Zhou Lab Publications
Dr. Yaoqi Zhou's Publications

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129
B.-R. Zhou, H. Feng, H. Kato, L. Dai, Y. Yang, Y. Zhou and Y. Bai, "Structural insights into the histone H1-nucleosome complex", Proc. Natl. Acad. Sci. (USA) in press (2013).
128
J. Wang, Y. Yang, Z. Cao, Z. Li, H. Zhao and Y. Zhou, "The role of semi-disorder in temperature adaptation of bacterial FlgM proteins", Biophys. J. in press (2013).
127
H. Zhao, Y. Yang, S. C. Janga, C. Kao, and Y. Zhou, "Prediction and validation of the unexplored RNA-binding protein atlas of the human proteome", Proteins, in press (2013). [TBA][List of >2000 Novel RBPs]

126
H. Zhao, Y. Yang and Y. Zhou, "Prediction of RNA binding proteins comes of age from low resolution to high resolution", Molecular Biosystems 9 , 2417-2425 (2013). [PDF]

125
T. Zhang, E. Faraggi, Z. Li, and Y. Zhou, "Intrinsically semi-disordered state and its role in induced folding and protein aggregation ", Cell Biochemistry & Biophys , in press (2013). [TBA]

124 DDIG-in
H. Zhao*, Y. Yang*, H. Lin, X. Zhang, M. Mort, D. N. Cooper, Y. Liu and Y. Zhou, "DDIG-in: Discriminating between disease-associated and neutral non-frameshifting micro-indels", Genome Biology 14 , R43 (2013). [PDF][DDIG-in Server ] [Disease INDEL set][Neutral INDEL set]

123
Y. Yang, H. Zhao, J. Wang, and Y. Zhou, "SPOT-Seq: Predicting protein-RNA complex structure and RNA-binding function by fold recognition and binding affinity prediction", Methods in Molecular Biology (Protein Structure Prediction, 3rd Edition), Edited by D. Kihara, Accepted (2013). [TBA]
122
Z. Li, Y. Yang, J. Zhan, L. Dai and Y. Zhou, "Energy Functions in De Novo Protein Design: Current Challenges and Future Prospects", Ann. Rev. Biophysics 42, 315-335 (2013). [E-reprint PDF] [List of Proteins]

121
J. Gao, E. Faraggi, Y. Zhou, J. Ruan, and L. Kurgan, "BEST: Improved Prediction of B-Cell Epitopes from Antigen Sequences", PLoS one 7, e40104 (2012). [PDF]

120 SPalign
Y. Yang, J. Zhan, H. Zhao, and Y. Zhou, "A new size-independent score for pairwise protein structure alignment and its assessment by structure classification and nucleic-acid binding prediction", Proteins 80, 2080-2088 (2012). [PDF][SPalign Programs and Server ]

119
T. Lu*, Y. Yang*, B. Yao, S. Liu, Y. Zhou, and C. Zhang, "Template-based structure prediction and classification of transcription factors in arabidopsis thaliana.", Protein Science 21, 828-838 (2012).[PDF]

118 SPINE-D
T. Zhang*, E. Faraggi*, B. Xue, A. K. Dunker, V. N. Uversky and Y. Zhou, ``SPINE-D: Accurate prediction of short and long disordered regions by a single neural-network-based method'', J. Biomol. Struc. Dyn. 29 , 799-813 (2012). [PDF][SPINE D Server]

117 SPINE X
E. Faraggi, T. Zhang, Y. Yang, L. Kurgan and Y. Zhou, ``SPINE X: Improving protein secondary structure prediction by multi-step learning coupled with prediction of solvent accessible surface area and backbone torsion angles'', J. Comput. Chem. 33 , 259-267 (2012). [PDF][SPINE X Server]

