S
Samarjeet Prasad
Researcher at National Institutes of Health
Publications - 14
Citations - 2353
Samarjeet Prasad is an academic researcher from National Institutes of Health. The author has contributed to research in topics: Computer science & Biology. The author has an hindex of 6, co-authored 10 publications receiving 1886 citations. Previous affiliations of Samarjeet Prasad include Johns Hopkins University & Johns Hopkins University School of Medicine.
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Journal ArticleDOI
A draft map of the human proteome
Min-Sik Kim,Sneha M. Pinto,Derese Getnet,Raja Sekhar Nirujogi,Srikanth S. Manda,Raghothama Chaerkady,Anil K. Madugundu,Dhanashree S. Kelkar,Ruth Isserlin,Shobhit Jain,Joji Kurian Thomas,Babylakshmi Muthusamy,Pamela Leal-Rojas,Pamela Leal-Rojas,Praveen Kumar,Nandini A. Sahasrabuddhe,Lavanya Balakrishnan,Jayshree Advani,Bijesh George,Santosh Renuse,Lakshmi Dhevi N. Selvan,Arun H. Patil,Vishalakshi Nanjappa,Aneesha Radhakrishnan,Samarjeet Prasad,Tejaswini Subbannayya,Rajesh Raju,Manish Kumar,Sreelakshmi K. Sreenivasamurthy,Arivusudar Marimuthu,Gajanan Sathe,Sandip Chavan,Keshava K. Datta,Yashwanth Subbannayya,Apeksha Sahu,Soujanya D. Yelamanchi,Savita Jayaram,Pavithra Rajagopalan,Jyoti Sharma,Krishna R Murthy,Nazia Syed,Renu Goel,Aafaque Ahmad Khan,Sartaj Ahmad,Gourav Dey,Keshav Mudgal,Aditi Chatterjee,Tai-Chung Huang,Jun Zhong,Xinyan Wu,Patrick G. Shaw,Donald Freed,Muhammad Saddiq Zahari,Kanchan K Mukherjee,Subramanian Shankar,Anita Mahadevan,Henry H N Lam,Chris J. Mitchell,Susarla K. Shankar,Parthasarathy Satishchandra,John T. Schroeder,Ravi Sirdeshmukh,Anirban Maitra,Steven D. Leach,Charles G. Drake,Marc K. Halushka,T. S. Keshava Prasad,Ralph H. Hruban,Candace L. Kerr,Candace L. Kerr,Gary D. Bader,Christine A. Iacobuzio-Donahue,Harsha Gowda,Akhilesh Pandey +73 more
TL;DR: A draft map of the human proteome is presented using high-resolution Fourier-transform mass spectrometry to discover a number of novel protein-coding regions, which includes translated pseudogenes, non-c coding RNAs and upstream open reading frames.
Journal ArticleDOI
Best Practices for Foundations in Molecular Simulations [Article v1.0].
Efrem Braun,Justin B. Gilmer,Heather B. Mayes,David L. Mobley,Jacob I. Monroe,Samarjeet Prasad,Daniel M. Zuckerman +6 more
TL;DR: This document provides a starting point for approaching molecular simulations, guiding beginning practitioners to what issues they need to know about before and while starting their first simulations, and why those issues are so critical.
Journal ArticleDOI
Best Practices for Alchemical Free Energy Calculations [Article v1.0].
Antonia S. J. S. Mey,Bryce K. Allen,Hannah E. Bruce Macdonald,John D. Chodera,David F. Hahn,Maximilian Kuhn,Julien Michel,David L. Mobley,Levi N. Naden,Samarjeet Prasad,Andrea Rizzi,Jenke Scheen,Michael R. Shirts,Gary Tresadern,Huafeng Xu +14 more
TL;DR: In this paper, the authors review current best practices for several popular application domains of alchemical free energy calculations performed with equilibrium simulations, in particular relative and absolute small molecule binding energy calculations to biomolecular targets.
Journal ArticleDOI
Best Practices for Alchemical Free Energy Calculations
Antonia S. J. S. Mey,Bryce K. Allen,Hannah E. Bruce Macdonald,John D. Chodera,Maximilian Kuhn,Julien Michel,David L. Mobley,Levi N. Naden,Samarjeet Prasad,Andrea Rizzi,Jenke Scheen,Michael R. Shirts,Gary Tresadern,Huafeng Xu +13 more
TL;DR: Current best practices for several popular application domains of alchemical free energy calculations, including relative and absolute small molecule binding free energy Calculations to biomolecular targets are reviewed.
Journal ArticleDOI
Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge
Gerhard König,Gerhard König,Frank C. Pickard,Jing Huang,Andrew C. Simmonett,Florentina Tofoleanu,Juyong Lee,Pavlo O. Dral,Samarjeet Prasad,Michael R. Jones,Yihan Shao,Walter Thiel,Bernard R. Brooks +12 more
TL;DR: This work uses predictions of the distribution coefficients between water and cyclohexane from the SAMPL5 challenge to estimate the hydrophobicity of different explicit solvent simulation techniques, and compares pure molecular mechanics with quantum-mechanical calculations based on QM/MM schemes that treat the solvent at the MM level.