Assessing therapeutic potential of molecules: molecular property diagnostic suite for tuberculosis (MPDSTB)

Anamika Singh Gaur; Anshu Bhardwaj; Arun Sharma; Lijo John; M. Ram Vivek; Neha Tripathi; Prasad V. Bharatam; Rakesh Kumar; Sridhara Janardhan; Abhaysinh Mori; Anirban Banerji; Andrew M. Lynn; Anmol J. Hemrom; Anurag Passi; Aparna Singh; Asheesh Kumar; Charuvaka Muvva; Chinmai Madhuri; Chinmayee Choudhury; D. Arun Kumar; Deepak Pandit; Deepak R. Bharti; Devesh Kumar; Er Azhagiya Singam; Gajendra Ps Raghava; Hari Sailaja; Harish Jangra; Kaamini Raithatha; Karunakar Tanneeru; Kumardeep Chaudhary; M. Karthikeyan; M. Prasanthi; Nandan Kumar; N. Yedukondalu; Neeraj K. Rajput; P. Sri Saranya; Pankaj Narang; Prasun Dutta; R. Venkata Krishnan; Reetu Sharma; R. Srinithi; Ruchi Mishra; S. Hemasri; Sandeep Singh; Subramanian Venkatesan; Suresh Kumar; Uca Jaleel; Vijay Khedkar; Yogesh Joshi; G. Narahari Sastry

doi:10.1007/s12039-017-1268-4

Assessing therapeutic potential of molecules: molecular property diagnostic suite for tuberculosis (MPDS^TB)

Anamika Singh Gaur, Anshu Bhardwaj, Arun Sharma, Lijo John, M. Ram Vivek, Neha Tripathi, Prasad V. Bharatam, Rakesh Kumar, Sridhara Janardhan, Abhaysinh Mori, Anirban Banerji, Andrew M. Lynn, Anmol J. Hemrom, Anurag Passi, Aparna Singh, Asheesh Kumar, Charuvaka Muvva, Chinmai Madhuri, Chinmayee Choudhury, D. Arun KumarDeepak Pandit, Deepak R. Bharti, Devesh Kumar, Er Azhagiya Singam, Gajendra Ps Raghava, Hari Sailaja, Harish Jangra, Kaamini Raithatha, Karunakar Tanneeru, Kumardeep Chaudhary, M. Karthikeyan, M. Prasanthi, Nandan Kumar, N. Yedukondalu, Neeraj K. Rajput, P. Sri Saranya, Pankaj Narang, Prasun Dutta, R. Venkata Krishnan, Reetu Sharma, R. Srinithi, Ruchi Mishra, S. Hemasri, Sandeep Singh, Subramanian Venkatesan, Suresh Kumar, Uca Jaleel, Vijay Khedkar, Yogesh Joshi, G. Narahari Sastry

Research output: Contribution to journal › Article › peer-review

21 Scopus citations

Abstract

Abstract: Molecular Property Diagnostic Suite (MPDS ^TB) is a web tool (http://mpds.osdd.net) designed to assist the in silico drug discovery attempts towards Mycobacterium tuberculosis (Mtb). MPDS ^TB tool has nine modules which are classified into data library (1–3), data processing (4–5) and data analysis (6–9). Module 1 is a repository of literature and related information available on the Mtb. Module 2 deals with the protein target analysis of the chosen disease area. Module 3 is the compound library consisting of 110.31 million unique molecules generated from public domain databases and custom designed search tools. Module 4 contains tools for chemical file format conversions and 2D to 3D coordinate conversions. Module 5 helps in calculating the molecular descriptors. Module 6 specifically handles QSAR model development tools using descriptors generated in the Module 5. Module 7 integrates the AutoDock Vina algorithm for docking, while module 8 provides screening filters. Module 9 provides the necessary visualization tools for both small and large molecules. The workflow-based open source web portal, MPDS ^TB 1.0.1 can be a potential enabler for scientists engaged in drug discovery in general and in anti-TB research in particular. Graphical Abstract: SYNOPSIS: A web-based MPDS ^TB Galaxy tool is developed for assessing therapeutic potential of molecules. MPDS ^TB is categorized into Data Library, Data Processing and Data Analysis. It can be a potential enabler for scientists engaged in drug discovery in general and in anti-TB research in particular. [Figure not available: see fulltext.]

Original language	English
Pages (from-to)	515-531
Number of pages	17
Journal	Journal of Chemical Sciences
Volume	129
Issue number	5
DOIs	https://doi.org/10.1007/s12039-017-1268-4
State	Published - 1 May 2017
Externally published	Yes

Keywords

Tuberculosis
chemoinformatics
drug discovery portal
neglected diseases
open science
web-based technology

Access to Document

10.1007/s12039-017-1268-4

Cite this

Gaur, A. S., Bhardwaj, A., Sharma, A., John, L., Vivek, M. R., Tripathi, N., Bharatam, P. V., Kumar, R., Janardhan, S., Mori, A., Banerji, A., Lynn, A. M., Hemrom, A. J., Passi, A., Singh, A., Kumar, A., Muvva, C., Madhuri, C., Choudhury, C., ... Sastry, G. N. (2017). Assessing therapeutic potential of molecules: molecular property diagnostic suite for tuberculosis (MPDS^TB). Journal of Chemical Sciences, 129(5), 515-531. https://doi.org/10.1007/s12039-017-1268-4

