DBI | R/D

Department Facilities

A) Infrastructural Facilities: Resources
1. High Performance Computing cluster system
2. High End Servers and workstations
3. Computers with higher configurations
4. 20, 10 and 5 KVA UPSs
5. Smart Class Room Facilities
6. In-house protein database
7. E-book database
1. Installation Packages: Miniconda,Anaconda
2. Sequence Alignment tools and server : BLASTp, ClustalW, ClustalW Omega
3. Secondary structure Prediction servers : Psipred, Jpred
4. Molecular modelling : Modeller, Robetta, Phyre, ITASSER
5. Visualization software : Pymol, UCSF Chimera
6. Structure Validation : SAVES server , Procheck
7. Molecular dynamics package : Gromacs2023 , Desmond, AMBER2018
8. Small Molecule Compound Databases : Enamine , ZINC, DrugBank, ChemDiv
9. Docking software : AutoDock Vina , Schrodinger Package, AutoDock
10. Network Analysis Software : R package
11. Commercial Software’s- Schrödinger package for molecular Modeling and Drug Design and Cambridge Structural Database (CSD) etc.,
12. Small and Macro molecule structure determination software : SHELXS, SHELXL, CCP4, CNS1.2, Coot etc.,
13. Bioinformatics Software/Tools: VMD/Rasmol, Pymol, Gaussian, Gromacs, Desmond, Chemoffice etc.,
14. Small Molecule Structure Solving Package Program: WingX, Olex2
15. Small Molecule program: ShelxS, ShelxL, ShelxT
16. Small Molecule Structure Validation: CheckCIF
17. Small Molecule Structure Deposition CCDC:
18. Macromolecule Structure Deposition: PDB
19. Macromolecule Structure Solving Package Program: CCP4, PHENIX, CNS – Currently Not available.
20. Macromolecule Program: Molrep, Phaser, Refmac, Coot.
21. Macromolecule Structure Validation : PDB Validation Server, Procheck .
22. Sequencing data Quality checking: FastQC Software .
23. Adapter Removal: TrimGalore, Fastp.
24. Assembled Genome: 1Unicycler Software.
25. Evaluate Genome Assembly: QUAST (Quality Assessment Tool for Genome Assemblies)
26. Genome Annotation: RAST (Rapid Annotation System Technology), PROKKA Software (Prokaryotic Genome Annotation)
27. Antimicrobial Resistance and Virulence gene prediction: ABRicate software
28. Plasmid Prediction and Visualization: PLSDB, Proksee
29. DNA-DNA Hybridization: TYGS ( type strain genome server)
30. Average Nucleotide Identity: FastANI
31. Prophage Identification: PHASTER ( PHAge Search Tool Enhanced Release)
32. Secondary metabolites Prediction: antiSMASH
B) Wet-Lab Facilities: Resources
1. AKTATM protein purification system
2. ELISA plate reader and washer
3. Vibration free incubator
4. BioSpectrometer
5. Nano Spectrophotometer
6. Multi Plate Reader
7. Gradient PCRs
8. Biophotometer Plus
9. UV - VIS - Spectrophotometer
10. Ice Flakers
11. Circulatory Water Bath
12. Bio Safety Cabinets
13. Co2 incubator
14. Deep Freezers (-80 ˚C and -20 ˚C)
15. Polaroid Stereo Zoom Microscope
16. Fluorescence Microscope
17. Western Blot Unit
18. Gel Documentation system
19. High Speed Cooling Centrifuges
20. Ultra Sonicators
21. Stackable Orbital Shaker
22. Gel Rocker

C) Databases & Other Information Resources:

The department currently uses the databases and resources that are freely (open access) available over the internet like NCBI, EBI, ExPASy, PDB, etc.,

NCSp: A novel search engine for the proteins involved in the Notch crosstalk signaling pathways: A Database Madhumathi S, Santhosh R, Dhanalakshmi R, Rahul C.N, Jeyakanthan J and Sekar K. J. Biosci., (2023)
Click Here to Open

HTNpedia: A Knowledgebase for Hypertension research Lakshmanan Loganathan, Jeyakanthan Jeyaraman and Karthikeyan Muthusamy. Journal of Combinatorial Chemistry & High Throughput Screening., (2023)
Click Here to Open

Comprehensive Dataset for CKD (CD-CKD) Gopinath K, Jayakumararaj R, Karthikeyan M
Click Here to Open

IMRPS: Inserted and Modified Residues in Protein Structures: A Database Rajendran Santhosh, Namrata Bankoti, Gurudarshan Manickam, Jeyakanthan J and K. Sekar. J. APPL. CRYST., (2020)
Click Here to Open

MRPC: Missing Regions in Polypeptide Chains - A Knowledgebase Rajendran Santhosh, Namrata Bankoti, Padmashri Adgonda Malgonnavar, Daliah Michael, Jeyaraman Jeyakanthan and K. Sekar J. APPL. CRYST., (2019)
Click Here to Open

ACMS : A database of alternate conformations found in the atoms of main and side chains of protein structures R. Santhosh, P. Chandrasekaran , Daliah Michael, K. Rangachari, Namrata Bankoti, J. Jeyakanthan and K. Sekar J. APPL. CRYST., (2019)
Click Here to Open

Diffraction precision index of macromolecular structures: A web based database R. Santhosh, E. Velayudham, Daliah Michael, Namrata Bankoti, P. Chandrasekaran, D. Karthikeyan, S. Pavithra, M. Gurusaran, K. P. R. Nisha, S.N. Satheesh, K. Rangachari, J. Jeyakanthan and K. Sekar RJLBPCS., (2019)
Click Here to Open

NIMS: A database on Nucleobase compounds and their Interactions in Macromolecular Structures. R. Santhosh, S.N. Satheesh, M. Gurusaran, Daliah Michael, K. Sekar and J. Jeyakanthan. Journal of Applied Crystallography. (2016)
Click Here to Open

Diabetes Associated Protein Database (DAPD) Gopinath K, Jayakumararaj R, Karthikeyan M IEEE Transactions on Computational Biology and Bioinformatics (2015)
Click Here to Open

Database on Anti-Diabetic Medicinal Plants (DADMP) used by Valaiyans of Alagarkoil, Tamilnadu, India. Jayakumararaj Ramaraj, Ramya Subramanian, Gopinath Krishnasamy, Karthikeyan Muthusamy ICMS Australia (2011)
Click Here to Open

Tool development for Prediction of pIC50 values from the IC50 values - A pIC50 value calculator. Selvaraj, C., Tripathi, S.K., Reddy, K.K., Singh, S.K., Current Trends in Biotechnology & Pharmacy (2011)
Click Here to Open

MIPS: Metal Interactions in Protein Structures. Hemavathi K, Kalaivani Mani, UdayaKumar A, Sowmiya Govindaraj, Jeyakanthan Jeyaraman and K.Sekar. J. APPL. CRYST (2010).
Click Here to Open

PlaneFinder: A methodology to find the best plane for a set of atoms involved in the metal coordination in the protein structures.
Click Here to Open

PDB Goodies A a web-based GUI to manipulate the Protein Data Bank file
Click Here to Open

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Department Facilities

A) Infrastructural Facilities: Resources

B) Wet-Lab Facilities: Resources

C) Databases & Other Information Resources:

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