spatial epigenome datasets have been generated, presenting rich opportunities for studying the regulation mechanisms in solid tissue sections. However, visual exploration of these datasets requires extensive computational processing of raw data, presenting a challenge for researchers without advanced computational skills to fully explore and analyze such datasets. Results: Here, we introduce AtlasXplore, a web-based platform that enables scientists to interactively navigate a growing collection of spatial epigenome data using an expanding set of tools.", | ||
| "authors": [ | ||
| { | ||
| "name": "Barnett J." | ||
| }, | ||
| { | ||
| "name": "Jafar T." | ||
| }, | ||
| { | ||
| "name": "Rao P." | ||
| }, | ||
| { | ||
| "name": "Silverman J." | ||
| }, | ||
| { | ||
| "name": "Sotudeh N." | ||
| }, | ||
| { | ||
| "name": "Wang L." | ||
| } | ||
| ], | ||
| "date": "2023-08-01T00:00:00Z", | ||
| "journal": "Bioinformatics", | ||
| "title": "AtlasXplore: a web platform for visualizing and sharing spatial epigenome data" | ||
| }, | ||
| "pmcid": "PMC10394123", | ||
| "pmid": "37478350", | ||
| "type": [ | ||
| "Primary" | ||
| ] | ||
| } | ||
| ], | ||
| "toolType": [ | ||
| "Web application" | ||
| ], | ||
| "topic": [ | ||
| { | ||
| "term": "Epigenomics", | ||
| "uri": "http://edamontology.org/topic_3173" | ||
| }, | ||
| { | ||
| "term": "Imaging", | ||
| "uri": "http://edamontology.org/topic_3382" | ||
| } | ||
| ] | ||
| } |
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