P. Cieplak

发表

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

P. Kollman, T. Fox, I. Gould, 1995 .

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

P. Kollman, D. Case, P. Cieplak, 1998 .

How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?

P. Kollman, P. Cieplak, Junmei Wang, 2000 .

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models.

P. Kollman, D. Case, Y. Duan, 2000, Accounts of chemical research.

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

P. Kollman, P. Cieplak, T. Cheatham, 1999, Journal of biomolecular structure & dynamics.

Allosteric transition and binding of small molecule effectors causes curvature change in central β-sheets of selected enzymes

Piotr Cieplak, Miguel Argáez, Leticia Velázquez, 2011, Journal of molecular modeling.

The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families

Benjamin J. Raphael, Susan S. Taylor, David A W Soergel, 2007, PLoS biology.

A well-behaved electrostatic potential-based method using charge restraints for deriving atomic char

P. Kollman, W. Cornell, P. Cieplak, 1993 .

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

P. Kollman, I. Gould, W. Cornell, 1996 .

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

P. Kollman, W. Cornell, P. Cieplak, 1993 .

New-generation amber united-atom force field.

P. Kollman, Y. Duan, P. Cieplak, 2006, The journal of physical chemistry. B.

Quantitative profiling of protease specificity

P. Cieplak, J. Smith, B. Ratnikov, 2020, bioRxiv.

Resolving the Ligand-Binding Specificity in c-MYC G-Quadruplex DNA: Absolute Binding Free Energy Calculations and SPR Experiment.

P. Cieplak, Danzhou Yang, L. Wickstrom, 2017, The journal of physical chemistry. B.

Basis for substrate recognition and distinction by matrix metalloproteinases

Jeffrey W. Smith, A. Godzik, A. Strongin, 2014, Proceedings of the National Academy of Sciences.

Correction: CleavPredict: A Platform for Reasoning about Matrix Metalloproteinases Proteolytic Events

Jeffrey W. Smith, P. Cieplak, M. Kazanov, 2015, PloS one.

Structural determinants of limited proteolysis.

Ying Zhang, Adam Godzik, Piotr Cieplak, 2011, Journal of proteome research.

Polarization effects in molecular mechanical force fields

Piotr Cieplak, François-Yves Dupradeau, Yong Duan, 2009, Journal of physics. Condensed matter : an Institute of Physics journal.

Characterization of the Zika virus two‐component NS2B‐NS3 protease and structure‐assisted identification of allosteric small‐molecule antagonists

A. Strongin, P. Cieplak, A. Terskikh, 2017, Antiviral research.

Lawrence Berkeley National Laboratory Title The Sorcerer II Global Ocean Sampling Expedition : Expanding the Universe of Protein Families Permalink

Benjamin J. Raphael, Susan S. Taylor, David A W Soergel, 2007 .

Predictive models of protease specificity based on quantitative protease-activity profiling data.

M. Gelfand, P. Cieplak, M. Kazanov, 2019, Biochimica et biophysica acta. Proteins and proteomics.

Matrix Metalloproteinase Proteolysis of the Myelin Basic Protein Isoforms Is a Source of Immunogenic Peptides in Autoimmune Multiple Sclerosis

Piotr Cieplak, Boris I. Ratnikov, Jeffrey W. Smith, 2009, PloS one.

Application of the quantum mechanics and free energy perturbation methods to study molecular processes

U. Singh, P. Kollman, P. Cieplak, 1987 .

Ab initio study of the potential energy surface of CH4‐H2O

P. Cieplak, M. Szczęśniak, asiński, 1993 .

Hydration of the tautomeric forms of 2-oxopyrimidine: A Monte Carlo simulation

P. Cieplak, M. Geller, 1985 .

Inflammatory Proprotein Convertase-Matrix Metalloproteinase Proteolytic Pathway in Antigen-presenting Cells as a Step to Autoimmune Multiple Sclerosis*

Jeffrey W. Smith, A. Strongin, Roy M. Williams, 2009, The Journal of Biological Chemistry.

Fission and Neuronal Injury-Amyloid-Related Mitochondrial β S-Nitrosylation of Drp 1 Mediates

Adam Godzik, Piotr Cieplak, Stuart A. Lipton, 2014 .

