Neeraj Kumar, PhD

nsonu11@gmail.com
Phone - +91-9459686718; +91-7018886792

Present Address: Permanent Address:

Biotechnology Division Ward No. 3
CSIR – IHBT VPO Lower Dehlan
Post Box No. 6 District & Tehsil Una
Palampur, Kangra H.P. 174306
H.P. 176061

SUMMARY
Neeraj has a demonstrated history of working in structural bioinformatics and machine
intelligence-driven solutions for virtual screening and drug discovery domains. He is a team
player, always willing and interested for working on new ideas for AI-driven drug discovery,
competitive benchmarking analysis and design, implement, supervise and analyze complete
project.

WORK AND RESEARCH EXPERIENCE

1. Machine Intelligence algorithm development and August 2016 - Present
Structural Bioinformatics
CSIR-IHBT Palampur
Projects carried out:
1. Development, testing and benchmarking of machine intelligence-driven framework for
optimized hit selection in virtual screening.
2. Machine intelligence-guided selection of optimized inhibitors for human
immunodeficiency virus (HIV) from natural products.
Approaches and Techniques:

• MI-driven framework development for Drug Discovery

• Machine and Deep Learning algorithm development in R and Python
• h2o deep learning, Keras, TensorFlow, PyTorch.
• Benchmarking of ML and DL, troubleshooting and performance analysis
• Automation using Linux shell and Perl
• Data collection, processing and visualization for Cheminformatics
• MI-driven virtual screening
• Ab-initio 3D structure building, Homology model building, Rosetta, AlphaFold
• Automated molecular Docking, Molecular Dynamics Simulation (AutoDock Tools,
AutoDock Vina, Galaxy, PyRx, racoon, Gromacs, MM-PBSA, VMD, Chimera,
Modeller)
• GitHub and GitLab data submission

2. Structural Bioinformatics December 2015 - March 2016

CSIR-IMTECH Chandigarh
• Homology model building,
• Automated Molecular Docking (AutoDock Tools, AutoDock Vina, Galaxy, PyRx,
racoon)
• Molecular Dynamics Simulation (Gromacs)

3. Structural Bioinformatics August 2013 - July 2014

NIPER Kolkata; CSIR-IICB Kolkata (Project Trainee)
Projects carried out:
1. Molecular Dynamics Simulation (MDS) study of promoter DNA
Approaches and Techniques:

• Molecular Docking (AutoDock Tools, AutoDock Vina)

• Molecular Dynamics Simulation (Gromacs)

EDUCATION AND QUALIFICATION

PhD (Computational Biology and Bioinformatics) August 2016 – October 2022
Specialization (AI-driven Cheminformatics)
AcSIR, Ghaziabad, U.P. and CSIR-IHBT Palampur, India (Thesis defense: 03.02.2023)

M.S. Pharm (Pharmacy) July 2012 – June 2014

National Institute of Pharmaceutical Education and Research, Kolkata, WB, India

Bachelors of Pharmacy (B. Pharmacy) July 2008 – June 2012

Punjab Technical University, Jalandhar, Punjab India
SKILLS
Linux OS Bash Shell Scripting (Automation) R Programming
Python TensorFlow, Algorithm development Molecular Docking
MD Simulation PyTorch, Keras Machine Learning
Big-Data handling Pipeline development, RDKit Perl

ACHIEVEMENTS
• Qualified UGC – NFSC for PhD.
• GPAT-2011 and 2012 Qualified.
• GATE 2013 and GATE 2014 Qualified.
• Qualified NIPER-JEE July 2012 and July 2015.

CONFERENCE AND SYMPOSIUM

• Poster presented in International Conference on Drug Discovery (ICDD) held at BITS
Pilani & KK Birla Goa Campus, Goa, India from November 10 &11, 2022.
• Poster presented in 17th International Conference on Bioinformatics (InCoB) held at
Jawaharlal Nehru University, New Delhi, India from September 26-28, 2018.
• Participated in Training program on Laboratory Safety organized by CSIR- Indian Institute
of Chemical Biology, Kolkata (6th Sept 2012)
• Participated in International Symposium on Challenges in Chemical Biology – 2013

