Profile Details

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USD 25 /hr

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Hire Samee U.

Pakistan

USD 25 /hr

Computational Structural Biologist | Molecular Dynamics Simulations | Structural Bioinformatics | De novo protein design

Profile Summary

Highly Skilled Computational Structural Biologist with expertise in proteins and nucleic acids structure modeling, docking, molecular dynamics simulation, and binding energy calculations; mmgbsa/mmbsa, metadynamics, fep. Exceptional in scientific writing, editing and proofreading. With a keen eye for detail, I deliver top-notch results that are not only accurate, but also communicate complex scientific concepts in a clear and concise manner. Choose me for your next project and receive professional support in advancing your research endeavors. I am fully confident in my ability to provide expert support in the following areas: 1) Services in Manuscript writing and Peer review: Manuscript preparation, Journal recommendations, submission to a Journal, Journal cover letter preparation and Reviewer response submission 2) De novo protein design and Simulations of epitopes, miniproteins, proteins and vaccine structures || Similar to my paper here || DOI: https://doi.org/10.1093/biomethods/bpad021 3) Molecular Dynamic Simulation (Gromacs or Amber upto 500ns) includes: || Similar to My paper here || DOI: 10.1016/j.molliq.2021.117975 RNA and DNA simulation Proteins simulation Small molecule simulation Biomaterials simulation Membranes(POPC, POPE, DMPC, DMMP) simulation 4) Molecular modeling & Docking || Similar to My paper here || DOI: 10.1016/j.molliq.2022.119393 Ligand and protein interactions Protein protein interactions Peptide protein interactions Ligand/peptide/protein interactions with DNA and RNA 5) Structural Analysis of Mutations (Wild versus Mutant MD simulations): || Similar to my paper here || DOI: 10.3389/fgene.2022.1117500 **Some list of general open source tools I will use in your project work** AlphaFold. Rosetta, Amber, VMD, CHARMGUI, Siremol, Desmond, OpenMM, Swiss model, FoldX, Modeller, HADDOCK, Autodock, SwissDock, Cluspro, Zdock Gnuplot, ggplot, Matplotlib, Xmgrace, Stata, Origin ImageJ, Bio-Blender, Icy, NumPy, Biopython Linux, R, PyTorch, NVIDIA CUDA, Anaconda, Jupyter Notebook Please visit my LinkedIn and ResearchGate profile for my Professional skills and expertise: https://www.linkedin.com/in/samee-ullah-structural-biologist/ https://www.researchgate.net/profile/Samee-Ullah-11

Subject Matter Expertise

• ★ Computational Biology
• ★ Structural Biology
• ★ Structural Bioinformatics
• ☆ Materials Science & Engineering
• ☆ Molecular Modeling
• ☆ Molecular Docking
• ☆ Chemoinformatics
• ☆ Biomaterials
• ☆ Virology
• ☆ Coronaviruses
• ☆ Biochemistry
• ☆ Molecular Biology
• ☆ Omics
• ☆ PCR
• ☆ Mutagenesis
• ☆ Biophysics
• ☆ Data Analysis
• ☆ Computer Simulation/Computational Modeling
• ☆ Data Visualization
• ☆ Bioinformatics
• ☆ Gene & Protein Expression Analysis
• ☆ Systems Biology
• ☆ Biomolecular Engineering
• ☆ Protein/Enzyme Engineering
• ☆ Antibody Engineering
• ☆ Phylogenetics
• ☆ Publishing
• ☆ Python
• ☆ R
• ☆ Drug Discovery
• ☆ High Throughput Screening (HTS)
• ☆ Drug Target Identification
• ☆ Medicinal Chemistry
• ☆ Drug Design
• ☆ Drug Development
• ☆ Small Molecule Drug Development
• ☆ Infectious Disease
• ☆ Viral Diseases
• ☆ COVID-19
• ☆ Tropical Medicine
• ☆ Rare Diseases
• ☆ Amyloidosis
• ☆ Health Informatics
• ☆ Traditional Medicine
• ☆ Medical Sciences
• ☆ Cancer Research
• ☆ Cancer Biology
• ☆ Product Design
• ☆ CAD & 3D Modeling
• ☆ Design for Manufacturing
• ☆ 2D Drawing
• ☆ Peer Review
• ☆ Research Methodology
• ☆ Literature Search
• ☆ Research Summaries & Abstracts
• ☆ Technical & Scientific Writing
• ☆ Journal Selection
• ☆ Manuscript & Journal Article Writing
• ☆ Scientific Proofreading & Editing
• ☆ Proofreading & Editing

