Piotr Cieplak

Publication Activity (10 Years)

Years Active: 1993-2021
Publications (10 Years): 2

Top Topics

Protein Complexes

Qualitative And Quantitative

Top Venues

Database J. Biol. Databases Curation

PLoS Comput. Biol.

Publications

Boris I. Ratnikov, Piotr Cieplak, Albert G. Remacle, Elise Nguyen, Jeffrey W. Smith
Quantitative profiling of protease specificity. PLoS Comput. Biol. 17 (2) (2021)
Sonu Kumar, Piotr Cieplak
CaspNeuroD: a knowledgebase of predicted caspase cleavage sites in human proteins related to neurodegenerative diseases. Database J. Biol. Databases Curation 2016 (2016)
Enguerran Vanquelef, Sabrina Simon, Gaelle Marquant, Elodie Garcia, Geoffroy Klimerak, Jean Charles Delepine, Piotr Cieplak, François-Yves Dupradeau
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. 39 (Web-Server-Issue) (2011)
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
PMAP: databases for analyzing proteolytic events and pathways. Nucleic Acids Res. 37 (Database-Issue) (2009)
François-Yves Dupradeau, Christine Cézard, Rodolphe Lelong, Élodie Stanislawiak, Julien Pêcher, Jean Charles Delepine, Piotr Cieplak
R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries. Nucleic Acids Res. 36 (Database-Issue) (2008)
Zhi-Xiang Wang, Wei Zhang, Chun Wu, Hongxing Lei, Piotr Cieplak, Yong Duan
Erratum - Strike a balance: Optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides. J. Comput. Chem. 27 (8) (2006)
Zhi-Xiang Wang, Wei Zhang, Chun Wu, Hongxing Lei, Piotr Cieplak, Yong Duan
Strike a balance: Optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides. J. Comput. Chem. 27 (6) (2006)
Adam Jarmula, Piotr Cieplak, William R. Montfort
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. 19 (2) (2005)
Yong Duan, Chun Wu, Shibasish Chowdhury, Mathew C. Lee, Guoming Xiong, Wei Zhang, Rong Yang, Piotr Cieplak, Ray Luo, Taisung Lee, James W. Caldwell, Junmei Wang, Peter A. Kollman
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J. Comput. Chem. 24 (16) (2003)
Adam Jarmula, Piotr Cieplak, Andrzej Les, Wojciech Rode
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. 17 (10) (2003)
Marek Orzechowski, Piotr Cieplak, Lucjan Piela
Theoretical calculation of the coiled-coil stability in water in the context of its possible use as a molecular rack. J. Comput. Chem. 23 (1) (2002)
Piotr Cieplak, James W. Caldwell, Peter A. Kollman
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. 22 (10) (2001)
Junmei Wang, Piotr Cieplak, Peter A. Kollman
How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 21 (12) (2000)
Piotr Cieplak, Wendy D. Cornell, Christopher I. Bayly, Peter A. Kollman
Application of the Multimolecule and Multiconformational RESP Methodology to Biopolymers: Charge Derication for DNA, RNA, and Proteins. J. Comput. Chem. 16 (11) (1995)
Allison E. Howard, Piotr Cieplak, Peter A. Kollman
A Molecular Mechanical Model That Reproduces the Relative Energies for Chair and Twist-Boat Conformations of 1, 3-Dioxanes. J. Comput. Chem. 16 (2) (1995)
Piotr Cieplak, Peter A. Kollman
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. 7 (3) (1993)