@article{104c2d8671e14befaf6c428afd3898f6,

title = "Assessing therapeutic potential of molecules: molecular property diagnostic suite for tuberculosis (MPDSTB)",

abstract = "Abstract: Molecular Property Diagnostic Suite (MPDS TB) is a web tool (http://mpds.osdd.net) designed to assist the in silico drug discovery attempts towards Mycobacterium tuberculosis (Mtb). MPDS TB tool has nine modules which are classified into data library (1–3), data processing (4–5) and data analysis (6–9). Module 1 is a repository of literature and related information available on the Mtb. Module 2 deals with the protein target analysis of the chosen disease area. Module 3 is the compound library consisting of 110.31 million unique molecules generated from public domain databases and custom designed search tools. Module 4 contains tools for chemical file format conversions and 2D to 3D coordinate conversions. Module 5 helps in calculating the molecular descriptors. Module 6 specifically handles QSAR model development tools using descriptors generated in the Module 5. Module 7 integrates the AutoDock Vina algorithm for docking, while module 8 provides screening filters. Module 9 provides the necessary visualization tools for both small and large molecules. The workflow-based open source web portal, MPDS TB 1.0.1 can be a potential enabler for scientists engaged in drug discovery in general and in anti-TB research in particular. Graphical Abstract: SYNOPSIS: A web-based MPDS TB Galaxy tool is developed for assessing therapeutic potential of molecules. MPDS TB is categorized into Data Library, Data Processing and Data Analysis. It can be a potential enabler for scientists engaged in drug discovery in general and in anti-TB research in particular. [Figure not available: see fulltext.]",

keywords = "Tuberculosis, chemoinformatics, drug discovery portal, neglected diseases, open science, web-based technology",

author = "Gaur, \{Anamika Singh\} and Anshu Bhardwaj and Arun Sharma and Lijo John and Vivek, \{M. Ram\} and Neha Tripathi and Bharatam, \{Prasad V.\} and Rakesh Kumar and Sridhara Janardhan and Abhaysinh Mori and Anirban Banerji and Lynn, \{Andrew M.\} and Hemrom, \{Anmol J.\} and Anurag Passi and Aparna Singh and Asheesh Kumar and Charuvaka Muvva and Chinmai Madhuri and Chinmayee Choudhury and Kumar, \{D. Arun\} and Deepak Pandit and Bharti, \{Deepak R.\} and Devesh Kumar and Singam, \{Er Azhagiya\} and Raghava, \{Gajendra Ps\} and Hari Sailaja and Harish Jangra and Kaamini Raithatha and Karunakar Tanneeru and Kumardeep Chaudhary and M. Karthikeyan and M. Prasanthi and Nandan Kumar and N. Yedukondalu and Rajput, \{Neeraj K.\} and Saranya, \{P. Sri\} and Pankaj Narang and Prasun Dutta and Krishnan, \{R. Venkata\} and Reetu Sharma and R. Srinithi and Ruchi Mishra and S. Hemasri and Sandeep Singh and Subramanian Venkatesan and Suresh Kumar and Uca Jaleel and Vijay Khedkar and Yogesh Joshi and Sastry, \{G. Narahari\}",

note = "Publisher Copyright: {\textcopyright} 2017, Indian Academy of Sciences.",

year = "2017",

month = may,

day = "1",

doi = "10.1007/s12039-017-1268-4",

language = "English",

volume = "129",

pages = "515--531",

journal = "Journal of Chemical Sciences",

issn = "0974-3626",

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Gaur, AS, Bhardwaj, A, Sharma, A, John, L, Vivek, MR, Tripathi, N, Bharatam, PV, Kumar, R, Janardhan, S, Mori, A, Banerji, A, Lynn, AM, Hemrom, AJ, Passi, A, Singh, A, Kumar, A, Muvva, C, Madhuri, C, Choudhury, C, Kumar, DA, Pandit, D, Bharti, DR, Kumar, D, Singam, EA, Raghava, GP, Sailaja, H, Jangra, H, Raithatha, K, Tanneeru, K, Chaudhary, K, Karthikeyan, M, Prasanthi, M, Kumar, N, Yedukondalu, N, Rajput, NK, Saranya, PS, Narang, P, Dutta, P, Krishnan, RV, Sharma, R, Srinithi, R, Mishra, R, Hemasri, S, Singh, S, Venkatesan, S, Kumar, S, Jaleel, U, Khedkar, V, Joshi, Y & Sastry, GN 2017, 'Assessing therapeutic potential of molecules: molecular property diagnostic suite for tuberculosis (MPDS^TB)', Journal of Chemical Sciences, vol. 129, no. 5, pp. 515-531. https://doi.org/10.1007/s12039-017-1268-4

TY - JOUR

T1 - Assessing therapeutic potential of molecules

T2 - molecular property diagnostic suite for tuberculosis (MPDSTB)

AU - Gaur, Anamika Singh

AU - Bhardwaj, Anshu

AU - Sharma, Arun

AU - John, Lijo

AU - Vivek, M. Ram

AU - Tripathi, Neha

AU - Bharatam, Prasad V.