Development of Polarizable Gaussian Model for Molecular Mechanical Calculations I: Atomic Polarizability Parameterization To Reproduce ab Initio Anisotropy.

Y. Duan, P. Cieplak, Junmei Wang, 2019, Journal of chemical theory and computation.

Amino acid sequence conservation of the algesic fragment of myelin basic protein is required for its interaction with CDK5 and function in pain

A. Strongin, P. Cieplak, V. Shubayev, 2018, The FEBS journal.

PyRESP: A Program for Electrostatic Parameterizations of Additive and Induced Dipole Polarizable Force Fields.

Y. Duan, P. Cieplak, R. Luo, 2022, Journal of chemical theory and computation.

Effect of phosphorylation and single nucleotide polymorphisms on caspase substrates processing

P. Cieplak, Sonu Kumar, 2018, Apoptosis.

Caspase Cleavage Sites in the Human Proteome: CaspDB, a Database of Predicted Substrates

P. Cieplak, G. Salvesen, Sonu Kumar, 2014, Apoptosis.

A technique to study molecular recognition in drug design: Preliminary application of free energy derivatives to inhibition of a malarial cysteine protease

P. Kollman, P. Cieplak, 1996, Journal of molecular recognition : JMR.

Toxoplasma gondii serine hydrolases regulate parasite lipid mobilization during growth and replication within the host

M. Bogyo, P. Cieplak, J. Long, 2020, bioRxiv.

Erratum - Strike a balance: Optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides

Wei Zhang, Yong Duan, Piotr Cieplak, 2006, J. Comput. Chem..

Internal Cleavages of the Autoinhibitory Prodomain Are Required for Membrane Type 1 Matrix Metalloproteinase Activation, although Furin Cleavage Alone Generates Inactive Proteinase*

A. Strongin, P. Cieplak, Ilian A Radichev, 2010, The Journal of Biological Chemistry.

Molecular Basis for the Cu Binding-Induced Destabilization of b2-Microglobulin Revealed by Molecular Dynamics Simulation

P. Cieplak, Lisa Yan, N. Deng, 2006 .

Neglected N-Truncated Amyloid-β Peptide and Its Mixed Cu–Zn Complexes

P. Cieplak, T. Frączyk, 2022, The Protein Journal.

High-Resolution Analysis and Functional Mapping of Cleavage Sites and Substrate Proteins of Furin in the Human Proteome

A. Strongin, M. Chee, E. Chudin, 2013, PloS one.

S-nitrosylated TDP-43 triggers aggregation, cell-to-cell spread, and neurotoxicity in hiPSCs and in vivo models of ALS/FTD

Gene W. Yeo, S. Lipton, J. Yates, 2021, Proceedings of the National Academy of Sciences.

A Note on the Potential BCG Vaccination – COVID-19 Molecular Link

A. Strongin, P. Cieplak, A. Sloutsky, 2020, Coronaviruses.

Theoretical study of the free‐radical copolymerization of styrene with methyl methacrylate: Comparative study to the styrene–acrylonitrile monomer system

P. Cieplak, A. Kaim, 2004 .

Selective function-blocking monoclonal human antibody highlights the important role of membrane type-1 matrix metalloproteinase (MT1-MMP) in metastasis

A. Strongin, P. Cieplak, A. Remacle, 2016, Oncotarget.

Calculation of the free energy of association of nucleic acid bases in vacuo and water solution

P. Kollman, P. Cieplak, 1988 .

Interactions between motor domains in kinesin-14 Ncd - a molecular dynamics study.

P. Cieplak, J. Ludwiczak, E. Szczęsna, 2019, The Biochemical journal.

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

A. Godzik, S. Lipton, P. Cieplak, 2009, Science.

Accurate Reproduction of Quantum Mechanical Many-Body Interactions in Peptide Main-Chain Hydrogen-Bonding Oligomers by the Polarizable Gaussian Multipole Model.