116
S. J. Fleishman, T. A. Whitehead, E.-M. Strauch, J. E. Corn, S. Qin, H.-X. Zhou, J. C. Mitchell, O. N. Demerdash, M. Takeda-Shitaka, G. Terashi, I. H. Moal, X. Li, P. A. Bates, M. Zacharias, H. Park, J. Ko, H. Lee, C. Seok, T. Bourquard, J. Bernauer, A. Poupon, J. Aze, S. Soner, S. K. Ovali, P. Ozbek, N. Ben Tal, T. Haliloglu, H. Hwang, T. Vreven, B. G. Pierce, Z. Weng, L. Perez-Cano, C. Pons, J. Fernadez-Recio, F. Jiang, F. Yang, X. Gong, L. Cao, X. Xu, B. Liu, P. Wang, C. Li, C. Wang, C. H. Robert, M. Guharoy, S. Liu, Y. Huang, L. Li , D. Guo, Y. Chen, Y. Xiao, N. London, Z. Itzhaki, O. Schueler-Furman, Y. Inbar, V. Patapov, M. Cohen, G. Schreiber, Y. Tsuchiya, E. Kanamori, D. M. Standley, H. Nakamura, K. Kinoshita, C. M. Driggers, R. G. Hall, J. L. Morgan, V. L. Hsu, J. Zhan, Y. Yang, Y. Zhou, P. L. Kastritis, A. M. J. J. Bonvin, W. Zhang, C. J. Camacho, K. P. Kilambi, A. Sircar, J. J. Gray, M, Ohue, N. Uchikoga, Y. Matsuzaki, T. Ishida, Y. Akiyama, R. Khashan, S. Bush, D. Fouches, A. Tropsha, J. Esquivel-Rodrigez, D. Kihara, P. B. Stranges, R. Jacak, B. Kuhlman, S. Huang, X. Zou, S. J. Wodak, J. Janin, and D. Baker, "Community-wide assessment of protein-interface modeling suggests improvements to design methodology", J. Molec. Biol. 114, 289-302 (2011). [pdf]

115 SPOT
H. Zhao*, Y. Yang*, and Y. Zhou, "Highly accurate and high-resolution function prediction of RNA binding proteins by fold recognition and binding affinity prediction", RNA Biology 8, 988-996 (2011). [pdf][SPOT server for RNA-binding prediction ][RB-C174][RB-C257]

114 SPARKS X
Y. Yang, E. Faraggi, H. Zhao and Y. Zhou, ''Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of the query and corresponding native properties of templates'' Bioinformatics 27, 2076-2082 (2011). [PDF] [Journal access] [Server]
113
M. Mizianty, T. Zhang, B. Xue, Y. Zhou, A. K. Dunker, V. N. Uversky and L. Kurgan, "In-silico prediction of disorder content using hybrid sequence representation", BMC Bioinformatics 12, 245 (2011). [Open Access]

112
H. Cheng, W. S. Chan, Z. Li, D. Wang, S. Liu, Y. Zhou, "Small open reading frames: Current prediction techniques and future prospect" Current Protein and Peptide Science 12, 503-507 (2011). [PDF]

111
L. Dai and Y. Zhou, "Characterizing the existing and potential structural space of proteins by large-scale multiple loop permutations" J. Molec. Biol. 408, 585-595 (2011). [PDF] [MLP2843 database]

110 OSCAR
S. Liang, Y. Zhou, N. Grishin, and D. M. Standley, "Protein side chain modeling with orientation dependent atomic force fields derived by series expansions.", J. Comput. Chem. 32, 1680-1686 (2011). [PDF]
109 SPOT
H. Zhao*, Y. Yang*, and Y. Zhou, "Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets" Nucleic Acids Research 39, 3017-3025 (2011). [pdf][SPOT server for RNA-binding prediction ] [Dataset]

108
Y. Zhou, Y. Duan, Y. Yang, E. Faraggi, H. Lei, ``Trends in template/fragment-free protein structure prediction" (Invited feature article) Theor. Chem. Accounts 128, 3-16 (2011). [Open Access PDF]

107
T. Zhang, E. Faraggi, and Y. Zhou, ``Fluctuations of backbone torsion angles obtained from NMR-determined structures and their prediction.'' Proteins 78, 3353-3362 (2010). [PDF][SPINE XI Server]

106 SPOT
H. Zhao*, Y. Yang*, and Y. Zhou, ``Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function.'' Bioinformatics 26, 1857-1863 (2010). [PDF][SPOT server and DDNA3 energy function ]

105 RosettaDesign-SR
L. Dai*, Y. Yang*, H. Kim and Y. Zhou, ``Improving computational protein design by using structure-derived sequence profile.'' Proteins 78, 2338-2348 (2010). [PDF]

