Peptide mimetics as enzyme inhibitors: Use of free energy perturbation calculations to evaluate isosteric replacement for amide bonds in a potent HIV protease inhibitor. - Piotr Cieplak; Peter A. Kollman (J. Comput. Aided Mol. Des., 1993)

Application of the Multimolecule and Multiconformational RESP Methodology to Biopolymers: Charge Derication for DNA, RNA, and Proteins. - Piotr Cieplak; Wendy D. Cornell; Christopher I. Bayly; Peter A. Kollman (J. Comput. Chem., 1995)

A Molecular Mechanical Model That Reproduces the Relative Energies for Chair and Twist-Boat Conformations of 1, 3-Dioxanes. - Allison E. Howard; Piotr Cieplak; Peter A. Kollman (J. Comput. Chem., 1995)

How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? - Junmei Wang; Piotr Cieplak; Peter A. Kollman (J. Comput. Chem., 2000)

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 (J. Comput. Chem., 2001)

Theoretical calculation of the coiled-coil stability in water in the context of its possible use as a molecular rack. - Marek Orzechowski; Piotr Cieplak; Lucjan Piela (J. Comput. Chem., 2002)

Relative free energies of binding to thymidylate synthase of 2- and/or 4-thio and/or 5-fluoro analogues of dUMP. - Adam Jarmula; Piotr Cieplak; Andrzej Les; Wojciech Rode (J. Comput. Aided Mol. Des., 2003)

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; Guoming Xiong; Wei Zhang; Rong Yang; Piotr Cieplak; Ray Luo 001; Tai-Sung Lee; James W. Caldwell; Junmei Wang; et al. (J. Comput. Chem., 2003)

5, 10-Methylene-5, 6, 7, 8-tetrahydrofolate conformational transitions upon binding to thymidylate synthase: molecular mechanics and continuum solvent studies. - Adam Jarmula; Piotr Cieplak; William R. Montfort (J. Comput. Aided Mol. Des., 2005)

Strike a balance: Optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides. - Zhi-Xiang Wang; Wei Zhang; Chun Wu; Hongxing Lei; Piotr Cieplak; Yong Duan (J. Comput. Chem., 2006)

Erratum - Strike a balance: Optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides. - Zhi-Xiang Wang; Wei Zhang; Chun Wu; Hongxing Lei; Piotr Cieplak; Yong Duan (J. Comput. Chem., 2006)

R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries. - François-Yves Dupradeau; Christine Cézard; Rodolphe Lelong; Élodie Stanislawiak; Julien Pêcher; Jean Charles Delepine; Piotr Cieplak (Nucleic Acids Res., 2008)

PMAP: databases for analyzing proteolytic events and pathways. - Yoshinobu Igarashi; Emily Heureux; Kutbuddin S. Doctor; Priti Talwar; Svetlana Gramatikova; Kosi Gramatikoff; Ying Zhang 004; Michael L. Blinov; Salmaz S. Ibragimova; Sarah E. Boyd; Boris I. Ratnikov; Piotr Cieplak; et al. (Nucleic Acids Res., 2009)

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; Geoffroy Klimerak; Jean Charles Delepine; Piotr Cieplak; François-Yves Dupradeau (Nucleic Acids Res., 2011)

CaspNeuroD: a knowledgebase of predicted caspase cleavage sites in human proteins related to neurodegenerative diseases. - Sonu Kumar; Piotr Cieplak (Database J. Biol. Databases Curation, 2016)

Quantitative profiling of protease specificity. - Boris I. Ratnikov; Piotr Cieplak; Albert G. Remacle; Elise Nguyen; Jeffrey W. Smith (PLoS Comput. Biol., 2021)

Refinement of Atomic Polarizabilities for a Polarizable Gaussian Multipole Force Field with Simultaneous Considerations of Both Molecular Polarizability Tensors and In-Solution Electrostatic Potentials. - Yong Duan; Junmei Wang; Piotr Cieplak; Ray Luo 001 (J. Chem. Inf. Model., 2025)