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Chemistry

D-Index
49
Citations
58009
World Ranking
14618
National Ranking
3733

Overview

Piotr Cieplak is affiliated with the Discovery Institute in the United States and has contributed extensively to research in biochemistry, genetics, molecular biology, and medicine. Their publications span multiple subfields such as molecular biology, atomic and molecular physics and optics, infectious diseases, public health, environmental and occupational health, and cancer research.

Their research topics primarily focus on protein structure and dynamics, spectroscopy and quantum chemical studies, DNA and nucleic acid chemistry, and infectious disease-related studies including SARS-CoV-2 and COVID-19, Toxoplasma gondii, HIV, as well as vaccine and immunoinformatics approaches.

Cieplak's frequent coauthors include Yong Duan, Ray Luo, Haixin Wei, Shiji Zhao, and Sergey A. Shiryaev, reflecting strong collaborative ties in their research efforts.

The scientist has published in several notable venues, with the most frequent publication venues being the Journal of Chemical Theory and Computation, bioRxiv (Cold Spring Harbor Laboratory), Cell Chemical Biology, The Journal of Chemical Physics, and Biophysical Journal.

Some recent papers authored or coauthored by Cieplak include:

  • Epitope-resolved profiling of the SARS-CoV-2 antibody response identifies cross-reactivity with endemic human coronaviruses, 2021, Cell Reports Medicine
  • The Antimalarial Natural Product Salinipostin A Identifies Essential α/β Serine Hydrolases Involved in Lipid Metabolism in P. falciparum Parasites, 2020, Cell Chemical Biology
  • S-nitrosylated TDP-43 triggers aggregation, cell-to-cell spread, and neurotoxicity in hiPSCs and in vivo models of ALS/FTD, 2021, Proceedings of the National Academy of Sciences
  • Efficient formulation of polarizable Gaussian multipole electrostatics for biomolecular simulations, 2020, The Journal of Chemical Physics
  • PyRESP: A Program for Electrostatic Parameterizations of Additive and Induced Dipole Polarizable Force Fields, 2022, Journal of Chemical Theory and Computation

Best Publications

  • A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

    Wendy D. Cornell;Piotr Cieplak;Piotr Cieplak;Christopher I. Bayly;Christopher I. Bayly;Ian R. Gould;Ian R. Gould

  • A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model

    Christopher I. Bayly;Piotr Cieplak;Wendy Cornell;Peter A. Kollman

  • How Well Does a Restrained Electrostatic Potential (RESP) Model Perform in Calculating Conformational Energies of Organic and Biological Molecules

    Junmei Wang;Piotr Cieplak;Piotr Cieplak;Peter A. Kollman

  • Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models

    Peter A. Kollman;Irina Massova;Carolina Reyes;Bernd Kuhn

  • A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.

    Yong Duan;Chun Wu;Shibasish Chowdhury;Mathew C. Lee

  • Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices

    Jayashree Srinivasan;Thomas E. Cheatham;Piotr Cieplak;Peter A. Kollman

  • Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation

    Wendy D. Cornell;Piotr Cieplak;Christopher I. Bayly;Peter A. Kollman

  • S-Nitrosylation of Drp1 Mediates β-Amyloid-Related Mitochondrial Fission and Neuronal Injury

    Dong-Hyung Cho;Tomohiro Nakamura;Jianguo Fang;Piotr Cieplak

  • The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building

    François-Yves Dupradeau;Adrien Pigache;Thomas Zaffran;Corentin Savineau

  • Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins

    Piotr Cieplak;Wendy D. Cornell;Christopher I. Bayly;Peter A. Kollman

  • A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat.

    Thomas E. Cheatham;Piotr Cieplak;Peter A. Kollman

  • R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments

    Enguerran Vanquelef;Sabrina Simon;Gaelle Marquant;Elodie Garcia

  • Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: aqueous solution free energies of methanol and N‐methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases

    Piotr Cieplak;James W. Caldwell;Peter A. Kollman

  • A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 1995, 117, 5179−5197

    Wendy D. Cornell;Piotr Cieplak;Christopher I. Bayly;Ian R. Gould

  • Polarization effects in molecular mechanical force fields.

    Piotr Cieplak;François Yves Dupradeau;Yong Duan;Junmei Wang

  • New-Generation Amber United-Atom Force Field

    Lijiang Yang;Chun Hu Tan;Meng Juei Hsieh;Junmei Wang

  • Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides.

    Zhi-Xiang Wang;Wei Zhang;Wei Zhang;Chun Wu;Chun Wu;Hongxing Lei

  • A theoretical study of tautomerism in the gas phase and aqueous solution: a combined use of state-of-the-art ab initio quantum mechanics and free energy perturbation methods

    Piotr Cieplak;Paul Bash;U. Chandra Singh;Peter A. Kollman

  • Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design.

    Shuanghong Huo;Junmei Wang;Piotr Cieplak;Piotr Cieplak;Peter A. Kollman

  • A new water potential including polarization: Application to gas‐phase, liquid, and crystal properties of water

    Piotr Cieplak;Peter Kollman;Terry Lybrand

Frequent Co-Authors

Peter A. Kollman
Peter A. Kollman University of California, San Francisco
Alex Y. Strongin
Alex Y. Strongin Sanford Burnham Prebys Medical Discovery Institute
Junmei Wang
Junmei Wang University of Pittsburgh
Ray Luo
Ray Luo University of California, Irvine
Jeffrey W. Smith
Jeffrey W. Smith Sanford Burnham Prebys Medical Discovery Institute
Adam Godzik
Adam Godzik University of California, Riverside
Matthew Bogyo
Matthew Bogyo Stanford University
Stuart A. Lipton
Stuart A. Lipton Scripps Research Institute
Thomas E. Cheatham
Thomas E. Cheatham University of Utah
Mark S. Chee
Mark S. Chee Illumina (United States)

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