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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