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Author Details

Piotr Cieplak
Sanford-Burnham-Prebys Medical Discovery Institute
1987
94
35
PMIDPaper TitleJournal TitlePublished Year
36696564Transferability of the Electrostatic Parameters of the Polarizable Gaussian Multipole Model.J Chem Theory Comput2023
37676646Streamlining and Optimizing Strategies of Electrostatic Parameterization.J Chem Theory Comput2023
38011215Dual function of Zika virus NS2B-NS3 protease.PLoS Pathog2023
36696564Transferability of the Electrostatic Parameters of the Polarizable Gaussian Multipole Model.J Chem Theory Comput2023
37441805Optimal Scheme to Achieve Energy Conservation in Induced Dipole Models.J Chem Theory Comput2023
38011215Dual function of Zika virus NS2B-NS3 protease.PLoS Pathog2023
37676646Streamlining and Optimizing Strategies of Electrostatic Parameterization.J Chem Theory Comput2023
37441805Optimal Scheme to Achieve Energy Conservation in Induced Dipole Models.J Chem Theory Comput2023
35169022S-Nitrosylation of p62 Inhibits Autophagic Flux to Promote α-Synuclein Secretion and Spread in Parkinson's Disease and Lewy Body Dementia.J Neurosci2022
35648338Neglected N-Truncated Amyloid-β Peptide and Its Mixed Cu-Zn Complexes.Protein J2022
36094401Accurate Reproduction of Quantum Mechanical Many-Body Interactions in Peptide Main-Chain Hydrogen-Bonding Oligomers by the Polarizable Gaussian Multipole Model.J Chem Theory Comput2022
35537209<i>PyRESP</i>: A Program for Electrostatic Parameterizations of Additive and Induced Dipole Polarizable Force Fields.J Chem Theory Comput2022
35317572Stress tensor and constant pressure simulation for polarizable Gaussian multipole model.J Chem Phys2022
35169022S-Nitrosylation of p62 Inhibits Autophagic Flux to Promote α-Synuclein Secretion and Spread in Parkinson's Disease and Lewy Body Dementia.J Neurosci2022
35648338Neglected N-Truncated Amyloid-β Peptide and Its Mixed Cu-Zn Complexes.Protein J2022
35537209<i>PyRESP</i>: A Program for Electrostatic Parameterizations of Additive and Induced Dipole Polarizable Force Fields.J Chem Theory Comput2022
36094401Accurate Reproduction of Quantum Mechanical Many-Body Interactions in Peptide Main-Chain Hydrogen-Bonding Oligomers by the Polarizable Gaussian Multipole Model.J Chem Theory Comput2022
35317572Stress tensor and constant pressure simulation for polarizable Gaussian multipole model.J Chem Phys2022
34043961Toxoplasma gondii serine hydrolases regulate parasite lipid mobilization during growth and replication within the host.Cell Chem Biol2021
33810667Determining the atomic charge of calcium ion requires the information of its coordination geometry in an EF-hand motif.J Chem Phys2021
33692125S-nitrosylated TDP-43 triggers aggregation, cell-to-cell spread, and neurotoxicity in hiPSCs and in vivo models of ALS/FTD.Proc Natl Acad Sci U S A2021
34043961Toxoplasma gondii serine hydrolases regulate parasite lipid mobilization during growth and replication within the host.Cell Chem Biol2021
33617527Quantitative profiling of protease specificity.PLoS Comput Biol2021
33495758Epitope-resolved profiling of the SARS-CoV-2 antibody response identifies cross-reactivity with endemic human coronaviruses.Cell Rep Med2021
33617527Quantitative profiling of protease specificity.PLoS Comput Biol2021
33810667Determining the atomic charge of calcium ion requires the information of its coordination geometry in an EF-hand motif.J Chem Phys2021
33692125S-nitrosylated TDP-43 triggers aggregation, cell-to-cell spread, and neurotoxicity in hiPSCs and in vivo models of ALS/FTD.Proc Natl Acad Sci U S A2021
33495758Epitope-resolved profiling of the SARS-CoV-2 antibody response identifies cross-reactivity with endemic human coronaviruses.Cell Rep Med2021
32962395Efficient formulation of polarizable Gaussian multipole electrostatics for biomolecular simulations.J Chem Phys2020
32743570Epitope-resolved profiling of the SARS-CoV-2 antibody response identifies cross-reactivity with an endemic human CoV.bioRxiv2020
32962395Efficient formulation of polarizable Gaussian multipole electrostatics for biomolecular simulations.J Chem Phys2020
32743570Epitope-resolved profiling of the SARS-CoV-2 antibody response identifies cross-reactivity with an endemic human CoV.bioRxiv2020
30645118Development of Polarizable Gaussian Model for Molecular Mechanical Calculations I: Atomic Polarizability Parameterization To Reproduce ab Initio Anisotropy.J Chem Theory Comput2019
