S. Piana

发表

Supporting Online Material Materials and Methods Figs. S1 to S10 Table S1 References Movies S1 to S3 Atomic-level Characterization of the Structural Dynamics of Proteins

Joseph A. Bank, J. A. Bank, R. Dror, 2022 .

Improved side-chain torsion potentials for the Amber ff99SB protein force field

R. Dror, K. Lindorff-Larsen, D. Shaw, 2010, Proteins.

Assessment of the utility of contact‐based restraints in accelerating the prediction of protein structure using molecular dynamics simulations

D. Shaw, S. Piana, M. Eastwood, 2015, Protein science : a publication of the Protein Society.

How Fast-Folding Proteins Fold

R. Dror, K. Lindorff-Larsen, D. Shaw, 2011, Science.

Systematic Validation of Protein Force Fields against Experimental Data

R. Dror, K. Lindorff-Larsen, D. Shaw, 2012, PloS one.

RNA force field with accuracy comparable to state-of-the-art protein force fields

Robert M. Dirks, D. Shaw, S. Piana, 2018, Proceedings of the National Academy of Sciences.

Evaluating the Effects of Cutoffs and Treatment of Long-range Electrostatics in Protein Folding Simulations

Kresten Lindorff-Larsen, Ron O. Dror, John K. Salmon, 2012, PloS one.

Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease.

Michele Parrinello, Paolo Carloni, M. Parrinello, 2002, Journal of molecular biology.

Drug resistance in HIV‐1 protease: Flexibility‐assisted mechanism of compensatory mutations

Ursula Rothlisberger, Paolo Carloni, S. Piana, 2002, Protein science : a publication of the Protein Society.

Structure and energy of a DNA dodecamer under tensile load

S. Piana, 2005, Nucleic acids research.

How robust are protein folding simulations with respect to force field parameterization?

K. Lindorff-Larsen, D. Shaw, S. Piana, 2011, Biophysical journal.

Insights On Protein Structure And Dynamics From Multiple Biased Molecular Dynamics Simulations

A. Laio, S. Piana, F. Marinelli, 2009 .

Picosecond to Millisecond Structural Dynamics in Human Ubiquitin.

K. Lindorff-Larsen, D. Shaw, P. Maragakis, 2016, The journal of physical chemistry. B.

Atomic-level description of ubiquitin folding

K. Lindorff-Larsen, D. Shaw, S. Piana, 2013, Proceedings of the National Academy of Sciences.

Structure and dynamics of an unfolded protein examined by molecular dynamics simulation.

K. Lindorff-Larsen, D. Shaw, P. Maragakis, 2012, Journal of the American Chemical Society.

A bias-exchange approach to protein folding.

A. Laio, S. Piana, 2007, The journal of physical chemistry. B.

Water dispersion interactions strongly influence simulated structural properties of disordered protein states.

Paul Robustelli, D. Shaw, S. Piana, 2015, The journal of physical chemistry. B.

Computational design and experimental testing of the fastest-folding β-sheet protein.

M. Gruebele, K. Lindorff-Larsen, D. Shaw, 2011, Journal of molecular biology.

Developing a molecular dynamics force field for both folded and disordered protein states

Paul Robustelli, D. Shaw, S. Piana, 2018, Proceedings of the National Academy of Sciences.

Predicting the effect of a point mutation on a protein fold: the villin and advillin headpieces and their Pro62Ala mutants.

A. Laio, S. Piana, C. Ampe, 2008, Journal of molecular biology.

Exploring the folding free energy landscape of insulin using bias exchange metadynamics.

S. Piana, F. Marinelli, I. Yarovsky, 2009, The journal of physical chemistry. B.

The mechanism of coupled folding-upon-binding of an intrinsically disordered protein

Paul Robustelli, D. Shaw, S. Piana, 2020, bioRxiv.

Identification of two distinct inactive conformations of the β2-adrenergic receptor reconciles structural and biochemical observations

Ron O Dror, R. Dror, M. Jensen, 2009, Proceedings of the National Academy of Sciences.

Millisecond-scale molecular dynamics simulations on Anton

J. P. Grossman, Joseph A. Bank, Martin M. Deneroff, 2009, Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis.

Hybrid QM/MM Car—Parrinello Simulations of Catalytic and Enzymatic Reactions

A. Laio, S. Piana, J. VandeVondele, 2010 .

Understanding the Kinetics of Barium Sulfate Precipitation from Water and Water–Methanol Solutions

S. Piana, J. Gale, F. Jones, 2008 .

Millisecond-scale molecular dynamics simulations on Anton

J. P. Grossman, Joseph A. Bank, Martin M. Deneroff, 2009, Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis.

Assessment of Pollutants in Wet and Dry Depositions in a Suburban Area around a Waste-to-Energy Plant (WEP) in Northern Italy

S. Piana, F. Ventura, L. V. Antisari, 2013 .

Climate change effects on bread wheat phenology and grain quality: A case study in the north of Italy

S. Piana, M. Naldi, J. Fiori, 2022, Frontiers in Plant Science.

Development of Force Field Parameters for the Simulation of Single- and Double-Stranded DNA Molecules and DNA–Protein Complexes

Michael V. LeVine, D. Shaw, S. Piana, 2022, The journal of physical chemistry. B.

Assisted desolvation as a key kinetic step for crystal growth.

S. Piana, J. Gale, F. Jones, 2006, Journal of the American Chemical Society.

Understanding the barriers to crystal growth: dynamical simulation of the dissolution and growth of urea from aqueous solution.

