D. Riccardi

发表

Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes.

Guohui Li, Q. Cui, Hua Guo, 2006, The journal of physical chemistry. B.

pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols.

Q. Cui, D. Riccardi, P. Schaefer, 2005, The journal of physical chemistry. B.

Proton transfer in carbonic anhydrase is controlled by electrostatics rather than the orientation of the acceptor.

Hua Guo, Qiang Cui, Q. Cui, 2008, Biochemistry.

Ensemble docking to difficult targets in early‐stage drug discovery: Methodology and application to fibroblast growth factor 23

Jeremy C. Smith, J. Baudry, D. Riccardi, 2018, Chemical biology & drug design.

A computationally identified compound antagonizes excess FGF-23 signaling in renal tubules and a mouse model of hypophosphatemia

Jeremy C. Smith, J. Baudry, D. Riccardi, 2016, Science Signaling.

Validation of thermophysical data for scientific and engineering applications.

D. Riccardi, V. Diky, E. Paulechka, 2019, The Journal of chemical thermodynamics.

Survey of Data and Models for Refrigerant Mixtures Containing Halogenated Olefins.

D. Riccardi, I. Bell, M. McLinden, 2021, Journal of chemical and engineering data.

Environmental Mercury Chemistry - In Silico.

Sarah J. Cooper, Jerry M. Parks, Jeremy C. Smith, 2019, Accounts of chemical research.

Corrections to standard state in combustion calorimetry: an update and a web-based tool.

D. Riccardi, E. Paulechka, M. D. R. D. Silva, 2021, The Journal of chemical thermodynamics.

Toward molecular models of proton pumping: Challenges, methods and relevant applications

Q. Cui, Xiao Zhu, D. Riccardi, 2012, Science China Chemistry.

Proton transfer function of carbonic anhydrase: Insights from QM/MM simulations.

Q. Cui, D. Riccardi, Shuo Yang, 2010, Biochimica et biophysica acta.

Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer.

D. York, Q. Cui, D. Riccardi, 2005, Physical chemistry chemical physics : PCCP.

Why Mercury Prefers Soft Ligands

Jerry M. Parks, Jeremy C. Smith, D. Riccardi, 2013 .

Interactions of the osmolyte glycine betaine with molecular surfaces in water: thermodynamics, structural interpretation, and prediction of m-values.

Megan B. Kratz, D. Riccardi, M. Record, 2009, Biochemistry.

X-ray Structure of a Hg2+ Complex of Mercuric Reductase (MerA) and Quantum Mechanical/Molecular Mechanical Study of Hg2+ Transfer between the C-Terminal and Buried Catalytic Site Cysteine Pairs

Dong-Qing Wei, Hao-Bo Guo, Jerry M. Parks, 2014, Biochemistry.

Mercury methylation by HgcA: theory supports carbanion transfer to Hg(II).

Jerry M. Parks, Jeremy C. Smith, Jeremy C Smith, 2014, Inorganic chemistry.

Cys.sqlite: A Structured-Information Approach to the Comprehensive Analysis of Cysteine Disulfide Bonds in the Protein Databank

Theodore L Fobe, Andrei Kazakov, Demian Riccardi, 2019, J. Chem. Inf. Model..

Towards improved FAIRness of the ThermoML Archive

D. Riccardi, V. Diky, E. Paulechka, 2022, J. Comput. Chem..

Activation loop plasticity and active site coupling in the MAP kinase, ERK2

D. Riccardi, L. Pegram, Natalie Ahn, 2023, bioRxiv.

HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales

Jeremy C. Smith, Jerry M. Parks, Demian Riccardi, 2015, J. Chem. Inf. Model..

Cluster-Continuum Calculations of Hydration Free Energies of Anions and Group 12 Divalent Cations.

Jerry M. Parks, Jeremy C. Smith, D. Riccardi, 2013, Journal of chemical theory and computation.

Quasi-Chemical Theory and the Standard Free Energy of H+(aq)

L. Pratt, D. Riccardi, P. Grabowski, 2002 .

Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules.

Qiang Cui, Q. Cui, D. Riccardi, 2005, The Journal of chemical physics.

Importance of van der Waals Interactions in QM/MM Simulations.

Qiang Cui, Guohui Li, Q. Cui, 2004, The journal of physical chemistry. B.

"Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis.

Thomas Frauenheim, Xavier Prat-Resina, Marcus Elstner, 2006, Journal of the American Chemical Society.

Evaluating elastic network models of crystalline biological molecules with temperature factors, correlated motions, and diffuse x-ray scattering.

George N Phillips, Qiang Cui, G. Phillips, 2010, Biophysical journal.

Highly mechanosensitive ion channels from graphene-embedded crown ethers

A. Smolyanitsky, D. Riccardi, K. Kroenlein, 2018, Nature Materials.

pKa analysis for the zinc-bound water in human carbonic anhydrase II: Benchmark for "multiscale" QM/MM simulations and mechanistic implications.

Qiang Cui, Q. Cui, D. Riccardi, 2007, The journal of physical chemistry. A.

Proton transfer in carbonic anhydrase is controlled by electrostatics rather than the orientation of the acceptor.

Q. Cui, Hua Guo, D. Riccardi, 2008, Biochemistry.

Application of elastic network models to proteins in the crystalline state.

George N Phillips, Qiang Cui, G. Phillips, 2009, Biophysical journal.