dbHDPLS: A database of human disease-related protein-ligand structures

Zhu, Muchun; Song, Xiaoping; Zhang, Youzhi; Wang, Wenyan; Wang, Bing

doi:10.1016/j.compbiolchem.2018.12.023

Cited by 7 publications

(4 citation statements)

References 42 publications

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“…Protein–ligand interactions modulate innumerable physiological events, including, but not limited to, cell signaling, 1 infection and disease onset, 2 immune response, 3 aging, 4 cell death, 5 etc. Inhibition of ligand binding is therefore a core mechanism of action of many therapeutic agents.…”

Section: Introductionmentioning

confidence: 99%

Protein–Ligand CH−π Interactions: Structural Informatics, Energy Function Development, and Docking Implementation

Yao

Woods

2023

J. Chem. Theory Comput.

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Here, we develop an empirical energy function based on quantum mechanical data for the interaction between methane and benzene that captures the contribution from CH−π interactions. Such interactions are frequently observed in protein−ligand crystal structures, particularly for carbohydrate ligands, but have been hard to quantify due to the absence of a model for CH−π interactions in typical molecular mechanical force fields or docking scoring functions. The CH−π term was added to the AutoDock Vina (AD VINA) scoring function enabling its performance to be evaluated against a cohort of more than 1600 occurrences in 496 experimental structures of protein−ligand complexes. By employing a conformational grid search algorithm, inclusion of the CH−π term was shown to improve the prediction of the preferred orientation of flexible ligands in protein-binding sites and to enhance the detection of carbohydrate-binding sites that display CH−π interactions. Last but not least, this term was also shown to improve docking performance for the CASF-2016 benchmark set and a carbohydrate set.

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Section: Introductionmentioning

confidence: 99%

Protein–Ligand CH−π Interactions: Structural Informatics, Energy Function Development, and Docking Implementation

Yao

Woods

2023

J. Chem. Theory Comput.

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“…A huge amount of biological information generated from laboratory experiments is warehoused in databases, which are freely available through the internet. NCBI ( https://www.ncbi.nlm.nih.gov/ ), Protein Information Resource (PIR) ( https://proteininformationresource.org/ ), DDBJ ( https://www.ddbj.nig.ac.jp/index-e.html ), ExPASy ( https://www.expasy.org/ ), Protein ligand interaction database (PLID) ( https://ngdc.cncb.ac.cn/databasecommons/database/id/3794 ), TTRMDB ( http://vit.ac.in/ttrmdb ), and dbHDPLS ( https://www.dlearningapp.com/web/dbDPLS/index.php ) are a few examples of large and popular databases providing information on proteins, protein families and also provide users with online software tools for bioinformatics analyses ( Reddy et al, 2008 ; Zhu et al, 2019 ; Srinivasan, Natarajan & Rajasekaran, 2020 ). Bioinformatics databases dedicated to viruses are available.…”

Section: Introductionmentioning

confidence: 99%

ArVirInd—a database of arboviral antigenic proteins from the Indian subcontinent

Atre

Alagarasu

Shil

2022

PeerJ

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Background Studies on antigenic proteins for arboviruses are important for providing diagnostics and vaccine development. India and its neighboring countries have a huge burden of arboviral diseases. Data mining for country-specific sequences from existing bioinformatics databases is cumbersome and time-consuming. This necessitated the development of a database of antigenic proteins from arboviruses isolated from the countries of the Indian subcontinent. Methods Arboviral antigenic protein sequences were obtained from the NCBI and other databases. In silico antigenic characterization was performed (Epitope predictions) and data was incorporated into the database. The front end was designed and developed using HTML, CSS, and PHP. For the backend of the database, we have used MySQL. Results A database, named ArVirInd, is created as a repository of information on curated antigenic proteins. This enlists sequences by country and year of outbreak or origin of the viral strain. For each entry, antigenic information is provided along with functional sites, etc. Researchers can search this database by virus/protein name, country, and year of collection (or in combination) as well as peptide search for epitopes. It is available publicly via the Internet at http://www.arvirind.co.in. ArVirInd will be useful in the study of immune informatics, diagnostics, and vaccinology for arboviruses.

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“…Huge amount of biological information generated from laboratory experiments are warehoused into databases, which are freely available through the internet. NCBI, Protein Information resource (PIR), DDBJ, ExPASy, PLID, TTRMDB and dbHDPLS are a few examples of large and popular databases providing information on proteins, protein families and also pro-vides users with online software tools for bioinformatics analyses (Reddy et al, 2008;Zhu et al, 2019;Srinivasan et al, 2020). Bioinformatics databases dedicated for viruses are available.…”

Section: Introductionmentioning

confidence: 99%

ArVirInd - a database of arboviral antigenic proteins from the Indian subcontinent

Atre

Alagarasu

Shil

2021

Preprint

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Studies on antigenic proteins for arboviruses are important for providing diagnostics and vaccine development. India and its neighbouring countries have huge burden of arboviral diseases. Data mining for country-specific sequences from existing databases is cumbersome and time-consuming. This necessitated the development of a database of antigenic proteins from arbo-viruses isolated from the countries of the Indian subcontinent. Arboviral antigenic protein sequences were obtained from the NCBI and other databases. In silico antigenic characterization was performed (Epitope predictions) and data incorporated in the database. The front end is designed and developed using HTML, CSS and PHP. For the backend of the database, we have used MySQL. A database, named ArVirInd, is created as a repository of information on antigenic proteins. This enlists sequences by country and year of outbreak or origin of the viral strain. For each entry antigenic information is provided along with functional sites, etc. Researchers can search this database by virus/protein name, country and year of collection (or in combination). It is available publicly via Internet at http://www.arvirind.co.in. ArVirInd will be useful in the study of immuno-informatics, diagnostics and vaccinology for arboviruses.

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dbHDPLS: A database of human disease-related protein-ligand structures

Cited by 7 publications

References 42 publications

Protein–Ligand CH−π Interactions: Structural Informatics, Energy Function Development, and Docking Implementation

Protein–Ligand CH−π Interactions: Structural Informatics, Energy Function Development, and Docking Implementation

ArVirInd—a database of arboviral antigenic proteins from the Indian subcontinent

ArVirInd - a database of arboviral antigenic proteins from the Indian subcontinent

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