Y. Duan, P. Cieplak, R. Luo, 2022, Journal of chemical theory and computation.

S-Nitrosylation of p62 Inhibits Autophagic Flux to Promote α-Synuclein Secretion and Spread in Parkinson's Disease and Lewy Body Dementia

S. Lipton, P. Cieplak, J. Nolan, 2022, The Journal of Neuroscience.

Image and Memory

P. Cieplak, 2009 .

Determining the atomic charge of calcium ion in a calcium-binding protein requires the information of its dynamic coordination geometry in aqueous solution

P. Cieplak, M. Cheung, Jaebeom Han, 2020, 2011.07639.

Penultimate unit effects in the free-radical copolymerization of styrene with acrylonitrile according to theoretical thermochemistry

P. Cieplak, A. Kaim, E. Megiel, 2002 .

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

Wei Zhang, Yong Duan, Rong Yang, 2003, J. Comput. Chem..

S-nitrosylation-mediated redox transcriptional switch modulates neurogenesis and neuronal cell death.

Jeffrey D. Zaremba, A. Godzik, Jiankun Cui, 2014, Cell reports.

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

Piotr Cieplak, François-Yves Dupradeau, Jean Charles Delepine, 2011, Nucleic Acids Res..

Synthesis of novel beta-lactone inhibitors of fatty acid synthase.

Jeffrey W. Smith, P. Cieplak, D. Romo, 2008, Journal of medicinal chemistry.

Synthesis, Physicochemical Studies, Molecular Dynamics Simulations, and Metal-Ion-Dependent Antiproliferative and Antiangiogenic Properties of Cone ICL670-Substituted Calix[4]arenes.

P. Cieplak, C. Cézard, E. Guillon, 2012, ChemPlusChem.

The effect of 5-substitution in the pyrimidine ring of dUMP on the interaction with thymidylate synthase: molecular modeling and QSAR.

P. Cieplak, T. M. Krygowski, W. Rode, 2007, Bioorganic & medicinal chemistry.

PMAP: databases for analyzing proteolytic events and pathways

Sarah Boyd, Jeffrey W. Smith, Michael L. Blinov, 2008, Nucleic Acids Res..

Molecular Dynamics and Free Energy Study of the Conformational Equilibria in the UUUU RNA Hairpin.

P. Cieplak, N. Deng, 2007, Journal of chemical theory and computation.

How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?

Junmei Wang, Peter A. Kollman, Piotr Cieplak, 2000, J. Comput. Chem..

Transferability of the Electrostatic Parameters of the Polarizable Gaussian Multipole Model.

Y. Duan, P. Cieplak, R. Luo, 2023, Journal of chemical theory and computation.

Free energy profile of RNA hairpins: a molecular dynamics simulation study.

Piotr Cieplak, P. Cieplak, Nan-Jie Deng, 2010, Biophysical journal.

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

Piotr Cieplak, François-Yves Dupradeau, Rodolphe Lelong, 2010, Physical chemistry chemical physics : PCCP.

Further evidence for the inseparability of the theoretical enthalpic terminal and penultimate unit effects in the radical copolymerization of styrene with acrylonitrile

P. Cieplak, A. Kaim, 2003 .

CaspNeuroD: a knowledgebase of predicted caspase cleavage sites in human proteins related to neurodegenerative diseases

Sonu Kumar, Piotr Cieplak, P. Cieplak, 2016, Database J. Biol. Databases Curation.

Letter to the Editor: Caspase cleavage sites in the human proteome: CaspDB, a database of predicted substrates

P. Cieplak, 2015, Apoptosis.

Induced polarization restricts the conformational distribution of a light-harvesting molecular triad in the ground state.

P. Cieplak, M. Cheung, Pengzhi Zhang, 2017, Physical chemistry chemical physics : PCCP.

Peptide mimetics as enzyme inhibitors: Use of free energy perturbation calculations to evaluate isosteric replacement for amide bonds in a potent HIV protease inhibitor

Peter A. Kollman, Piotr Cieplak, P. Kollman, 1993, J. Comput. Aided Mol. Des..

Relative free energies of binding to thymidylate synthase of 2- and/or 4-thio and/or 5-fluoro analogues of dUMP

Piotr Cieplak, Adam Jarmula, Wojciech Rode, 2003, J. Comput. Aided Mol. Des..