104
Y. Zhou and E. Faraggi, ``Prediction of one-dimensional structural properties of proteins by integrated neural network'' in H. Rangwala and G. Karypis (Eds.) Protein Structure Prediction: Method and Algorithms (Chapter 4, pp. 45-74), Hoboken, NJ: Wiley (2010).[PDF]

103 SPINE XI
E. Faraggi*, Y. Yang*, S. Zhang and Y. Zhou, ``Predicting continuous local structure and the effect of its substitution for secondary structure in fragment-free protein structure prediction'', Structure 17,1515-1527 (2009) [PDF] [SPINE X Server][SPINE XI Server]

102 DDNA2
B. Xu*, Y. Yang*, H. Liang and Y. Zhou, ``An all-atom knowledge-based energy function for protein-DNA threading, decoy discrimination, and prediction of transcription-factor binding profiles'', Proteins 76, 718-730 (2009) [PDF] [Corrected Table 4] [DDNA 2 Download ] [List of Protein-DNA complexes]

101 DEMPIRE
S. Liang, G. Wang, and Y. Zhou, ``Refining near-native protein-protein docking decoys by local re-sampling and energy minimization'', Proteins 76, 309--316 (2009) [PDF]

100 SPINE-2D
B. Xue, E. Faraggi, and Y. Zhou, ``Predicting residue-residue contact maps by a two-layer, integrated neural-network method.'', Proteins 76, 176-183 (2009) [SPINE-2D server ][PDF][Download] [500 Training] [500 Testing]

99
S. Liang, L. Li, W.L. Hsu, V. N. Uversky, Y. Zhou, A. K. Dunker and S. O. Meroueh, ``Exploring the molecular design of protein interaction sites with molecular dynamics and free energy calculations'', Biochemistry 48, 399-414 (2009).[PDF]

98 ENDES
S. Liang, S. O. Meroueh, Guangce Wang, Chao Qiu and Y. Zhou, ``Consensus scoring for enriching near-native structures from protein-protein docking decoys'', Proteins 75, 397-403 (2009) [ENDES download ] [ENDES download] [PDF]

97 Real-SPINE 3.0
E. Faraggi, B. Xue, and Y. Zhou, ``Improving the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins by fast guided-learning through a two-layer neural network.'', Proteins 74, 857-871 (2009) [Real-SPINE 3.0 server ][PDF] [Data Set]

96
H. Lei, C. Wu, Z. X. Wang, Y. Zhou, and Y. Duan, ``Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations'', J. Chem. Phys.128, 235105 (2008). [PDF]

95
Z. Luo, J. Ding and Y. Zhou, ``Folding mechanisms of individual beta-hairpins in a Go model of Pin1 WW domain by all-atom molecular dynamics simulations'', J. Chem. Phys. 128, 225103 (2008)[PDF]

94 SP5
W. Zhang, S. Liu and Y. Zhou, ``SP5: Improving protein fold recognition by using predicted torsion angles and profile-based gap penalty'', PLoS ONE 3, e2325 (2008)[PDF] [SP5 server] [List of Prefab pairs]

93 DFIRE2
Y. Yang and Y. Zhou, ``Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely-related all-atom statistical energy functions.'', Protein Science 17 1212-1219, (2008)[PDF] [DFIRE2]

92 dDFIRE
Y. Yang and Y. Zhou, ``Specific interactions for ab initio folding of protein terminal regions with secondary structures.'', Proteins 72, 793-803 (2008)[PDF] [dDFIRE]

91 Real-SPINE 2.0
B. Xue, O. Dor, E. Faraggi and Y. Zhou, ``Real value prediction of backbone torsion angles.'', Proteins 72, 427-433 (2008) [Real-SPINE 2.0 server ][PDF]

90 SKSP
W. Zhang, A. K. Dunker, and Y. Zhou, ``Assessing secondary-structure assignment of protein structures by using pairwise sequence-alignment benchmarks.'', Proteins 71, 61--67 (2008) [SKSP server ][PDF] [List of Prefab pairs (Table IV)]

89
Z. Luo, J. Ding, and Y. Zhou, ``Temperature-Dependent Folding Pathways of Pin1 WW Domain: An All-Atom Molecular Dynamics Simulation of a Gō Model.'', Biophys. J.93, 2152--2161 (2007) [PDF]