S. Piana, J. Gale, 2005, Journal of the American Chemical Society.

The effects of biochar on the physical properties of bare soil

S. Piana, L. Pieri, F. Ventura, 2012, Earth and Environmental Science Transactions of the Royal Society of Edinburgh.

The mechanism of catalytic enantioselective fluorination: computational and experimental studies.

S. Piana, U. Rothlisberger, A. Togni, 2002, Angewandte Chemie.

Hybrid Car-Parrinello/molecular mechanics modelling of transition metal complexes: Structure, dynamics and reactivity

S. Piana, U. Rothlisberger, P. Maurer, 2002 .

Simulating micrometre-scale crystal growth from solution

S. Piana, J. Gale, M. Reyhani, 2005, Nature.

PNAS201713027 1..10

Robert M. Dirks, D. Shaw, S. Piana, 2018 .

Aspartic acid as a crystal growth catalyst

S. Piana, J. Gale, F. Jones, 2007 .

The nature of the adsorption of nucleobases on the gold [111] surface.

S. Piana, A. Bilić, 2006, The journal of physical chemistry. B.

Folding pathways for initiator and effector procaspases from computer simulations

S. Piana, U. Rothlisberger, Zoe Taylor, 2005, Proteins.

Identifying localized changes in large systems: Change-point detection for biomolecular simulations

Stefano Piana, Ron O Dror, David E Shaw, 2015, Proceedings of the National Academy of Sciences.

A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations

Alessandro Laio, Fabio Pietrucci, Stefano Piana, 2009, PLoS Comput. Biol..

Protonation States of Methionine Aminopeptidase and Their Relevance for Inhibitor Binding and Catalytic Activity*

S. Piana, G. Folkers, C. Klein, 2003, Journal of Biological Chemistry.

Structure-based thermodynamic analysis of caspases reveals key residues for dimerization and activity.

S. Piana, U. Rothlisberger, M. Sulpizi, 2003, Biochemistry.

The mechanism of coupled folding-upon-binding of an intrinsically disordered protein.

Paul Robustelli, D. Shaw, S. Piana, 2020, Journal of the American Chemical Society.

Refinement of protein structure homology models via long, all‐atom molecular dynamics simulations

Stefano Piana, Alpan Raval, Michael P Eastwood, 2012, Proteins.

Atomic-Level Description of Protein Folding inside the GroEL Cavity.

D. Shaw, S. Piana, 2018, The journal of physical chemistry. B.

Protein folding kinetics and thermodynamics from atomistic simulation

Kresten Lindorff-Larsen, K. Lindorff-Larsen, D. Shaw, 2012, Proceedings of the National Academy of Sciences.

Conformational flexibility of the catalytic Asp dyad in HIV‐1 protease: An ab initio study on the free enzyme

Paolo Carloni, S. Piana, P. Carloni, 2000, Proteins.

Demonstrating an Order-of-Magnitude Sampling Enhancement in Molecular Dynamics Simulations of Complex Protein Systems.

Stefano Piana, David E Shaw, Albert C Pan, 2016, Journal of chemical theory and computation.

Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations.

Stefano Piana, David E Shaw, John L Klepeis, 2014, Current opinion in structural biology.

Atomistic description of the folding of a dimeric protein.

Kresten Lindorff-Larsen, K. Lindorff-Larsen, D. Shaw, 2013, The journal of physical chemistry. B.

Field examination of the hydrological behaviour of a typical vertisol in a cropped area

S. Piana, A. Guarnieri, L. Cavazza, 2013 .

Development of a force field for the simulation of single-chain proteins and protein-protein complexes.

Paul Robustelli, D. Shaw, S. Piana, 2020, Journal of chemical theory and computation.

Ab initio molecular dynamics-based assignment of the protonation state of pepstatin A/HIV-1 protease cleavage site.

M. Parrinello, S. Piana, P. Carloni, 2001, Journal of the American Chemical Society.

Molecular dynamics simulations of structural changes during procaspase 3 activation

S. Piana, U. Rothlisberger, 2004, Proteins.

Interaction Networks in Protein Folding via Atomic-Resolution Experiments and Long-Time-Scale Molecular Dynamics Simulations

Kresten Lindorff-Larsen, Victor Muñoz, Clara M. Santiveri, 2015, Journal of the American Chemical Society.

Three-dimensional kinetic Monte Carlo simulation of crystal growth from solution

S. Piana, J. Gale, 2006 .

Atomic-Level Characterization of the Structural Dynamics of Proteins

Joseph A. Bank, J. A. Bank, R. Dror, 2010, Science.

Automated Event Detection and Activity Monitoring in Long Molecular Dynamics Simulations.

Stefano Piana, Willy Wriggers, Michael P Eastwood, 2009, Journal of chemical theory and computation.

Atomic-Level Characterization of the Structural Dynamics of Proteins

Joseph A. Bank, R. Dror, J. Salmon, 2010, Science.

Reaction Mechanism of HIV-1 Protease by Hybrid Car-Parrinello/Classical MD Simulations

Ursula Rothlisberger, Paolo Carloni, S. Piana, 2004 .

Atomistic description of the folding of a dimeric protein.

K. Lindorff-Larsen, D. Shaw, S. Piana, 2013, The journal of physical chemistry. B.

Evaluating the Effects of Cutoffs and Treatment of Long-range Electrostatics in Protein Folding Simulations

Robert M. Dirks, R. Dror, J. Salmon, 2012, PloS one.