INTERACTIONS BETWEEN SOLUTE AND SOLVENT MOLECULES IN NUCLEIC ACID BASES SOLUTIONS

P. Cieplak, M. Geller, A. Leś, 1981 .

Conformations of duplex structures formed by oligodeoxynucleotides covalently linked to the intercalator 2-methoxy-6-chloro-9-aminoacridine.

P. Kollman, P. Cieplak, S. N. Rao, 1987, Journal of biomolecular structure & dynamics.

S-nitrosylation of Drp1 links excessive mitochondrial fission to neuronal injury in neurodegeneration.

A. Godzik, S. Lipton, P. Cieplak, 2010, Mitochondrion.

5,10-Methylene-5,6,7,8-tetrahydrofolate conformational transitions upon binding to thymidylate synthase: molecular mechanics and continuum solvent studies

Piotr Cieplak, Adam Jarmula, William R. Montfort, 2005, J. Comput. Aided Mol. Des..

Hydration of Benzoic Acid in Benzene Solution

P. Cieplak, E. Wiȩckowska, W. Pawłowski, 1990 .

Dual function of Zika virus NS2B-NS3 protease

R. Liddington, P. Cieplak, A. Terskikh, 2021, bioRxiv.

Sequence‐derived structural features driving proteolytic processing

Piotr Cieplak, Andrei L Osterman, M. Gelfand, 2014, Proteomics.

Development of polarizable models for molecular mechanical calculations I: parameterization of atomic polarizability.

Jie Li, Ray Luo, Piotr Cieplak, 2011, The journal of physical chemistry. B.

Development of polarizable models for molecular mechanical calculations II: induced dipole models significantly improve accuracy of intermolecular interaction energies.

Jie Li, Ray Luo, Piotr Cieplak, 2011, The journal of physical chemistry. B.

CleavPredict: A Platform for Reasoning about Matrix Metalloproteinases Proteolytic Events

Piotr Cieplak, Marat D. Kazanov, Boris I. Ratnikov, 2015, PloS one.

Substrate Cleavage Analysis of Furin and Related Proprotein Convertases

Piotr Cieplak, Michal Lebl, Robert Day, 2008, Journal of Biological Chemistry.

History, trauma and remembering in Kivu Ruhorahoza’s Grey Matter (2011)

P. Cieplak, 2018 .

High-Throughput Multiplexed Peptide-Centric Profiling Illustrates Both Substrate Cleavage Redundancy and Specificity in the MMP Family.

Piotr Cieplak, David A. Routenberg, Muskan Kukreja, 2015, Chemistry & biology.

Molecular basis for the Cu2+ binding-induced destabilization of beta2-microglobulin revealed by molecular dynamics simulation.

P. Cieplak, Lisa Yan, N. Deng, 2006, Biophysical journal.

Peptide Sequence Region That is Essential for the Interactions of the Enterotoxigenic Bacteroides fragilis Metalloproteinase II with E-cadherin.

A. Strongin, P. Cieplak, A. Remacle, 2014, Journal of proteolysis.

Substrate Cleavage Profiling Suggests a Distinct Function of Bacteroides fragilis Metalloproteinases (Fragilysin and Metalloproteinase II) at the Microbiome-Inflammation-Cancer Interface*

A. Strongin, P. Čapek, P. Cieplak, 2013, The Journal of Biological Chemistry.

Structural and functional diversity of metalloproteinases encoded by the Bacteroides fragilis pathogenicity island

A. Strongin, R. Liddington, P. Cieplak, 2014, The FEBS journal.

Chapter 2: Images of After: Gilles Peress and Sebastião Salgado

P. Cieplak, 2017 .

The Wnt/Planar Cell Polarity Protein-tyrosine Kinase-7 (PTK7) Is a Highly Efficient Proteolytic Target of Membrane Type-1 Matrix Metalloproteinase

A. Strongin, P. Cieplak, Ilian A Radichev, 2010, The Journal of Biological Chemistry.

Interaction of the cryptic fragment of myelin basic protein with mitochondrial voltage-dependent anion-selective channel-1 affects cell energy metabolism.