30645118Development of Polarizable Gaussian Model for Molecular Mechanical Calculations I: Atomic Polarizability Parameterization To Reproduce ab Initio Anisotropy.J Chem Theory Comput2019
31416830Interactions between motor domains in kinesin-14 Ncd - a molecular dynamics study.Biochem J2019
31330204Predictive models of protease specificity based on quantitative protease-activity profiling data.Biochim Biophys Acta Proteins Proteom2019
31416830Interactions between motor domains in kinesin-14 Ncd - a molecular dynamics study.Biochem J2019
31330204Predictive models of protease specificity based on quantitative protease-activity profiling data.Biochim Biophys Acta Proteins Proteom2019
29329315Role of N-glycosylation in activation of proMMP-9. A molecular dynamics simulations study.PLoS One2018
29954845Interaction of the cryptic fragment of myelin basic protein with mitochondrial voltage-dependent anion-selective channel-1 affects cell energy metabolism.Biochem J2018
30079618Amino acid sequence conservation of the algesic fragment of myelin basic protein is required for its interaction with CDK5 and function in pain.FEBS J2018
29329315Role of N-glycosylation in activation of proMMP-9. A molecular dynamics simulations study.PLoS One2018
29453691Effect of phosphorylation and single nucleotide polymorphisms on caspase substrates processing.Apoptosis2018
30079618Amino acid sequence conservation of the algesic fragment of myelin basic protein is required for its interaction with CDK5 and function in pain.FEBS J2018
29954845Interaction of the cryptic fragment of myelin basic protein with mitochondrial voltage-dependent anion-selective channel-1 affects cell energy metabolism.Biochem J2018
29453691Effect of phosphorylation and single nucleotide polymorphisms on caspase substrates processing.Apoptosis2018
27835863Selective function-blocking monoclonal human antibody highlights the important role of membrane type-1 matrix metalloproteinase (MT1-MMP) in metastasis.Oncotarget2017
28347746Matrix metalloproteinases - From the cleavage data to the prediction tools and beyond.Biochim Biophys Acta Mol Cell Res2017
28815237Induced polarization restricts the conformational distribution of a light-harvesting molecular triad in the ground state.Phys Chem Chem Phys2017
28461069Characterization of the Zika virus two-component NS2B-NS3 protease and structure-assisted identification of allosteric small-molecule antagonists.Antiviral Res2017
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Collaborators

Yong Duan
Co-authored papers 16
Ray Luo
Co-authored papers 11
Junmei Wang
Co-authored papers 10
Peter A Kollman
Co-authored papers 10
Adam Godzik
University of California Riverside
Co-authored papers 7
Stuart A Lipton
The Scripps Research Institute, University of California
Co-authored papers 5
Tomohiro Nakamura
The Scripps Research Institute
Co-authored papers 5
Mark S Chee
Medical Research Council Laboratory of Molecular Biology
Co-authored papers 4
Andrei L Osterman
Sanford Burnham Prebys Medical Discovery Institute
Co-authored papers 4
Veronica I Shubayev
Co-authored papers 3
Tai-Sung Lee
Co-authored papers 2
Mars Stone
Vitalant Research Institute
Co-authored papers 2
Matthew C Lee
Co-authored papers 2
Shuanghong Huo
Co-authored papers 2
Xuemei Han
Co-authored papers 2
Thomas E Cheatham
Co-authored papers 2
John R Yates
TheScripps Research Institute
Co-authored papers 2
Jun Wang
Co-authored papers 2
Lukasz Jaroszewski
University of California Riverside School of Medicine
Co-authored papers 1
Tingjun Hou
Co-authored papers 1
Karin A Remington
The J. Craig Venter Institute.
Co-authored papers 1
Maria T Diaz-Meco
Co-authored papers 1
Susan T Mashiyama
University of California san francisco
Co-authored papers 1
Vineet Bafna
University of California San Diego
Co-authored papers 1
Anthony B Pinkerton
Sanford Burnham Prebys Medical Discovery Institute
Co-authored papers 1
Steven E Brenner
University of California berkeley
Co-authored papers 1
Weizhong Li
J. Craig Venter Institute
Co-authored papers 1
Wei Wang
IBM Thomas J Watson Research Center, University of California Los Angeles, University of North Carolina at Chapel Hill
Co-authored papers 1
Carolina Reyes
Co-authored papers 1
Scott D Rychnovsky
University of California irvine
Co-authored papers 1
Release 1.2