AU - Kumar, Rakesh

AU - Janardhan, Sridhara

AU - Mori, Abhaysinh

AU - Banerji, Anirban

AU - Lynn, Andrew M.

AU - Hemrom, Anmol J.

AU - Passi, Anurag

AU - Singh, Aparna

AU - Kumar, Asheesh

AU - Muvva, Charuvaka

AU - Madhuri, Chinmai

AU - Choudhury, Chinmayee

AU - Kumar, D. Arun

AU - Pandit, Deepak

AU - Bharti, Deepak R.

AU - Kumar, Devesh

AU - Singam, Er Azhagiya

AU - Raghava, Gajendra Ps

AU - Sailaja, Hari

AU - Jangra, Harish

AU - Raithatha, Kaamini

AU - Tanneeru, Karunakar

AU - Chaudhary, Kumardeep

AU - Karthikeyan, M.

AU - Prasanthi, M.

AU - Kumar, Nandan

AU - Yedukondalu, N.

AU - Rajput, Neeraj K.

AU - Saranya, P. Sri

AU - Narang, Pankaj

AU - Dutta, Prasun

AU - Krishnan, R. Venkata

AU - Sharma, Reetu

AU - Srinithi, R.

AU - Mishra, Ruchi

AU - Hemasri, S.

AU - Singh, Sandeep

AU - Venkatesan, Subramanian

AU - Kumar, Suresh

AU - Jaleel, Uca

AU - Khedkar, Vijay

AU - Joshi, Yogesh

AU - Sastry, G. Narahari

PY - 2017/5/1

Y1 - 2017/5/1

N2 - Abstract: Molecular Property Diagnostic Suite (MPDS TB) is a web tool (http://mpds.osdd.net) designed to assist the in silico drug discovery attempts towards Mycobacterium tuberculosis (Mtb). MPDS TB tool has nine modules which are classified into data library (1–3), data processing (4–5) and data analysis (6–9). Module 1 is a repository of literature and related information available on the Mtb. Module 2 deals with the protein target analysis of the chosen disease area. Module 3 is the compound library consisting of 110.31 million unique molecules generated from public domain databases and custom designed search tools. Module 4 contains tools for chemical file format conversions and 2D to 3D coordinate conversions. Module 5 helps in calculating the molecular descriptors. Module 6 specifically handles QSAR model development tools using descriptors generated in the Module 5. Module 7 integrates the AutoDock Vina algorithm for docking, while module 8 provides screening filters. Module 9 provides the necessary visualization tools for both small and large molecules. The workflow-based open source web portal, MPDS TB 1.0.1 can be a potential enabler for scientists engaged in drug discovery in general and in anti-TB research in particular. Graphical Abstract: SYNOPSIS: A web-based MPDS TB Galaxy tool is developed for assessing therapeutic potential of molecules. MPDS TB is categorized into Data Library, Data Processing and Data Analysis. It can be a potential enabler for scientists engaged in drug discovery in general and in anti-TB research in particular. [Figure not available: see fulltext.]

AB - Abstract: Molecular Property Diagnostic Suite (MPDS TB) is a web tool (http://mpds.osdd.net) designed to assist the in silico drug discovery attempts towards Mycobacterium tuberculosis (Mtb). MPDS TB tool has nine modules which are classified into data library (1–3), data processing (4–5) and data analysis (6–9). Module 1 is a repository of literature and related information available on the Mtb. Module 2 deals with the protein target analysis of the chosen disease area. Module 3 is the compound library consisting of 110.31 million unique molecules generated from public domain databases and custom designed search tools. Module 4 contains tools for chemical file format conversions and 2D to 3D coordinate conversions. Module 5 helps in calculating the molecular descriptors. Module 6 specifically handles QSAR model development tools using descriptors generated in the Module 5. Module 7 integrates the AutoDock Vina algorithm for docking, while module 8 provides screening filters. Module 9 provides the necessary visualization tools for both small and large molecules. The workflow-based open source web portal, MPDS TB 1.0.1 can be a potential enabler for scientists engaged in drug discovery in general and in anti-TB research in particular. Graphical Abstract: SYNOPSIS: A web-based MPDS TB Galaxy tool is developed for assessing therapeutic potential of molecules. MPDS TB is categorized into Data Library, Data Processing and Data Analysis. It can be a potential enabler for scientists engaged in drug discovery in general and in anti-TB research in particular. [Figure not available: see fulltext.]

KW - Tuberculosis

KW - chemoinformatics

KW - drug discovery portal

KW - neglected diseases

KW - open science

KW - web-based technology

UR - https://www.scopus.com/pages/publications/85020527564

U2 - 10.1007/s12039-017-1268-4

DO - 10.1007/s12039-017-1268-4

M3 - Article

AN - SCOPUS:85020527564

SN - 0974-3626

VL - 129

SP - 515

EP - 531

JO - Journal of Chemical Sciences

JF - Journal of Chemical Sciences

IS - 5