Piotr Cieplak

17 papers Journal 17
YearRankTypeTitle / Venue / Authors
2025 J jnl
Refinement of Atomic Polarizabilities for a Polarizable Gaussian Multipole Force Field with Simultaneous Considerations of Both Molecular Polarizability Tensors and In-Solution Electrostatic Potentials.
J. Chem. Inf. Model.
Yong Duan, Junmei Wang, Piotr Cieplak, Ray Luo
2021 J jnl
Quantitative profiling of protease specificity.
PLoS Comput. Biol.
Boris I. Ratnikov, Piotr Cieplak, Albert G. Remacle, Elise Nguyen, Jeffrey W. Smith
2016 J jnl
CaspNeuroD: a knowledgebase of predicted caspase cleavage sites in human proteins related to neurodegenerative diseases.
Database J. Biol. Databases Curation
Sonu Kumar, Piotr Cieplak
2011 J jnl
R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments.
Nucleic Acids Res.
Enguerran Vanquelef, Sabrina Simon, Gaelle Marquant, Elodie Garcia, Geoffroy Klimerak, Jean Charles Delepine, Piotr Cieplak, François-Yves Dupradeau
2009 J jnl
PMAP: databases for analyzing proteolytic events and pathways.
Nucleic Acids Res.
Yoshinobu Igarashi, Emily Heureux, Kutbuddin S. Doctor, Priti Talwar, Svetlana Gramatikova, Kosi Gramatikoff, Ying Zhang, Michael L. Blinov, Salmaz S. Ibragimova, Sarah E. Boyd, Boris I. Ratnikov, Piotr Cieplak, Adam Godzik, Jeffrey W. Smith, Andrei Osterman, Alexey M. Eroshkin
2008 J jnl
R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries.
Nucleic Acids Res.
François-Yves Dupradeau, Christine Cézard, Rodolphe Lelong, Élodie Stanislawiak, Julien Pêcher, Jean Charles Delepine, Piotr Cieplak
2006 J jnl
Erratum - Strike a balance: Optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides.
J. Comput. Chem.
Zhi-Xiang Wang, Wei Zhang, Chun Wu, Hongxing Lei, Piotr Cieplak, Yong Duan
2006 J jnl
Strike a balance: Optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides.
J. Comput. Chem.
Zhi-Xiang Wang, Wei Zhang, Chun Wu, Hongxing Lei, Piotr Cieplak, Yong Duan
2005 J jnl
5, 10-Methylene-5, 6, 7, 8-tetrahydrofolate conformational transitions upon binding to thymidylate synthase: molecular mechanics and continuum solvent studies.
J. Comput. Aided Mol. Des.
Adam Jarmula, Piotr Cieplak, William R. Montfort
2003 J jnl
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.
J. Comput. Chem.
Yong Duan, Chun Wu, Shibasish Chowdhury, Mathew C. Lee, Guoming Xiong, Wei Zhang, Rong Yang, Piotr Cieplak, Ray Luo, Tai-Sung Lee, James W. Caldwell, Junmei Wang, Peter A. Kollman
2003 J jnl
Relative free energies of binding to thymidylate synthase of 2- and/or 4-thio and/or 5-fluoro analogues of dUMP.
J. Comput. Aided Mol. Des.
Adam Jarmula, Piotr Cieplak, Andrzej Les, Wojciech Rode
2002 J jnl
Theoretical calculation of the coiled-coil stability in water in the context of its possible use as a molecular rack.
J. Comput. Chem.
Marek Orzechowski, Piotr Cieplak, Lucjan Piela
2001 J jnl
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.
J. Comput. Chem.
Piotr Cieplak, James W. Caldwell, Peter A. Kollman
2000 J jnl
How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
J. Comput. Chem.
Junmei Wang, Piotr Cieplak, Peter A. Kollman
1995 J jnl
A Molecular Mechanical Model That Reproduces the Relative Energies for Chair and Twist-Boat Conformations of 1, 3-Dioxanes.
J. Comput. Chem.
Allison E. Howard, Piotr Cieplak, Peter A. Kollman
1995 J jnl
Application of the Multimolecule and Multiconformational RESP Methodology to Biopolymers: Charge Derication for DNA, RNA, and Proteins.
J. Comput. Chem.
Piotr Cieplak, Wendy D. Cornell, Christopher I. Bayly, Peter A. Kollman
1993 J jnl
Peptide mimetics as enzyme inhibitors: Use of free energy perturbation calculations to evaluate isosteric replacement for amide bonds in a potent HIV protease inhibitor.
J. Comput. Aided Mol. Des.
Piotr Cieplak, Peter A. Kollman