A. Strongin, P. Cieplak, V. Shubayev, 2018, The Biochemical journal.

The antimalarial natural product salinipostin A identifies essential α/β serine hydrolases involved in lipid metabolism in P. falciparum parasites

Roger G. Linington, Kenji L. Kurita, M. Bogyo, 2019, bioRxiv.

Frustration-driven transitions on fractals

M. Cieplak, P. Cieplak, M. Załuska-Kotur, 1986 .

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

Peter A. Kollman, Piotr Cieplak, Christopher I. Bayly, 1995, J. Comput. Chem..

Mixed spin glass in Ising systems

M. Cieplak, P. Cieplak, M. Załuska-Kotur, 1987 .

Calculation of free energy changes in ion–water clusters using nonadditive potentials and the Monte Carlo method

Terry P. Lybrand, Peter A. Kollman, Piotr Cieplak, 1987 .

Nucleic Acid Force Fields

P. Cieplak, 2002 .

ArC2H2: a challenging system for ab initio calculations

P. Cieplak, R. Kendall, M. Szczęśniak, 1997 .

Walking on the free energy hypersurface of the 18‐crown‐6 ion system using free energy derivatives

Peter A. Kollman, Piotr Cieplak, David A. Pearlman, 1994 .

Selective and potent furin inhibitors protect cells from anthrax without significant toxicity.

A. Strongin, R. Liddington, P. Cieplak, 2010, The international journal of biochemistry & cell biology.

Matrix metalloproteinases - From the cleavage data to the prediction tools and beyond.

Piotr Cieplak, Alex Y Strongin, A. Strongin, 2017, Biochimica et biophysica acta. Molecular cell research.

New Details of HCV NS3/4A Proteinase Functionality Revealed by a High-Throughput Cleavage Assay

A. Strongin, M. Chee, E. Chudin, 2012, PloS one.

A monoclonal antibody interferes with TIMP-2 binding and incapacitates the MMP-2-activating function of multifunctional, pro-tumorigenic MMP-14/MT1–MMP

A. Strongin, P. Cieplak, N. Behrendt, 2013, Oncogenesis.

Death, Image, Memory

P. Cieplak, 2017 .

Alternative African cinemas: a case study of Rwanda

P. Cieplak, 2010 .

Chapter 1: Image, Evidence, Memory

P. Cieplak, 2017 .

Ab initio study of intermolecular potential of H2O trimer

P. Cieplak, S. Scheiner, M. Szczęśniak, 1991 .

Chapter 3: Images of Before: Personal Archives and the Kigali Genocide Memorial

P. Cieplak, 2017 .

Chapter 5: ‘I Remember Them’— Keepers of Memory (2004)

P. Cieplak, 2017 .

Epitope-resolved profiling of the SARS-CoV-2 antibody response identifies cross-reactivity with endemic human coronaviruses

Zane W. Fink, M. Caligiuri, M. Chee, 2020, Cell Reports Medicine.

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

Terry P. Lybrand, Peter A. Kollman, Piotr Cieplak, 1990 .

Development of polarizable models for molecular mechanical calculations. 3. Polarizable water models conforming to Thole polarization screening schemes.

Ray Luo, Piotr Cieplak, Qin Cai, 2012, The journal of physical chemistry. B.

On the use of electrostatic potential derived charges in molecular mechanics force fields. The relative solvation free energy of cis‐ and trans‐N‐methyl‐acetamide

Peter A. Kollman, Piotr Cieplak, P. Kollman, 1991 .

Molecular Dynamics Simulations Find That 3‘ Phosphoramidate Modified DNA Duplexes Undergo a B to A Transition and Normal DNA Duplexes an A to B Transition

P. Kollman, P. Cieplak, T. Cheatham, 1997 .

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

Peter A. Kollman, Piotr Cieplak, Paul A. Bash, 1987 .

R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries

Piotr Cieplak, François-Yves Dupradeau, Christine Cézard, 2007, Nucleic Acids Res..

Toxoplasma gondii serine hydrolases regulate parasite lipid mobilization during growth and replication within the host.

