Molecular property diagnostic suite (MPDS): Development of disease-specific open source web portals for drug discovery

Nagamani, Selvaraman; Gaur, Anamika Singh; Tanneeru, Karunakar; Muneeswaran, Gurusamy; Madugula, Sita Sirisha; Consortium, MPDS; Druzhilovskiy, Dmitry S.; Poroikov, Vladimir; Sastry, G. Narahari

doi:10.1080/1062936x.2017.1402819

Cited by 11 publications

(6 citation statements)

References 51 publications

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“…Molecular property diagnostic suite is a galaxy-based open-source computational drug discovery software developed in our group. The MPDS has been generated for different diseases namely tuberculosis [ 3 , 4 ], diabetes [ 5 ], COVID-19, etc. The modules in MPDS are classified into disease-dependent and disease-independent modules.…”

Section: Resultsmentioning

confidence: 99%

“…Development of open-source drug discovery software along with disease-specific information, a robust compound library, and fragment library is essential for the identification of potential lead compounds with improved activity. One such effort from our group is the development of open-source computational drug discovery software MPDS [ 4 , 5 ].…”

Section: Introductionmentioning

confidence: 99%

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Towards systematic exploration of chemical space: building the fragment library module in molecular property diagnostic suite

et al. 2022

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A fragment-based drug discovery (FBDD) approach has traditionally been of utmost significance in drug design studies. It allows the exploration of large chemical space to find novel scaffolds and chemotypes which can be improved into selective inhibitors with good affinity. In the current work, several public domain chemical libraries (ChEMBL, DrugCentral, PDB ligands, COCONUT, and SAVI) comprising bioactive and virtual molecules were retrieved to develop a fragment library. A systematic fragmentation method that breaks a given molecule into rings, linkers, and substituents was used to cleave the molecules and the fragments were analyzed. Further, only the ring framework was taken into the consideration to develop a fragment library that consists of a total number of 107,614 unique fragments. This set represents a rich diverse structure framework that covers a wide variety of yet-to-be-explored fragments for a wide range of small molecule-based applications. This fragment library is an integral part of the molecular property diagnostic suite (MPDS) suite that can be used with other modeling and informatics methods for FBDD approaches. The fragment library module of MPDS can be accessed at http://mpds.neist.res.in:8085 . Graphical abstract Supplementary Information The online version contains supplementary material available at 10.1007/s11030-022-10506-5.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Towards systematic exploration of chemical space: building the fragment library module in molecular property diagnostic suite

et al. 2022

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“…The modules in MPDS are categorized into (i) data library (that consists of information on genes and targets speci c to a disease or disorder, a molecular repository, druglike fragments, literature, etc.,) (ii) data processing (computation of molecular descriptors/ ngerprints, le format converter) (iii) data analysis (QSAR, docking, drug-likeness lter, and visualization tool), (iv) Advanced modules (which include various predictive modules for disease-disease interaction, big data analysis, and machine learning tools). MPDS is also equipped with a work ow management system that enables the users to easily integrate multiple tools from the available modules and customize the existing work ows as per the requirements [32][33][34]41]. The utility and scope of open-source packages are well documented in the literature [42][43].…”

Section: Genesis Of Galaxy Based Mpdsmentioning

confidence: 99%

Molecular Property Diagnostic Suite Compound Library (MPDS-CL): A Structure based Classification of the Chemical Space

John

Nagamani

Mahanta

et al. 2023

Preprint

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Molecular Property Diagnostic Suite-Compound Library (MPDS-CL), is an open-source galaxy-based cheminformatics web-portal which presents a structure-based classification of the molecules. A structure-based classification of nearly 150 million unique compounds, which are obtained from 42 publicly available databases were curated for redundancy removal through 97 hierarchically well-defined atom composition-based portions. These are further subjected to 56-bit fingerprint-based classification algorithm which led to a formation of 56 structurally well-defined classes. The classes thus obtained were further divided into clusters based on their molecular weight. Thus, the entire set of molecules was put in 56 different classes and 625 clusters. This led to the assignment of a unique ID, named as MPDS-Aadhar card, for each of these 149 169 443 molecules. Aadhar card is akin to the unique number given to citizens in India (similar to the SSN in US, NINO in UK). MPDS-CL unique features are: a) several search options, such as exact structure search, substructure search, property-based search, fingerprint-based search, using SMILES, InChIKey and key-in; b) automatic generation of information for the processing for MPDS and other galaxy tools; c) providing the class and cluster of a molecule which makes it easier and fast to search for similar molecules and d) information related to the presence of the molecules in multiple databases. The MPDS-CL can be accessed at http://mpds.neist.res.in:8086/.