88 EMPIRE
S. Liang, S. Liu, C. Zhang and Y. Zhou, ``A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys.'', Proteins 69, 244--253 (2007) [PDF] [Download] Server [On the Cover]

87
Y. Chen, Y. Zhou and J. Ding, ``The helix-coil transition revisited.'', Proteins 69, 58--68 (2007) [PDF]

86 DDOMAIN
H. Zhou, B. Xue, and Y. Zhou, ``DDOMAIN: Dividing structures into domains using a normalized domain-domain interaction profile'', Protein Sci.16,947--955 (2007)[DDOMAIN server] [DDOMAIN download] [PDF]

85 SP4
S. Liu, C. Zhang, S. Liang, and Y. Zhou, ``Fold Recognition by Concurrent Use of Solvent Accessibility and Residue Depth'', Proteins68, 636--645, (2007)[SP4 Server] [PDF] [SALIGN Benchmark] [On the Cover]

84 Real-SPINE
O. Dor and Y. Zhou, ``Real-SPINE: An integrated system of neural networks for real-value prediction of protein structural properties'', Proteins 68, 76--81, (2007)[SPINE/Real-SPINE Server] [PDF]

83 SPINE
O. Dor and Y. Zhou, ``Achieving 80% ten-fold cross-validated accuracy for secondary structure prediction by large-scale training'', Proteins 66, 838--845, (2007)[SPINE Server & Downloads] [PDF]

2005-2006
82.
Y. Zhou, H. Zhou, and M. Karplus, ``Cooperativity in Scapharca dimeric hemoglobin: Simulation of binding intermediates and elucidation of the role of interfacial water'', Rend. Fis. Acc. Lincei, 17:191-211 (2006) [Reprinted from #54].

81 PINUP
S. Liang, C. Zhang, S. Liu and Y. Zhou, ``Protein binding site prediction with an empirical scoring function'', Nucl. Acids Res. 34, 3698-3707 (2006). [PINUP Server] [PINUP 64 bits downloads] [PDF]

80 MC2
C. Zhang, S. Liu and Y. Zhou, ``MC2: Identifying high-quality protein-interaction modules by clique merging'', J. Proteome Res. 5, 801--807 (2006). [MC2 Server] [PDF]

79
S. Liu, C. Zhang and Y. Zhou, ``Uneven size distribution of mammalian genes in the number of tissues expressed and in the number of co-expressed genes'', Human Molec. Genetics 15, 1313--1318 (2006) [Cover Article]. Abstract. [PDF]

78
Y. Zhou, H. Zhou, C. Zhang and S. Liu, ``What is a desirable statistical energy function for proteins and how can it be obtained?'', Cell Biochem. Biophys. 46, 165--174 (2006) [Review].[PDF]

77
Z. Xu and C. Zhang and S. Liu and Y. Zhou, ``QBES: Predicting real values of solvent accessibility from sequences by efficient, constrained energy optimization'', Proteins 63, 961--966 (2006). [PDF]

76
Z. Zhou, H. Feng, H. Zhou, Y. Zhou and Y. Bai, ``Design and folding of a multi-domain protein'', Biochemistry 44, 12107--12112 (2005). [PDF]

75 SPEM
H. Zhou and Y. Zhou, ``SPEM: Improving multiple-sequence alignment with sequence profiles and predicted secondary structures'', Bioinformatics 21, 3615--3621 (2005). [PDF] [SPEM download] [SPEM Server]

74
H. Zhou and Y. Zhou, ``SPARKS 2 and SP3 servers in CASP 6.'', Proteins (Supplement CASP issue), Suppl 7 152--156 (2005). [PDF]

73
H. Li and Y. Zhou, ``Fold helical proteins by energy minimization in dihedral space and a DFIRE-based statistical energy function'', J. Bioinfo. Comput. Biol. 3, 1151-1170 (2005). [PDF]

72
B. P. Pandey, C. Zhang, X. Yuan, J. Zi and Y. Zhou, ``Protein flexibility prediction by an all-atom mean-field statistical theory'', Protein Science 14, 1772--1777 (2005). [PDF]

