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Demian Riccardi, Ph.D. - Publications

Affiliations: 
2006 University of Wisconsin, Madison, Madison, WI 
Area:
computational chemistry and biophysics
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21 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Fobe TL, Kazakov A, Riccardi D. Cys.sqlite: A Structured-Information Approach to the Comprehensive Analysis of Cysteine Disulfide Bonds in the Protein Databank. Journal of Chemical Information and Modeling. PMID 30694665 DOI: 10.1021/Acs.Jcim.8B00950  0.313
2019 Asaduzzaman A, Riccardi D, Afaneh AT, Cooper SJ, Smith JC, Wang F, Parks JM, Schreckenbach G. Environmental Mercury Chemistry - In Silico. Accounts of Chemical Research. PMID 30689347 DOI: 10.1021/Acs.Accounts.8B00454  0.355
2017 Velazquez HA, Riccardi D, Xiao Z, Quarles LD, Yates CR, Baudry J, Smith JC. Ensemble Docking to Difficult Targets in Early-Stage Drug Discovery: Methodology and Application to Fibroblast Growth Factor 23. Chemical Biology & Drug Design. PMID 28944571 DOI: 10.1111/Cbdd.13110  0.312
2014 Lian P, Guo HB, Riccardi D, Dong A, Parks JM, Xu Q, Pai EF, Miller SM, Wei DQ, Smith JC, Guo H. 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. Biochemistry. 53: 7211-22. PMID 25343681 DOI: 10.1021/Bi500608U  0.347
2013 Riccardi D, Guo HB, Parks JM, Gu B, Liang L, Smith JC. Cluster-Continuum Calculations of Hydration Free Energies of Anions and Group 12 Divalent Cations. Journal of Chemical Theory and Computation. 9: 555-69. PMID 26589054 DOI: 10.1021/Ct300296K  0.393
2013 Riccardi D, Guo HB, Parks JM, Gu B, Summers AO, Miller SM, Liang L, Smith JC. Why mercury prefers soft ligands Journal of Physical Chemistry Letters. 4: 2317-2322. DOI: 10.1021/Jz401075B  0.355
2012 Riccardi D, Zhu X, Goyal P, Yang S, Hou G, Cui Q. Toward molecular models of proton pumping: Challenges, methods and relevant applications Science China Chemistry. 55: 3-18. DOI: 10.1007/S11426-011-4458-9  0.667
2010 Riccardi D, Cui Q, Phillips GN. Evaluating elastic network models of crystalline biological molecules with temperature factors, correlated motions, and diffuse X-ray scattering Biophysical Journal. 99: 2616-2625. PMID 20959103 DOI: 10.1016/J.Bpj.2010.08.013  0.446
2010 Riccardi D, Yang S, Cui Q. Proton transfer function of carbonic anhydrase: Insights from QM/MM simulations Biochimica Et Biophysica Acta - Proteins and Proteomics. 1804: 342-351. PMID 19679196 DOI: 10.1016/J.Bbapap.2009.07.026  0.572
2009 Capp MW, Pegram LM, Saecker RM, Kratz M, Riccardi D, Wendorff T, Cannon JG, Record MT. Interactions of the osmolyte glycine betaine with molecular surfaces in water: thermodynamics, structural interpretation, and prediction of m-values. Biochemistry. 48: 10372-9. PMID 19757837 DOI: 10.1021/Bi901273R  0.367
2009 Riccardi D, Cui Q, Phillips GN. Application of elastic network models to proteins in the crystalline state. Biophysical Journal. 96: 464-75. PMID 19167297 DOI: 10.1016/J.Bpj.2008.10.010  0.482
2009 Riccardi D, Cui Q, Phillips GN. Application of elastic network models to proteins in the crystalline state (Biophysical Journal (2009) 96, (464-475)) Biophysical Journal. 96: 2548. DOI: 10.1016/j.bpj.2009.02.007  0.369
2008 Riccardi D, König P, Guo H, Cui Q. Proton transfer in carbonic anhydrase is controlled by electrostatics rather than the orientation of the acceptor. Biochemistry. 47: 2369-78. PMID 18247480 DOI: 10.1021/Bi701950J  0.586
2007 Riccardi D, Cui Q. pK a analysis for the zinc-bound water in human carbonic anhydrase II: Benchmark for "multiscale" QM/MM simulations and mechanistic implications Journal of Physical Chemistry A. 111: 5703-5711. PMID 17506534 DOI: 10.1021/Jp070699W  0.547
2006 Riccardi D, König P, Prat-Resina X, Yu H, Elstner M, Frauenheim T, Cui Q. "Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis. Journal of the American Chemical Society. 128: 16302-11. PMID 17165785 DOI: 10.1021/Ja065451J  0.62
2006 Riccardi D, Schaefer P, Yang Y, Yu H, Ghosh N, Prat-Resina X, König P, Li G, Xu D, Guo H, Elstner M, Cui Q. Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes. The Journal of Physical Chemistry. B. 110: 6458-69. PMID 16570942 DOI: 10.1021/Jp056361O  0.673
2005 Riccardi D, Schaefer P, Cui Q. PK a calculations in solution and proteins with QM/MM free energy perturbation simulations: A quantitative test of QM/MM protocols Journal of Physical Chemistry B. 109: 17715-17733. PMID 16853267 DOI: 10.1021/Jp0517192  0.579
2005 Range K, Riccardi D, Cui Q, Elstner M, York DM. Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer. Physical Chemistry Chemical Physics : Pccp. 7: 3070-9. PMID 16186912 DOI: 10.1039/B504941E  0.541
2005 Schaefer P, Riccardi D, Cui Q. Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules. The Journal of Chemical Physics. 123: 014905. PMID 16035867 DOI: 10.1063/1.1940047  0.543
2004 Riccardi D, Li G, Cui Q. Importance of van der Waals Interactions in QM/MM Simulations. The Journal of Physical Chemistry. B. 108: 6467-78. PMID 18950136 DOI: 10.1021/Jp037992Q  0.537
2002 Grabowski P, Riccardi D, Gomez MA, Asthagiri D, Pratt LR. Quasi-chemical theory and the standard free energy of H+(aq) Journal of Physical Chemistry A. 106: 9145-9148. DOI: 10.1021/Jp026291A  0.359
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