Allen L.R.; Krivov S.V.; Paci E., Analysis of the free-energy surface of proteins from reversible folding simulations, «PLOS COMPUTATIONAL BIOLOGY», 2009, 5, Article number: e1000428, pp. 1 - 10 [articolo]
Glowacki D.R.; Paci E.; Shalashilin D.V., Boxed molecular dynamics: A simple and general technique for accelerating rare event kinetics and mapping free energy in large molecular systems, «JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL», 2009, 113, pp. 16603 - 16611 [articolo]
Brooks B.R.; Brooks III C.L.; Mackerell Jr. A.D.; Nilsson L.; Petrella R.J.; Roux B.; Won Y.; Archontis G.; Bartels C.; Boresch S.; Caflisch A.; Caves L.; Cui Q.; Dinner A.R.; Feig M.; Fischer S.; Gao J.; Hodoscek M.; Im W.; Kuczera K.; Lazaridis T.; Ma J.; Ovchinnikov V.; Paci E.; Pastor R.W.; Post C.B.; Pu J.Z.; Schaefer M.; Tidor B.; Venable R.M.; Woodcock H.L.; Wu X.; Yang W.; York D.M.; Karplus M., CHARMM: The biomolecular simulation program, «JOURNAL OF COMPUTATIONAL CHEMISTRY», 2009, 30, pp. 1545 - 1614 [articolo]
Noronha M.; Santos R.; Paci E.; Santos H.; Macanita A.L., Fluorescence Lifetimes of Tyrosine Residues in Cytochrome c″ as Local Probes to Study Protein Unfolding, «JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL», 2009, 113, pp. 4466 - 4474 [articolo]
Forman J.R.; Yew Z.T.; Qamar S.; Sandford R.N.; Paci E.; Clarke J., Non-Native Interactions Are Critical for Mechanical Strength in PKD Domains, «STRUCTURE», 2009, 17, pp. 1582 - 1590 [articolo]
Allen L.R.; Paci E., Orientational averaging of dye molecules attached to proteins in Förster resonance energy transfer measurements: Insights from a simulation study, «THE JOURNAL OF CHEMICAL PHYSICS», 2009, 131, Article number: 065101, pp. 065101 - 065111 [articolo]
Periole X.; Allen L.R.; Tamiola K.; Mark A.E.; Paci E., Probing the free energy landscape of the FBP28 WW domain using multiple techniques, «JOURNAL OF COMPUTATIONAL CHEMISTRY», 2009, 30, pp. 1059 - 1068 [articolo]
Rose R.J.; Welsh T.S.; Waksman G.; Ashcroft A.E.; Radford S.E.; Paci E., Donor-Strand Exchange in Chaperone-Assisted Pilus Assembly Revealed in Atomic Detail by Molecular Dynamics, «JOURNAL OF MOLECULAR BIOLOGY», 2008, 375, pp. 908 - 919 [articolo]
Yew Z.T.; Krivov S.; Paci E., Free-energy landscapes of proteins in the presence and absence of force, «JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL», 2008, 112, pp. 16902 - 16907 [articolo]
Caflisch A.; Paci E., Molecular Dynamics Simulations to Study Protein Folding and Unfolding, in: Protein Folding Handbook., Weinheim, WILEY-VCH Verlag GmbH & Co, 2008, pp. 1143 - 1169 [capitolo di libro]
Yew Z.T.; McLeish T.; Paci E., New dynamical window onto the landscape for forced protein unfolding, «PHYSICAL REVIEW LETTERS», 2008, 101, Article number: 248104, pp. 1 - 4 [articolo]
Best R.B.; Paci E.; Hummer G.; Dudko O.K., Pulling direction as a reaction coordinate for the mechanical unfolding of single molecules, «JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL», 2008, 112, pp. 5968 - 5976 [articolo]
Feige M.J.; Paci E., Rate of Loop Formation in Peptides: A Simulation Study, «JOURNAL OF MOLECULAR BIOLOGY», 2008, 382, pp. 556 - 565 [articolo]
Verger D.; Rose R.J.; Paci E.; Costakes G.; Daviter T.; Hultgren S.; Remaut H.; Ashcroft A.E.; Radford S.E.; Waksman G., Structural Determinants of Polymerization Reactivity of the P pilus Adaptor Subunit PapF, «STRUCTURE», 2008, 16, pp. 1724 - 1731 [articolo]
Feige M.J.; Groscurth S.; Marcinowski M.; Zu T.Y.; Truffault V.; Paci E.; Kessler H.; Buchner J., The structure of a folding intermediate provides insight into differences in immunoglobulin amyloidogenicity, «PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA», 2008, 105, pp. 13373 - 13378 [articolo]