71 SCUD
H. Li and Y. Zhou, ``SCUD: Fast structure clustering of decoys using reference state to remove overall rotation'', J. Comput. Chem. 26, 1189-1192 (2005). [PDF] [SCUD Server] [SCUD Download]

70
H. Zhou, C. Zhang, S. Liu, and Y. Zhou, ``Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis, and comparative analysis of domain combinations'', Nucl. Acids Res. (Server issue) 33, W193--W197 (2005). [PDF]

69
C. Zhang, S. Liu, and Y. Zhou, ``Docking prediction using biological information, ZDOCK sampling technique and clustering guided by the DFIRE statistical energy function'', Proteins (Special CAPRI issue) 60, 314--318 (2005) [Invited, Peer-reviewed Conference Paper]. [PDF]

68 DDNA
C. Zhang, S. Liu, Q. Zhu, and Y. Zhou, ``A knowledge-based energy function for protein-ligand, protein-protein and protein-DNA complexes'', J. Med. Chem. 48, 2325-2335 (2005). [PDF] [DDNA Server]

67 DOGMA
S. Liu, C. Zhang, and Y. Zhou, ``Domain Graph of Arabidopsis thaliana Proteome by comparative analysis'', J. Proteome Res. 4, 435-444 (2005). [PDF] [DOGMA Server/Database]

66 SP3 Method -- Ranked #2 in CM (SPARKS 2 as #1) and #5 in FR/H targets in 49 servers assessed at CASP6
H. Zhou, and Y. Zhou, ``Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments.'', Proteins. 58, 321-328 (2005). [PDF] [Server & Download] Independent LiveBench Performance CAFASP4 CASP6

2001-2004
65
Y. Bai, H. Zhou, and Y. Zhou, ``Critical nucleation size in the folding of small apparently two-state proteins.'', Protein Sci. 13, 1173-1181 (2004). [PDF]

64
C. Zhang, S. Liu, H. Zhou, and Y. Zhou, ``The dependence of all-atom statistical potentials on training structural database.'', Biophys. J. 86, 3349-3358 (2004). [PDF] [397 alpha proteins] [438 beta proteins]

63
C. Zhang, S. Liu, H. Zhou, and Y. Zhou, ``An accurate residue-level pair potential of mean force for folding and binding based on the distance-scaled ideal-gas reference state.'', Protein Sci. 13, 400-411 (2004). [PDF] [SCM Download]

62 -- DLOOP --
C. Zhang, S. Liu, and Y. Zhou, ``Accurate and efficient loop selections using DFIRE-based all-atom statistical potential.'', Protein Sci. 13, 391-399 (2004). [PDF] [Supplement Materials] [ Server]

61-- DCOMPLEX --
S. Liu, C. Zhang, H. Zhou, and Y. Zhou, ``A physical reference state unifies the structure-derived potential of mean force for protein folding and binding.'', Proteins 56, 93-101 (2004). [PDF] [ Server] [DCOMPLEX Download ]

60
H. Jang, C. K. Hall, and Y. Zhou, ``Thermodynamics and stability of a beta-sheet complex: Molecular dynamics simulations on simplified off-lattice protein models'', Protein Sci., 13, 40-53 (2004) [PDF]

59 -- SPARKS Method -- Ranked #1 in CM targets in 49 servers assessed in CASP6
H. Zhou and Y. Zhou,``Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition'', Proteins, 55, 1005-1013 (2004).[ Subject Area:Bioinformatics][ Server & Download] Abstract [PDF] [20X25 contact energy function] [Contact energy function usage] Independent LiveBench Performance [CASP6]

58
H. Jang, C. K. Hall, and Y. Zhou, ``Assembly and kinetic folding pathways of a tetrameric beta-sheet complex: Molecular dynamics simulations on simplified off-lattice protein models'', Biophys. J., 86, 31-49 (2004). [ Subject Area:Folding Kinetics/Thermodynamcs] [ PDF ]

57
H. Zhou and Y. Zhou, ``Quantifying the effect of burial of amino acid residues on protein stability'', Proteins, 54, 315-322 (2004). [ Subject Area:Bioinformatics] [ PDF ] List of 200 PDB structures

