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Neeraj Kumar CV

Neeraj Kumar has extensive experience in structural bioinformatics, machine learning, and AI-driven solutions for drug discovery. He has a PhD from AcSIR, Ghaziabad, India focused on machine intelligence approaches for virtual screening and drug discovery. He has worked on developing machine learning frameworks, performing virtual screening and molecular simulations, and publishing his work. He is looking for opportunities where he can apply his skills in AI, drug discovery, and computational biology.

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36 views6 pages

Neeraj Kumar CV

Neeraj Kumar has extensive experience in structural bioinformatics, machine learning, and AI-driven solutions for drug discovery. He has a PhD from AcSIR, Ghaziabad, India focused on machine intelligence approaches for virtual screening and drug discovery. He has worked on developing machine learning frameworks, performing virtual screening and molecular simulations, and publishing his work. He is looking for opportunities where he can apply his skills in AI, drug discovery, and computational biology.

Uploaded by

jyoti.v9196
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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

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