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Zhirong Liu - Publications

Affiliations: 
Physical Chemistry Peking University, Beijing, Beijing Shi, China 
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47 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
2020 Huang Q, Li M, Lai L, Liu Z. Allostery of multidomain proteins with disordered linkers. Current Opinion in Structural Biology. 62: 175-182. PMID 32151887 DOI: 10.1016/J.Sbi.2020.01.017  0.327
2019 Yu M, Chen Y, Wang ZL, Liu Z. Fluctuation correlations as major determinants of structure- and dynamics-driven allosteric effects. Physical Chemistry Chemical Physics : Pccp. PMID 30775734 DOI: 10.1039/C8Cp07859A  0.311
2018 Xiong J, Gao M, Zhou J, Liu S, Su Z, Liu Z, Huang Y. The influence of intrinsic folding mechanism of an unfolded protein on the coupled folding-binding process during target recognition. Proteins. PMID 30520528 DOI: 10.1002/Prot.25646  0.386
2018 Zhang L, Li M, Liu Z. A comprehensive ensemble model for comparing the allosteric effect of ordered and disordered proteins. Plos Computational Biology. 14: e1006393. PMID 30507941 DOI: 10.1371/Journal.Pcbi.1006393  0.33
2018 Yu M, Ma X, Cao H, Chong B, Lai L, Liu Z. Singular value decomposition for the correlation of atomic fluctuations with arbitrary angle. Proteins. PMID 30019778 DOI: 10.1002/Prot.25586  0.321
2018 Li M, Cao H, Lai L, Liu Z. Disordered linkers in mutli-domain allosteric proteins: entropic effect to favor the open state or enhanced local concentration to favor the closed state? Protein Science : a Publication of the Protein Society. PMID 30019371 DOI: 10.1002/Pro.3475  0.345
2018 Wang Z, Liu Z, Huang Z. Angle-adjustable density field formulation for the modeling of crystalline microstructure Physical Review B. 97. DOI: 10.1103/Physrevb.97.180102  0.306
2017 Zhang X, Tan D, Li Q, Li M, Gong Z, Tang C, Liu Z, Dong MQ, Lei X, Wang JH. Carboxylate-Selective Chemical Cross-Linkers for Mass Spectrometric Analysis of Protein Structures. Analytical Chemistry. PMID 29251911 DOI: 10.1021/Acs.Analchem.7B03789  0.332
2016 Li M, Sun T, Jin F, Yu D, Liu Z. Dimension conversion and scaling of disordered protein chains. Molecular Biosystems. PMID 27440558 DOI: 10.1039/C6Mb00415F  0.391
2016 Chan HS, Liu Z. Thermodynamics and kinetics of TopoII action: A consensus on T-segment curvature selection? Comment on "Disentangling DNA Molecules" by Alexander Vologodskii. Physics of Life Reviews. PMID 27265508 DOI: 10.1016/J.Plrev.2016.05.016  0.559
2016 Cao H, Huang Y, Liu Z. Interplay between binding affinity and kinetics in protein-protein interactions. Proteins. PMID 27018856 DOI: 10.1002/Prot.25041  0.392
2016 Yu C, Niu X, Jin F, Liu Z, Jin C, Lai L. Structure-based Inhibitor Design for the Intrinsically Disordered Protein c-Myc. Scientific Reports. 6: 22298. PMID 26931396 DOI: 10.1038/Srep22298  0.317
2015 Li M, Liu Z. Dimensions, energetics and denaturant effects of the protein unstructured state. Protein Science : a Publication of the Protein Society. PMID 26683260 DOI: 10.1002/Pro.2865  0.413
2015 Liu Z, Chan HS. Consistent rationalization of type-2 topoisomerases' unknotting, decatenating, supercoil-relaxing actions and their scaling relation. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 27: 354103. PMID 26291958 DOI: 10.1088/0953-8984/27/35/354103  0.59
2015 Zhang Y, Cao H, Liu Z. Binding cavities and druggability of intrinsically disordered proteins. Protein Science : a Publication of the Protein Society. 24: 688-705. PMID 25611056 DOI: 10.1002/Pro.2641  0.372
2015 Huang H, Liu Z, Zhang H, Duan W, Vanderbilt D. Emergence of a Chern-insulating state from a semi-Dirac dispersion Physical Review B - Condensed Matter and Materials Physics. 92. DOI: 10.1103/Physrevb.92.161115  0.325