56 -- THUMBUP/UMDHMM Methods --
H. Zhou and Y. Zhou, ``Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model based method'', Protein Sci., 12, 1547-1555 (2003). [ Subject Area:Bioinformatics] [ THUMBUP Server] [ UMBHMM Server] Abstract[PDF] 73 protein sequences topologies pdb list

55
Y. Zhou, C. Zhang, G. Stell, and J. Wang, ``Temperature dependence of the distribution of the first passage time: Results from all-atom discontinuous molecular dynamics simulations of the second -hairpin fragment of protein G", J. Am. Chem. Soc., 125, 6300-6305 (2003). [ Subject Area:Folding kinetics] [PDF]

54
Y. Zhou, H. Zhou, and M. Karplus, ``Cooperativity in Scapharca dimeric hemoglobin: Simulation of binding intermediates and elucidation of the role of interfacial water'', J. Mol. Biol., 326, 593--606 (2003). [ Subject Area: Binding Cooperativity, Protein Dynamics] Abstract [PDF]

53
A. Linhananta and Y. Zhou, ``The role of sidechain packing and native contact interactions in folding: Discontinuous molecular dynamics folding simulations of an all-atom Go model of fragment B of Staphylococcal protein A'', J. Chem. Phys., 117, 8983--8995 (2002). [ Subject Area: Folding Mechanism, Folding Kinetics, Protein Dynamics] [PDF]

52 -- DFIRE Method (DMONOMER/DMUTANT)--
H. Zhou and Y. Zhou, ``Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction'', Protein Science, 11, 2714--2726 (2002). [ Subject Area: Bioinformatics, Folding Stability, Structure Prediction] The 895 mutation list Abstract [PDF] [CORRECTIONS] Protein Science, 12, 2121 (2003). [ DMONMER Server] [ DMUTANT Server]

51
H. Zhou and Y. Zhou, ``The stability scale and atomic solvation parameters extracted from 1023 mutation experiments'', Proteins, 49, 483--492 (2002). [ Subject Area: Bioinformatics, Folding Stability] The 1023 mutation list [PDF]

50
A. Linhananta, H. Zhou and Y. Zhou, ``The dual role of a loop with low loop contact distance in folding and domain swapping'', Protein Science, 11, 1695-1701 (2002). [ Subject Area: Folding Mechanism, Folding Kinetics, Bioinformatics] Abstract [PDF]

49
H. Jang, C. K. Hall, and Y. Zhou ``Protein folding pathways and kinetics: Molecular dynamics simulations of -strand motifs'', Biophys. J. 83, 819-835 (2002). [ Subject Area: Folding Mechanism, Folding Kinetics] [PDF]

48
Y. Zhou and A. Linhananta, ``Role of hydrophilic and hydrophobic contacts in folding of the second -hairpin fragment of protein G: Molecular dynamics simulation studies of an all-atom model'', Proteins, 47, 154-162 (2002). [ Subject Area: Folding Mechanism, Folding Kinetics] Abstract [PDF]

47
Y. Zhou and A. Linhananta, ``Thermodynamics of an all-atom off-lattice model of the fragment B of Staphylococcal protein A: Implication for the origin of the cooperativity of protein folding'', J. Phys. Chem. B, 106, 1481-1485 (2002). [ Subject Area: Folding Thermodynamics, Folding Cooperativity] Abstract [PDF]

46
H. Jang, C. K. Hall, and Y. Zhou ``Folding thermodynamics of model four-strand antiparallel -sheet proteins'', Biophys. J. 82, 646-659 (2002). [Subject Area: Folding Thermodynamics] [PDF]

45
Y. Zhou, M. Karplus, K. D. Ball and R. S. Berry, ``The distance fluctuation criterion for melting: Comparison of square-well and Morse potential models for clusters and homopolymers'',J. Chem. Phys., 116, 2323-2329 (2002). [ Subject Area: Polymer Thermodynamics, Statistical Mechanics] [PDF]

44
H. Zhou and Y. Zhou, ``Folding rate prediction using total contact distance.'', Biophys. J. 82, 458--463 (2002). [ Subject Area: Folding Kinetics] [ Server] Abstract [ Residue ranges for some proteins] [PDF]

43
Y. Zhou, ``Fast and accurate thermodynamics of square-well systems from umbrella-sampling simulations of hard-sphere systems.'', J. Chem. Phys. 115, 7550-7553 (2001). [ Subject Area: Polymer Thermodynamics, Statistical Mechanics] [PDF]

