Piotr Cieplak - researchr alias

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Viewing Publication 1 - 16 from 16

2021

Quantitative profiling of protease specificityBoris I. Ratnikov, Piotr Cieplak, Albert G. Remacle, Elise Nguyen, Jeffrey W. Smith. ploscb, 17(2), 2021. [doi]

2016

CaspNeuroD: a knowledgebase of predicted caspase cleavage sites in human proteins related to neurodegenerative diseasesSonu Kumar, Piotr Cieplak. biodb, 2016, 2016. [doi]

2011

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragmentsEnguerran Vanquelef, Sabrina Simon, Gaelle Marquant, Elodie Garcia, Geoffroy Klimerak, Jean Charles Delepine, Piotr Cieplak, François-Yves Dupradeau. nar, 39(Web-Server-Issue):511-517, 2011. [doi]

2009

PMAP: databases for analyzing proteolytic events and pathwaysYoshinobu Igarashi, Emily Heureux, Kutbuddin S. Doctor, Priti Talwar, Svetlana Gramatikova, Kosi Gramatikoff, Ying Zhang, Michael L. Blinov, Salmaz S. Ibragimova, Sarah Boyd, Boris Ratnikov, Piotr Cieplak, Adam Godzik, Jeffrey W. Smith, Andrei Osterman, Alexey M. Eroshkin. nar, 37(Database-Issue):611-618, 2009. [doi]

2008

R.E.DD.B.: A database for RESP and ESP atomic charges, and force field librariesFrançois-Yves Dupradeau, Christine Cézard, Rodolphe Lelong, Élodie Stanislawiak, Julien Pêcher, Jean Charles Delepine, Piotr Cieplak. nar, 36(Database-Issue):360-367, 2008. [doi]

2006

Strike a balance: Optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptidesZhi-Xiang Wang, Wei Zhang, Chun Wu, Hongxing Lei, Piotr Cieplak, Yong Duan. jcc, 27(6):781-790, 2006. [doi]

Erratum - Strike a balance: Optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptidesZhi-Xiang Wang, Wei Zhang, Chun Wu, Hongxing Lei, Piotr Cieplak, Yong Duan. jcc, 27(8):994, 2006. [doi]

2005

5, 10-Methylene-5, 6, 7, 8-tetrahydrofolate conformational transitions upon binding to thymidylate synthase: molecular mechanics and continuum solvent studiesAdam Jarmula, Piotr Cieplak, William R. Montfort. jcamd, 19(2):123-136, 2005. [doi]

2003

2002

Theoretical calculation of the coiled-coil stability in water in the context of its possible use as a molecular rackMarek Orzechowski, Piotr Cieplak, Lucjan Piela. jcc, 23(1):106-110, 2002. [doi]

2001

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/Piotr Cieplak, James W. Caldwell, Peter A. Kollman. jcc, 22(10):1048-1057, 2001. [doi]

2000

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. jcc, 21(12):1049-1074, 2000. [doi]

1995

Application of the Multimolecule and Multiconformational RESP Methodology to Biopolymers: Charge Derication for DNA, RNA, and ProteinsPiotr Cieplak, Wendy D. Cornell, Christopher I. Bayly, Peter A. Kollman. jcc, 16(11):1357-1376, 1995.

A Molecular Mechanical Model That Reproduces the Relative Energies for Chair and Twist-Boat Conformations of 1, 3-DioxanesAllison E. Howard, Piotr Cieplak, Peter A. Kollman. jcc, 16(2):243-262, 1995.

1993

Peptide mimetics as enzyme inhibitors: Use of free energy perturbation calculations to evaluate isosteric replacement for amide bonds in a potent HIV protease inhibitorPiotr Cieplak, Peter A. Kollman. jcamd, 7(3):291-304, 1993.

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