Sam Paul D., Phd personal email
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Current Position:ICMR Research Scientist (Level 2), University of MadrasExperience:8 years PhD Research Experience 3 + 2 Postdoctoral Experience Research Focus:My research focuses on developing computational strategies to combat viral infections and drug resistance. I apply generative AI to predict viral mutations and design targeted inhibitors. With expertise in molecular modeling, protein-ligand docking, and structure-based drug design, my work contributes to advancing antiviral drug discovery.Key Contributions:1. MOLS 2.0 Software Package: Developed a novel software for peptide modeling and molecular docking, utilizing mutually orthogonal Latin squares (MOLS) for enhanced peptide-ligand interaction predictions.Link to software: https://sourceforge.net/projects/mols2-0/files/2. pepMOLS Server: Created an online server for peptide modeling, providing researchers with tools for advanced peptide structure prediction.Access the server: https://mols.co.inTop 5 Research Publications:1. Physical Chemistry Chemical Physics: DOI: 10.1039/D4CP01891E 2. Journal of Molecular Modeling: DOI: 10.1007/s00894-022-05413-33. Journal of Computer-Aided Molecular Design: DOI: 10.1007/s10822-018-0152-84. Journal of Molecular Graphics and Modelling: DOI: 10.1016/j.jmgm.2017.03.0085. Journal of Molecular Modeling: DOI: 10.1007/s00894-016-3106-xDoctoral Advisor:Dr. N. Gautham, PhD, FNAScLearn more: https://en.m.wikipedia.org/wiki/N._GauthamPositions/Awards:1. ICMR-Research Scientist II2. UGC- Dr. D S Kothari Postdoctoral Fellowship3. CSIR-Research Associateship4. UGC-BSR Meritorious Senior Research Fellowship5. UGC-BSR Meritorious Junior Research FellowshipPassion:I am committed to collaborating with scientists globally to drive drug discovery, using my expertise in computational modeling and structural biology to develop novel therapeutic solutions addressing urgent health challenges.
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Computational BiologistSekkei Bio Private Limited Dec 2024 - PresentChennai, Tamil Nadu, India -
Secretary, Physics Alumni Society - MccMadras Christian College Dec 2010 - PresentChennai, Tamil Nadu, IndiaInvolved in the following activities as Secretary, Physics Alumni Society:◦ Conducted 8 Physics Alumni Meets in MCC. ◦ The Prof. K.M. Karunakaran Endowment Fund we generated has enabled the Department of Physics to conduct the Endowment Lecture every year since 2012.◦ Since 2018, the Physics Alumni Society Scholarship (PASS) is provided every year to deserving students in the Physics department.For more information, kindly check our official website at https://mccpas.in -
Temporary Assistant Professor At Department Of Physics (Aided), MccMadras Christian College Aug 2018 - Sep 2018Chennai, Tamil Nadu, IndiaDuring this period, I handled part of the following subjects:Theory:1. Advanced Quantum Mechanics - Second Year M.Sc. Physics2. Physics of Appliances and Devices - Second Year B.Sc. Physics3. Social Ethics - First Year B.Sc. PhysicsPractical classes:1. B.Sc. Physics (First Year, Second Year, and Third Year)2. Under Graduate Allied Mathematics3. Under Graduate Allied Chemistry
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Icmr Project Research Scientist-IiUniversity Of Madras Jul 2023 - Dec 2024Chennai, Tamil Nadu, India -
Dr. D.S. Kothari Postdoctoral FellowUniversity Of Madras Feb 2019 - Dec 2022The following works were carried out:#1) Enhanced molecular simulations were carried out to understand the inhibition mechanism of Anti-CRISPR suppressor AcrIIA4 targeting SpyCas9.#2) Updates were made to iMOLSDOCK (Protein-Ligand Docking Tool developed at Centre of Advanced Study in Crystallography and Biophysics, University of Madras) in order to increase receptor flexibility, improve the scoring function, and speed up calculation. The computation time for peptide docking was lowered by two orders of magnitude, and for non peptide small molecule docking, it was roughly 14 times faster due to code optimization.#3) Served as Expert Member for problem statement [iMOLSDOCK - "Anti-COVID-19 drug repurposing using the MOLS algorithm" (PS No: DDT2-12 ; https://innovateindia.mygov.in/drug_ps/ddt2-12/)] in the Open Source Drug Discovery Hackathon against COVID-19, a joint initiative of AICTE, CSIR, and supported by Office of Principal Scientific Advisor, Government of India, NIC, and MyGov.
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Ugc - Bsr Senior Research Fellow At Centre Of Advanced Study In Crystallography And BiophysicsUniversity Of Madras 2015 - Apr 2017Chennai, Tamil Nadu, India#1) During my SRF, I worked on further extending iMOLSDOCK(peptide-protein induced-fit docking tool) to dock organic small molecules to receptor proteins. Small molecule ligands were validated using GAFF and MMFF94 force fields. The flexible residues of the receptor protein were validated using AMBER force field. Comparison of iMOLSDOCK, for small molecule - protein docking, with other tools revealed that iMOLSDOCK performed on par with the other tools in identifying near-native structures.#2) iMOLSDOCK was a FORTRAN-based command line program. To enable accessibility to academic users, I developed a Java-based GUI for iMOLSDOCK. A software package - MOLS 2.0 - comprising the already developed MOLS peptide modelling tool and the newly developed iMOLSDOCK was bundled and distributed freely for academic users.
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Ugc - Bsr Junior Research Fellow At Centre Of Advanced Study In Crystallography And BiophysicsUniversity Of Madras Apr 2012 - Mar 2015Chennai, Tamil Nadu, IndiaI worked on incorporating receptor flexibility in the protein-ligand docking tool, dubbed MOLSDOCK, developed in Prof. N. Gautham's Computational Biology Laboratory. The Induced-fit receptor flexibility, I incorporated, involved - (1) Protein parameterisation in addition to the already existing peptide ligand parameterisation, (2) Extension of the MOLS (mutually orthogonal Latin squares) sampling to include protein sampling along with the sampling of the docking pose of the peptide, and (3) Improvement of the scoring function to include protein structure optimisation. The induced-fit docking tool using MOLS - iMOLSDOCK - was benchmarked and validated for docking oligopeptides of length 3 - 8. The algorithm for iMOLSDOCK was written using FORTRAN, C, Perl, and Shell Scripting.
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Guest LecturerMadras Christian College Jun 2010 - Nov 2010Chennai Area, IndiaTaught Physics for Under Graduate students.
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Guest Lecturer, School Of Continuing Education, MccMadras Christian College Jun 2006 - Apr 2010Chennai, Tamil Nadu, IndiaTaught C, C++, and Java.
Sam Paul D., Phd Education Details
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Physics - Crystallography And Biophysics
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Physics
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Amm Matriculation School, Kotturpuram, Chennai, IndiaMaths,Physics,Computer Science
Frequently Asked Questions about Sam Paul D., Phd
What company does Sam Paul D., Phd work for?
Sam Paul D., Phd works for Sekkei Bio Private Limited
What is Sam Paul D., Phd's role at the current company?
Sam Paul D., Phd's current role is Computational Biologist.
What is Sam Paul D., Phd's email address?
Sam Paul D., Phd's email address is sa****@****ook.com
What schools did Sam Paul D., Phd attend?
Sam Paul D., Phd attended University Of Madras, Madras Christian College, Amm Matriculation School, Kotturpuram, Chennai, India.
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