M. Bogyo, P. Cieplak, J. Long, 2021, Cell chemical biology.

Mechanism of influence of phosphorylation on serine 124 on a decrease of catalytic activity of human thymidylate synthase.

Piotr Cieplak, P. Cieplak, Adam Jarmuła, 2010, Bioorganic & medicinal chemistry.

Epitope-resolved profiling of the SARS-CoV-2 antibody response identifies cross-reactivity with an endemic human CoV

Zane W. Fink, M. Caligiuri, M. Chee, 2020, bioRxiv.

Role of N-glycosylation in activation of proMMP-9. A molecular dynamics simulations study

P. Cieplak, Sonu Kumar, 2018, PloS one.

Free energy calculation on base specificity of drug – DNA interactions: Application to daunomycin and acridine intercalation into DNA

P. Kollman, P. Cieplak, P. Grootenhuis, 1990, Biopolymers.

Matrix Metalloproteinase (MMP) Proteolysis of the Extracellular Loop of Voltage-gated Sodium Channels and Potential Alterations in Pain Signaling*

A. Strongin, P. Cieplak, V. Shubayev, 2015, The Journal of Biological Chemistry.

Efficient formulation of polarizable Gaussian multipole electrostatics for biomolecular simulations.

Y. Duan, P. Cieplak, Junmei Wang, 2020, The Journal of chemical physics.

Development of polarizable models for molecular mechanical calculations. 4. van der Waals parametrization.

Jie Li, Ray Luo, Piotr Cieplak, 2012, The journal of physical chemistry. B.

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

Wei Zhang, Yong Duan, Piotr Cieplak, 2006, J. Comput. Chem..

Elucidating the Origin of Conformational Energy Differences in Substituted 1,3-Dioxanes: A Combined Theoretical and Experimental Study.

P. Kollman, P. Cieplak, S. Rychnovsky, 1996, The Journal of organic chemistry.

A molecular mechanical model that reproduces the relative energies for chair and twist‐boat conformations of 1,3‐dioxanes

Peter A. Kollman, Piotr Cieplak, Allison E. Howard, 1995, J. Comput. Chem..

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

Piotr Cieplak, Irwin D Kuntz, Shuanghong Huo, 2002, Journal of medicinal chemistry.

ACCURATE SOLVATION FREE ENERGIES OF ACETATE AND METHYLAMMONIUM IONS CALCULATED WITH A POLARIZABLE WATER MODEL

Elaine C. Meng, Peter A. Kollman, Piotr Cieplak, 1994 .

A second generation force field for the simulation of proteins

P. Kollman, T. Fox, I. Gould, 1995 .

Interactions of anesthetics with the membrane-water interface.

A. Pohorille, P. Cieplak, M. Wilson, 1996, Chemical physics.

Matrix metalloproteinase proteolysis of the mycobacterial HSP65 protein as a potential source of immunogenic peptides in human tuberculosis

A. Strongin, P. Cieplak, Wenhong Zhu, 2011, The FEBS journal.

Optimal Scheme to Achieve Energy Conservation in Induced Dipole Models.

Y. Duan, P. Cieplak, Shiji Zhao, 2023, Journal of chemical theory and computation.

Stress tensor and constant pressure simulation for polarizable Gaussian multipole model.

Y. Duan, P. Cieplak, R. Luo, 2022, The Journal of chemical physics.

High throughput substrate phage display for protease profiling.

Jeffrey W. Smith, P. Cieplak, B. Ratnikov, 2009, Methods in molecular biology.

Synthesis of novel beta-lactone inhibitors of fatty acid synthase.

Jeffrey W. Smith, P. Cieplak, D. Romo, 2008, Journal of medicinal chemistry.

Solvation of the tautomeric forms of 2-oxopyrimidine in carbon tetrachloride solution: A Monte Carlo simulation

P. Cieplak, M. Geller, 1985 .

Salt leverages polyethylene terephthalate hydrolase (PETase) enzymatic activity via the predicted conformational switch

P. Cieplak, S. Shiryaev, A. Chernov, 2021, bioRxiv.

No Job Name

P. Cieplak, T. Cheatham, I. Massova, 2022 .