Services

• Writing
• Research
• Data & AI

Writing Medical Writing, Technical Writing, General Proofreading & Editing

Research Scientific and Technical Research

Work Experience

Peer Review

Biology Methods and Protocols Journal - Oxford Press

September 2023 - Present

Peer Review

Gene Reports Journal - Elsevier

May 2022 - Present

Bioinformatician

National Institute of Health (NIH)

May 2020 - February 2022

Research Assistant - Research Associate

Quaid-i-Azam University

June 2016 - August 2017

Education

M.Phil (Bioinformatics)

Quaid-i-Azam University National Center for Bioinformatics

December 2017 - December 2019

Master (Microbiology)

Quaid-i-Azam University Faculty of Biological Sciences

January 2014 - January 2016

Certifications

• Behind the Scenes with Editors-in-Chief A Live Interactive Session on Research Writing, Journal Review, and Handling Rejection

  Enago Academy

  https://verified.sertifier.com/en/verify/09924937608256

  September 2022 - Present

• Recognized Reviewer Certificate

  Gene Reports Journal Elsevier publisher's

  https://www.researchgate.net/publication/362061694_Recognized_Reviewer_Certificate_to_SAMEE_ULLAH_in_recognition_of_the_review_contributed_to_the_Journal_of_Gene_Reports_Elsevier

  July 2022 - Present

• Focus on Peer Review

  Springer Nature

  https://www.researchgate.net/publication/360902160_Focus_on_Peer_Review_by_SPRINGER_NATURE_Certificate_of_Course_Completion

  May 2022 - Present

• An Introduction to Peer Review

  CLARIVATE Web of Science Academy

  https://www.researchgate.net/publication/360902270_An_Introduction_to_Peer_Review_by_CLARIVATE_Web_of_Science_Academy_Certificate_of_Course_Completion

  May 2022 - Present

• Good Citation Behavior

  CLARIVATE Web of Science Academy

  https://www.researchgate.net/publication/360902150_Good_Citation_Behavior_by_CLARIVATE_Web_of_Science_Academy_Certificate_of_Course_Completion

  May 2022 - Present

• Certified Peer Reviewer

  Elsevier Publisher's

  http://dx.doi.org/10.13140/RG.2.2.12515.84000

  May 2022 - Present

Publications

PREPRINT

Samee Ullah, Nasir Ali Khan (2023). Computational Insights on Xenobiotic Nuclear Receptor-Air Pollutant Interactions Through Molecular Docking and Dynamics Simulations .

Samee Ullah, Nasir Ali Khan (2023). Computational Insights on Xenobiotic Nuclear Receptor-Air Pollutant Interactions Through Molecular Docking and Dynamics Simulations .

Goswami A, Kumar SM, Ullah S, Gore M(2023). De novo design of anti-variant COVID-19 Vaccine .

Samee Ullah, Afreenish Amir, Aamer Ikram, Caterina Vicidomini, Rosanna Palumbo, Giovanni N. Roviello (2023). Computational insights on the destabilizing mutations in the binding site of 3CL-protease SARS-CoV-2 Omicron (VOC) .

Samee Ullah, Arpita Goswami, S. Madan Kumar, Milind M. Gore (2022). De novodesign of anti-variant COVID-19 Vaccine .