Workshops
• Participated in BioTecNika Schrodinger Joint Workshop on Computer - Aided Drug
Discovery Organized by Biotecnika Info Labs Pvt Ltd via virtual mode from 22nd July to
2nd August 2019.
• Participated in Faculty Development Programme on “Machine Learning – Foundation,
Methodologies and Interconnections” organized by Amity University, Noida UP India via
virtual mode from 16th – 21st August 2021.
• Participated in “Skill enhancement workshop on multi-omics data integration and data
analytics” organized by Centre for Computational Biology and Bioinformatics (CCBB),
Amity University, Noida UP India via virtual mode from 27th – 30th September 2022.
• Contributed as resource person in three-days workshop “Deep Bioinformatics Boot Camp-
2023” organized by the Himalayan Centre for High-throughput Computational Biology
(HiCGiCoB), a BIC of DBT, Govt of India at CSIR-Institute of Himalayan Bioresource
Technology, Palampur, Himachal Pradesh, held on August 28th-30th, 2023.

PUBLICATIONS

Publications from PhD work:

1. Neeraj Kumar, Vishal Acharya (2022) Machine intelligence-driven framework for

optimized hit selection in virtual screening Journal of Cheminformatics. DOI:
https://doi.org/10.1186/s13321-022-00630-7.
2. Neeraj Kumar, Vishal Acharya (2023) Machine intelligence-guided selection of
optimized inhibitors for human immunodeficiency virus (HIV) from natural products
Computers in Biology and Medicine. DOI:
https://doi.org/10.1016/j.compbiomed.2022.106525.
3. Neeraj Kumar, Vishal Acharya (2023) The machine-intelligence-driven virtual screening
methods in the era of big-data Medicinal Research Reviews (In Press)

Publications from other than PhD work

1. Desh Raj, Vinesh Sharma, Ashwani Upadhyaya, Neeraj Kumar, Robin Joshi, Vishal
Acharya, Dinesh Kumar & Vikram Patial (2021) Swertia purpurascens Wall ethanolic
extract mitigates hepatic fibrosis and restores hepatic hepcidin levels via inhibition of
TGFβ/SMAD/NFκB signaling in rats Journal of Ethnopharmacology. DOI:
https://doi.org/10.1016/j.jep.2021.114741.
2. Mousumi Sinha, Rahul Jagadeesan, Neeraj Kumar, Satabdi Saha, GuganKothandan &
Diwakar Kumar (2020) In-silico studies on Myo inositol-1-phosphatesynthase of
Leishmania donovani in search of anti-leishmaniasis Journal of Biomolecular Structure
and Dynamics. DOI: 10.1080/07391102.2020.1847194.
3. Anil Kumar, Srijana Mukhia, Neeraj Kumar, Vishal Acharya, Sanjay Kumar and Rakshak
Kumar (2020) A Broad Temperature Active Lipase Purified from a Psychrotrophic
Bacterium of Sikkim Himalaya with Potential Application in Detergent Formulation.
Front. Bioeng. Biotechnol. 8:642. doi: 10.3389/fbioe.2020.00642.
4. Nisha Gautam, Satbir Kaur, Kamaljeet Kaur, and Neeraj Kumar* (2019) A novel insight
of Asp193His mutation on epigenetic methyltransferase activity of human EZH2 protein:
An in-silico approach, Meta Gene, Volume 19,
https://doi.org/10.1016/j.mgene.2019.01.003.

Book chapter:

1. Kumar N., Acharya V. (2018) Metabolomics Resources: An Introduction of Databases

and Their Future Prospective. In: Yadav S., Kumar V., Singh S. (eds) Recent Trends and
Techniques in Plant Metabolic Engineering. Springer, Singapore.
https://doi.org/10.1007/978-981-13-2251-8_7.

Tools/Database:

• Automated - Hit Identification and Optimization Tool (A-HIOT) on GitLab:

https://gitlab.com/neeraj-24/A-HIOT.
• Clustering of uncharacterised data on GitLab: https://gitlab.com/neeraj-24/clustering-of-
uncharacterised-data
 REFERENCES

Dr. Vishal Acharya Dr. Ravi Shankar

CSIR- IHBT, Biotechnology Division CSIR- IHBT, Biotechnology Division

Senior Scientist & Assistant Professor Principal Scientist & Assistant
Functional Genomics and Complex Professor Studio of Computational
Systems Lab (FG&CSL Biology and Bioinformatics

Email: vishal@ihbt.res.in Email: ravish@ihbt.res.in

Dr. Rituraj Purohit

CSIR- IHBT, Biotechnology Division

Principal Scientist & Assistant Professor
Bioinformatics & Computational
structural biology Lab

Email: rituraj@ihbt.res.in