1994-2000
42
Y. Zhou, M. Cook, and M. Karplus, ``Protein motions at zero-total angular momentum: The importance of long-range correlations.'', Biophys. J. 79, 2902-2908 (2000). [PDF]

41
Y. Zhou and M. Karplus, ``Folding of a model three-helix bundle protein: A thermodynamic and kinetic analysis.'', J. Molec. Biol. 293, 917-951 (1999). [PDF]

40
Y. Zhou and M. Karplus, ``Interpreting the folding kinetics of helical proteins.'', Nature 401, 400-403 (1999). [PDF]

39
Y. Zhou, C. K. Hall, and M. Karplus, ``The calorimetric criterion for a two-state process revisited.'', Protein Science 8 , 1064 (1999). [PDF]

38
Y. Zhou, D. Vitkup, and M. Karplus, ``Native proteins are surface-molten solids: Application of the Lindemann criterion for the solid versus liquid state.'', J. Molec. Biol. 285 , 1371 (1999). [PDF]

37
Y. Zhou, ``Salt effects on protein titration and binding.'', J. Phys. Chem. 102, 10615 (1998). [PDF]

36
Y. Zhou and M. Karplus, ``Folding thermodynamics of a model three-helix bundle protein.'', Proc. Natl. Acad. Sci. (USA) 94, 14429 (1997). [PDF]

35
Y. Zhou, M. Karplus, J. M. Wichert, and C. K. Hall, ``Equilibrium thermodynamics of homopolymers and clusters: Molecular dynamics and Monte Carlo simulation studies of systems with square-well interactions.'', J. Chem. Phys. 107, 10691 (1997). [PDF]

34
Y. Zhou, C. K. Hall, and M. Karplus, ``A first-order disorder-to-order transition in an isolated homopolymer model.'', Phys. Rev. Lett. 77 , 2822 (1996). [PDF]

33
Y. Zhou and M. Karplus, ``Exact results for the effect of bond flexibility on the structure and the collapse transition of isolated square-well trimers.'', Molec. Phys. 89, 1707 (1996).

32
Y. Zhou and C. K. Hall, ``Solute excluded-volume effects on the stability of globular proteins: A statistical thermodynamic theory.'', Biopolymers 38 , 273 (1996).

31
S. Yeh, Y. Zhou, and G. Stell, ``Phase separation of ionic fluids: An extended Ebeling-Grigo approach.'', J. Phys. Chem. (H. L. Friedman Issue) 100 , 1415 (1996). [PDF]

30
Y. Zhou, C. K. Hall, and G. Stell, ``Exact results for isolated sticky chains.'', Molec. Phys. 86 , 1485 (1995).

29
Y. Zhou, S. W. Smith, and C. K. Hall, ``Linear dependence of thermodynamic properties of tangent hard-sphere chains on chain length.'', Molec. Phys. 86 , 1157 (1995).

28
Y. Zhou, C. K. Hall, and G. Stell, ``The thermodynamic perturbation theory for fused hard-sphere chain fluids.'', J. Chem. Phys. 103 , 2688 (1995).

27
L. A. Costa, Y. Zhou, C. K. Hall, and S. Carr, ``Fused hard-sphere chain molecules: Comparison between monte carlo simulation for the bulk pressure and generalized Flory theories.'', J. Chem. Phys. 102, 6212 (1995).

26
Y. Zhou and G. Stell, ``Criticality of charged systems: II. The binary mixture of hard spheres and ions.'', J. Chem. Phys. 102, 5796 (1995).

25
Y. Zhou, S. Yeh, and G. Stell, ``Criticality of charged systems: I. The restricted primitive model.'', J. Chem. Phys. 102, 5785 (1995).

24
Y. Zhou and G. Stell, ``Chemical association in simple models of molecular and ionic fluids IV. New approximation for the cavity function and an application to the theory of weak electrolytes.'', J. Chem. Phys. 102, 8089 (1995).

1985-1990

23
Y. Zhou and G. Stell, ``Analytical approach to molecular liquids: V. Symmetric dissociative dipolar dumbbells with the bonding length, /2 and related systems.'', J. Chem. Phys. 98, 5777 (1993).