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“…The Molecular Property Diagnostic Suite (MPDS) is a Galaxy (Gu et al, 2021; Galaxy community., 2022; Gaur et al, 2023) based open-source computational drug discovery platform. The development of MPDS is a result of our interest in developing open-source disease specific web portals (Gaur et al, 2017 and 2018; Nagamani et al, 2017). Galaxy offers the flexibility for users to deploy tools using multiple programming languages based on their preferences.…”

Section: Introductionmentioning

confidence: 99%

Molecular Property Diagnostic Suite for COVID-19 (MPDS^COVID-19): An open access disease specific drug discovery portal

Priyadarsinee,

Jamir,

Nagamani

et al. 2023

Preprint

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Computational drug discovery is intrinsically interdisciplinary and has to deal with the multifarious factors which are often dependent on the type of disease. Molecular Property Diagnostic Suite (MPDS) is a Galaxy based web portal which was conceived and developed as a disease specific web portal, originally developed for tuberculosis (MPDSTB). As specific computational tools are often required for a given disease, developing a disease specific web portal is highly desirable. This paper emphasises on the development of the customised web portal for COVID-19 infection and is referred to as MPDSCOVID-19. Expectedly, the MPDS suites of programs have modules which are essentially independent of a given disease, whereas some modules are specific to a particular disease. In the MPDSCOVID-19 portal, there are modules which are specific to COVID-19, and these are clubbed in SARS-COV-2 disease library. Further, the new additions and/or significant improvements were made to the disease independent modules, besides the addition of tools from galaxy toolshed. This manuscript provides a latest update on the disease independent modules of MPDS after almost 6 years, as well as provide the contemporary information and tool-shed necessary to engage in the drug discovery research of COVID-19. The disease independent modules include file format converter and descriptor calculation under the data processing module; QSAR, pharmacophore, scaffold analysis, active site analysis, docking, screening, drug repurposing tool, virtual screening, visualisation, sequence alignment, phylogenetic analysis under the data analysis module; and various machine learning packages, algorithms and in-house developed machine learning antiviral prediction model are available. The MPDS suite of programs are expected to bring a paradigm shift in computational drug discovery, especially in the academic community, guided through a transparent and open innovation approach. The MPDSCOVID-19 can be accessed at http://mpds.neist.res.in:8085.

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Molecular property diagnostic suite (MPDS): Development of disease-specific open source web portals for drug discovery

Cited by 11 publications

References 51 publications

Towards systematic exploration of chemical space: building the fragment library module in molecular property diagnostic suite

Towards systematic exploration of chemical space: building the fragment library module in molecular property diagnostic suite

Molecular Property Diagnostic Suite Compound Library (MPDS-CL): A Structure based Classification of the Chemical Space

Molecular Property Diagnostic Suite for COVID-19 (MPDS^COVID-19): An open access disease specific drug discovery portal

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Molecular property diagnostic suite (MPDS): Development of disease-specific open source web portals for drug discovery

Cited by 11 publications

References 51 publications

Towards systematic exploration of chemical space: building the fragment library module in molecular property diagnostic suite

Towards systematic exploration of chemical space: building the fragment library module in molecular property diagnostic suite

Molecular Property Diagnostic Suite Compound Library (MPDS-CL): A Structure based Classification of the Chemical Space

Molecular Property Diagnostic Suite for COVID-19 (MPDSCOVID-19): An open access disease specific drug discovery portal

Contact Info

Product

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Molecular Property Diagnostic Suite for COVID-19 (MPDS^COVID-19): An open access disease specific drug discovery portal