M RAM VIVEK
Articles written in Journal of Chemical Sciences
Volume 129 Issue 5 May 2017 pp 515-531 Regular Article
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
Molecular Property Diagnostic Suite (MPDSTB) is a web tool (http://mpds.osdd.net) designed to assist the in silico drug discovery attempts towards Mycobacterium tuberculosis (Mtb). (MPDSTB) 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 targetanalysis 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 toolsfor 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,(MPDSTB) 1.0.1 can be a potential enabler for scientists engaged in drug discovery in general and in anti-TB research in particular.
Volume 129 Issue 7 July 2017 pp 1053-1060 REGULAR ARTICLE
On the origin of spurious errors in many-body expansion for water cluster
SOUMEN SAHA M RAM VIVEK G NARAHARI SASTRY
Many-body expansion (MBE) has been carried out to investigate two- to five-body energy terms and their contributions to the interaction energy (IE) of (H₂O)₁₅ cluster. We have observed that the erroneous contribution of many-body terms on IE originated from cheaper convergence thresholds set as default in popular quantum mechanics packages. The propagation of errors from smaller to higher-body terms, due to the combinatorial nature of MBE, is also observed.
Volume 135, 2023
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