22
G. Stell and Y. Zhou, ``Microscopic modeling of association.'', Fluid Phase Equilibria 79, 1 (1992).

21
Y. Zhang, Y. Zhou, Z. Luo, and D. Hanson, ``Electron rearrangement and energy relaxation due to a core hole creation in molecules.'', J. Phys. Chem. 96, 2949 (1992).

20
Y. Zhou and G. Stell, ``Chemical association in simple models of molecular and ionic fluids III. The cavity functions.'', J. Chem. Phys. 96, 1507 (1992).

19
Y. Zhou and G. Stell, ``Chemical association in simple models of molecular and ionic fluids II. Thermodynamic properties.'', J. Chem. Phys. 96, 1504 (1992).

18
F. O. Raineri, Y. Zhou, H. L. Friedman, and G. Stell, ``Ion solvation dynamics in an interaction site model solvent.'', Chem. Phys. 152, 201 (1991).

17
Y. Zhou, H. L. Friedman, and G. Stell, ``Outer-sphere electron transfer reactions in model molecular solvents: The mean spherical approximation.'', Chem. Phys. 152, 185 (1991).

16
Y. Zhou and G. Stell, ``Nonlocal integral-equation approximations: II. The Lennard-Jones fluid.'', J. Chem. Phys. 92, 5544 (1990).

15
Y. Zhou and G. Stell, ``Nonlocal integral-equation approximations: I. The hydrostatic approximation with applications.'', J. Chem. Phys. 92, 5533 (1990).

14
Y. Zhou and G. Stell, ``Fluids inside a pore -- an integral-equation approach III. Water-in-oil microemulsions.'', Molec. Phys. 68, 1265 (1989).

13
Y. Zhou, H. L. Friedman, and G. Stell, ``Analytical approach to molecular liquids: IV. Solvation dynamics and electron-transfer reactions.'', J. Chem. Phys. 91, 4885 (1989).

12
Y. Zhou, H. L. Friedman, and G. Stell, ``Analytical approach to molecular liquids: III. The Born solvation free energy of two fixed ions in a dipolar solvent.'', J. Chem. Phys. 91, 4879 (1989).

11
Y. Zhou and G. Stell, ``Analytical approach to molecular liquids: II. Solvation of ions in molecular fluids.'', J. Chem. Phys. 91, 4869 (1989).

10
G. Stell and Y. Zhou, ``Analytical approach to molecular liquids: I. Site-site interaction model using an extended mean-spherical approximation.'', J. Chem. Phys. 91, 4861 (1989).

9
G. Stell and Y. Zhou, ``Chemical association in simple models of molecular and ionic fluids.'', J. Chem. Phys. 91, 3618 (1989).

8
Y. Zhou and G. Stell, ``The theory of semipermeable vesicles and membranes: An integral-equation approach. III. Vesicles with internal nonpermeating ions.'', J. Chem. Phys. 91, 3208 (1989).

7
Y. Zhou and G. Stell, ``Fluids inside a pore -- an integral-equation approach II. Cylindrical pores.'', Molec. Phys. 66, 791 (1989).

6
Y. Zhou and G. Stell, ``Fluids inside a pore -- an integral-equation approach I. General formalism and hard-spheres inside spherical and slit pores.'', Molec. Phys. 66, 767 (1989).

5
Y. Zhou and G. Stell, ``The theory of semipermeable vesicles and membranes: An integral-equation approach. II. Donnan equilibrium.'', J. Chem. Phys. 89, 7020 (1988).

4
Y. Zhou and G. Stell, ``The theory of semipermeable vesicles and membranes: An integral-equation approach. I. General formalism and application to a hard-sphere mixture.'', J. Chem. Phys. 89, 7010 (1988).

3
Y. Zhou and G. Stell, ``Equations of state for hard-sphere fluids.'', Int. J. Thermophys. 9, 953 (1988).

2
Y. Zhou, G. Stell, and H. L. Friedman, ``Note on standard free energy of transfer and partitioning of ionic species between two fluid phases.'', J. Chem. Phys. 89, 3836 (1988).

1
Y. Zhou and G. Stell, ``The hard-sphere fluid: New exact results with applications.'', J. Stat. Phys., Howard Reiss Issue 52, 1389 (1988).