2015 Liu Z, Chan HS. Erratum: Consistent rationalization of type-2 topoisomerases’ unknotting, decatenating, supercoil-relaxing actions and their scaling relation (2015J. Phys.: Condens. Matter27354103) Journal of Physics: Condensed Matter. 27: 459601. DOI: 10.1088/0953-8984/27/45/459601  0.539
2014 Liu Z, Huang Y. Advantages of proteins being disordered. Protein Science : a Publication of the Protein Society. 23: 539-50. PMID 24532081 DOI: 10.1002/Pro.2443  0.38
2013 Jia C, Wang J, Yao C, Cao Y, Zhong Y, Liu Z, Liu Z, Guo X. Conductance switching and mechanisms in single-molecule junctions. Angewandte Chemie (International Ed. in English). 52: 8666-70. PMID 23818452 DOI: 10.1002/Anie.201304301  0.306
2013 Jin F, Liu Z. Inherent relationships among different biophysical prediction methods for intrinsically disordered proteins Biophysical Journal. 104: 488-495. PMID 23442871 DOI: 10.1016/J.Bpj.2012.12.012  0.322
2013 Huang Y, Liu Z. Do intrinsically disordered proteins possess high specificity in protein-protein interactions? Chemistry (Weinheim An Der Bergstrasse, Germany). 19: 4462-7. PMID 23436397 DOI: 10.1002/Chem.201203100  0.379
2013 Liu Z, Huang Y. Evidences for the unfolding mechanism of three-dimensional domain swapping. Protein Science : a Publication of the Protein Society. 22: 280-6. PMID 23238853 DOI: 10.1002/Pro.2209  0.367
2013 Huang H, Duan W, Liu Z. The existence/absence of Dirac cones in graphynes New Journal of Physics. 15: 023004. DOI: 10.1088/1367-2630/15/2/023004  0.308
2012 Staneva I, Huang Y, Liu Z, Wallin S. Binding of two intrinsically disordered peptides to a multi-specific protein: a combined Monte Carlo and molecular dynamics study. Plos Computational Biology. 8: e1002682. PMID 23028280 DOI: 10.1371/Journal.Pcbi.1002682  0.729
2012 Huang Y, Cao H, Liu Z. Three-dimensional domain swapping in the protein structure space. Proteins. 80: 1610-9. PMID 22411444 DOI: 10.1002/Prot.24055  0.324
2011 Huang Y, Liu Z. Anchoring intrinsically disordered proteins to multiple targets: lessons from N-terminus of the p53 protein. International Journal of Molecular Sciences. 12: 1410-30. PMID 21541066 DOI: 10.3390/Ijms12021410  0.41
2011 Chan HS, Zhang Z, Wallin S, Liu Z. Cooperativity, local-nonlocal coupling, and nonnative interactions: principles of protein folding from coarse-grained models. Annual Review of Physical Chemistry. 62: 301-26. PMID 21453060 DOI: 10.1146/Annurev-Physchem-032210-103405  0.765
2011 Huang Y, Liu Z. Smoothing molecular interactions: the "kinetic buffer" effect of intrinsically disordered proteins. Proteins. 78: 3251-9. PMID 20949632 DOI: 10.1002/Prot.22820  0.376
2010 Huang Y, Liu Z. Nonnative interactions in coupled folding and binding processes of intrinsically disordered proteins. Plos One. 5: e15375. PMID 21079758 DOI: 10.1371/Journal.Pone.0015375  0.386
2010 Lin J, Wang N, Li Y, Liu Z, Tian S, Zhao L, Zheng Y, Liu S, Li S, Jin C, Xia B. LEC-BiFC: a new method for rapid assay of protein interaction. Biotechnic & Histochemistry : Official Publication of the Biological Stain Commission. 86: 272-9. PMID 20465514 DOI: 10.3109/10520295.2010.483068  0.313
2010 Liu Z, Zechiedrich L, Chan HS. Action at hooked or twisted-hooked DNA juxtapositions rationalizes unlinking preference of type-2 topoisomerases. Journal of Molecular Biology. 400: 963-82. PMID 20460130 DOI: 10.1016/J.Jmb.2010.05.007  0.603
2010 Liu Z, Zechiedrich L, Chan HS. Local site preference rationalizes disentangling by DNA topoisomerases. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 81: 031902. PMID 20365765 DOI: 10.1103/Physreve.81.031902  0.578
2010 Qi Y, Huang Y, Liang H, Liu Z, Lai L. Folding simulations of a de novo designed protein with a betaalphabeta fold. Biophysical Journal. 98: 321-9. PMID 20338854 DOI: 10.1016/J.Bpj.2009.10.018  0.381