JOURNAL ARTICLE

Samee Ullah (2023). Case report: A novel de novo loss of function variant in the DNA-binding domain of TBX2 causes severe osteochondrodysplasia . Frontiers in Genetics.

Samee Ullah, Arpita Goswami, Madan Kumar, S., Milind M Gore (2023). De novo design of anti-variant COVID-19 vaccine . Biology Methods and Protocols.

Rafeeq MM, Murad HAS, Najumuddin, Ullah S, Ahmed Z, Alam Q, Bilal M, Habib AH, Sain ZM, Khan MJ, et al.(2023). Case report: A novel <i>de novo</i> loss of function variant in the DNA-binding domain of TBX2 causes severe osteochondrodysplasia . Frontiers in genetics.

Ullah, Samee, Amir, Afreenish, Ikram, Aamer, Vicidomini, Caterina, Palumbo, Rosanna, Roviello, Giovanni N (2023). Computational insights on the destabilizing mutations in the binding site of 3CL-protease SARS-CoV-2 Omicron (VOC) . BioRxiv.

SAMEE ULLAH, Nasir Ali Khan (2023). Computational Insights on Xenobiotic Nuclear Receptor-Air Pollutant Interactions Through Molecular Docking and Dynamics Simulations . BioRxiv.

Samee Ullah, Adewale Oluwaseun Fadaka, Odunayo Anthonia Taiwo, Oluwatosin Adebisi Dosumu, Oluwafemi Paul Owolabi, Adebola Busola Ojo, Nicole Remaliah Samantha Sibuyi, Ashwil Klein, Abram Madimabe Madiehe, Mervin Meyer, et al. (2022). Computational prediction of potential drug-like compounds from Cannabis sativa leaf extracts targeted towards Alzheimer therapy . Journal of Molecular Liquids.

Samee Ullah, Domenica Musumeci, Aamer Ikram, Giovanni N. Roviello (2022). Novel insights on nucleopeptide binding: A spectroscopic and in silico investigation on the interaction of a thymine-bearing tetrapeptide with a homoadenine DNA . Journal of Molecular Liquids.

Musumeci, D., Ullah, S., Ikram, A., Roviello, G.N.(2022). Novel insights on nucleopeptide binding: A spectroscopic and in silico investigation on the interaction of a thymine-bearing tetrapeptide with a homoadenine DNA . Journal of Molecular Liquids. 347.

Ullah, Samee, Musumeci, Domenica, Ikram, Aamer, Roviello, Giovanni N. (2022). Novel insights on nucleopeptide binding: A spectroscopic and in silico investigation on the interaction of a thymine-bearing tetrapeptide with a homoadenine DNA . Journal of Molecular Liquids.

Fadaka, A.O., Taiwo, O.A., Dosumu, O.A., Owolabi, O.P., Ojo, A.B., Sibuyi, N.R.S., Ullah, S., Klein, A., Madiehe, A.M., Meyer, M., et al.(2022). Computational prediction of potential drug-like compounds from Cannabis sativa leaf extracts targeted towards Alzheimer therapy . Journal of Molecular Liquids. 360.

Goswami, A., Kumar, M. S., Gore, M. M. (2022). <italic>De novo </italic>design of anti-variant COVID vaccine with T-cell memory . BioRxiv.

Umair, M., Ikram, A., Salman, M., Alam, M.M., Badar, N., Rehman, Z., Tamim, S., Khurshid, A., Ahad, A., Ahmad, H., et al.(2021). Importation of SARS-CoV-2 Variant B.1.1.7 in Pakistan . Journal of Medical Virology. 93. (5). p. 2623-2625.

Ullah, Samee, Umair, Massab, Ikram, Aamer, Salman, Muhammad, Alam, Muhammad Masroor, Badar, Nazish, Rehman, Zaira, Tamim, Sana, Khurshid, Adnan, Ahad, Abdul, et al. (2021). Importation of SARS-CoV-2 Variant B.1.1.7 in Pakistan . Journal of Medical Virology.