2010 Ferguson A, Liu Z, Chan HS. Desolvation Barrier Effects Are a Likely Contributor to the Remarkable Diversity in the Folding Rates of Small Proteins [J. Mol. Biol. (2009) 389, 619–636] Journal of Molecular Biology. 401: 153. DOI: 10.1016/J.Jmb.2010.06.020  0.593
2009 Huang Y, Liu Z. Kinetic advantage of intrinsically disordered proteins in coupled folding-binding process: a critical assessment of the "fly-casting" mechanism. Journal of Molecular Biology. 393: 1143-59. PMID 19747922 DOI: 10.1016/J.Jmb.2009.09.010  0.391
2009 Ferguson A, Liu Z, Chan HS. Desolvation barrier effects are a likely contributor to the remarkable diversity in the folding rates of small proteins. Journal of Molecular Biology. 389: 619-36. PMID 19362564 DOI: 10.1016/J.Jmb.2009.04.011  0.659
2009 Liu Z, Deibler RW, Chan HS, Zechiedrich L. The why and how of DNA unlinking. Nucleic Acids Research. 37: 661-71. PMID 19240147 DOI: 10.1093/Nar/Gkp041  0.553
2009 Liu Z, Chan HS. Erratum: “Efficient chain moves for Monte Carlo simulations of a wormlike DNA model: Excluded volume, supercoils, site juxtapositions, knots, and comparisons with random-flight and lattice models” [J. Chem. Phys. 128, 145104 (2008)] The Journal of Chemical Physics. 131: 049902. DOI: 10.1063/1.3187933  0.59
2009 Ferguson A, Liu Z, Chan HS. Addendum to “Desolvation Barrier Effects Are a Likely Contributor to the Remarkable Diversity in the Folding Rates of Small Proteins” [J. Mol. Biol. 389 (2009) 619–636] Journal of Molecular Biology. 392: 242. DOI: 10.1016/J.Jmb.2009.07.011  0.608
2009 Badasyan A, Liu Z, Chan HS. Interplaying roles of native topology and chain length in marginally cooperative and noncooperative folding of small protein fragments International Journal of Quantum Chemistry. 109: 3482-3499. DOI: 10.1002/Qua.22272  0.776
2008 Badasyan A, Liu Z, Chan HS. Probing possible downhill folding: native contact topology likely places a significant constraint on the folding cooperativity of proteins with approximately 40 residues. Journal of Molecular Biology. 384: 512-30. PMID 18823994 DOI: 10.1016/J.Jmb.2008.09.023  0.78
2008 Liu Z, Chan HS. Efficient chain moves for Monte Carlo simulations of a wormlike DNA model: excluded volume, supercoils, site juxtapositions, knots, and comparisons with random-flight and lattice models. The Journal of Chemical Physics. 128: 145104. PMID 18412482 DOI: 10.1063/1.2899022  0.623
2006 Liu Z, Mann JK, Zechiedrich EL, Chan HS. Topological Information Embodied in Local Juxtaposition Geometry Provides a Statistical Mechanical Basis for Unknotting by Type-2 DNA Topoisomerases Journal of Molecular Biology. 361: 268-285. PMID 16842819 DOI: 10.1016/J.Jmb.2006.06.005  0.622
2006 Liu Z, Zechiedrich EL, Chan HS. Inferring global topology from local juxtaposition geometry: interlinking polymer rings and ramifications for topoisomerase action. Biophysical Journal. 90: 2344-55. PMID 16537549 DOI: 10.1529/Biophysj.105.076778  0.605
2005 Liu Z, Chan HS. Solvation and desolvation effects in protein folding: native flexibility, kinetic cooperativity and enthalpic barriers under isostability conditions. Physical Biology. 2: S75-85. PMID 16280624 DOI: 10.1088/1478-3975/2/4/S01  0.65
2005 Liu Z, Chan HS. Desolvation is a likely origin of robust enthalpic barriers to protein folding. Journal of Molecular Biology. 349: 872-89. PMID 15893325 DOI: 10.1016/J.Jmb.2005.03.084  0.638
2005 Kaya H, Liu Z, Chan HS. Chevron behavior and isostable enthalpic barriers in protein folding: successes and limitations of simple Gō-like modeling. Biophysical Journal. 89: 520-35. PMID 15863486 DOI: 10.1529/Biophysj.104.057471  0.753
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