103.   Xu, B.*, Yang, Y.*, Liang, H. and Zhou, Y., An all-atom knowledge-based energy function for protein-DNA threading, decoy discrimination, and prediction of transcription-factor binding profiles, Proteins, in Press (2009) [DDNA 2 Download ] [List of Protein-DNA complexes]

102.  Liang, S., Wang, G., and Zhou, Y., Refining near-native protein-protein docking decoys by local re-sampling and energy minimization, Proteins, in Press (2009). [PDF-TBA]

101.  Zhou, Y. and Faraggi, E., Prediction of one-dimensional structural properties of proteins by integrated neural network (Book Chapter), Protein Structure Prediction: Method and Algorithms, edited by H. Rangwala and G. Karypis, Wiley, 2009.

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

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

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

97.  Faraggi, E., Xue, B., and Zhou, Y., 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]

96.  Lei, H., Wu, C., Wang, Z. X., Zhou, Y., and Duan, Y., 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.  Luo, Z., Ding, J. and Zhou, Y., 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.  Zhang, W., Liu, S. and Zhou, Y., SP5: Improving protein fold recognition by using predictedtorsion angles and profile-based gap penalty, PLoS ONE 3, e2325 (2008). [PDF] [SP5 server] [List of Prefab pairs]

93.  Yang, Y. and Zhou, Y., 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] [DFIRE 2.0]

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

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

90.  Zhang, W., Dunker, A. K., and Zhou, Y., 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.  Luo, Z., Ding, J., and Zhou, Y., 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.  Liang, S., Liu, S., Zhang, C. and Zhou, Y., A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys., Proteins 69, 244--253 (2007). [PDF] [Server [On the Cover]

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

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

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

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

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

82.  Zhou, Y., Zhou, H., and Karplus, M., 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.  Liang, S., Zhang, C., Liu, S. and Zhou, Y., Protein binding site prediction with an empirical scoring function, Nucl. Acids Res. 34, 3698-3707 (2006). [PINUP Server] [PDF]

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

79.  Liu, S., Zhang, C. and Zhou, Y., 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.  Zhou, Y., Zhou, H., Zhang, C. and Liu, S., 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.  Xu, Z. and Zhang, C. and Liu, S. and Zhou, Y., QBES: Predicting real values of solventaccessibility from sequences by efficient, constrained energyoptimization, Proteins 63, 961--966 (2006). [PDF]

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

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

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

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

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

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

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

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

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

63.  Zhang, C., Liu, S., Zhou, H., and Zhou, Y., 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]

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

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

60.  Jang, H., Hall, C. K., and Zhou, Y., 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.  Zhou, H. and Zhou, Y., 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] [Abstract [ PDF] **Ranked #1 in CM targets in 49 servers assessed in CASP6 - [ Independent LiveBench Performance [CASP6]

58.  Jang, H., Hall, C. K., and Zhou, Y., 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.  Zhou, H. and Zhou, Y., Quantifying the effect of burial of amino acid residues on proteinstability, Proteins, 54, 315-322 (2004). SubjectArea:Bioinformatics [PDF ] [List of 200 PDB structures]

56.  Zhou, H. and Zhou, Y., Predicting the topology of transmembrane helical proteins usingmean 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.  Zhou, Y., Zhang, C., Stell, G., and J. Wang, Temperature dependence of thedistribution of the first passage time: Results from all-atomdiscontinuous 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.  Zhou, Y., Zhou, H., and Karplus, M., Cooperativity in Scapharca dimerichemoglobin: Simulation of binding intermediates and elucidation ofthe role of interfacial water, J. Mol. Biol., 326,593--606 (2003). Subject Area: BindingCooperativity, Protein Dynamics] [Abstract] [PDF]

53.  Zhou, H. and Zhou, Y., 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]

52.  Zhou, Y. and Linhananta, A., 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]

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

50.  Linhananta, A. and Zhou, Y., The role of sidechain packing and native contact interactions infolding: Discontinuous molecular dynamics folding simulations of anall-atom Go model of fragment B of Staphylococcal proteinA, J. Chem. Phys., 117, 8983--8995 (2002). Subject Area: Folding Mechanism, FoldingKinetics, Protein Dynamics] [PDF]

49.  Zhou, H. and Zhou, Y., Distance-scaled, finite ideal-gas reference state improvesstructure-derived potentials of mean force for structure selectionand stability prediction, Protein Science, 11,2714--2726 (2002). Subject Area: Bioinformatics, Folding Stability, StructurePrediction [The895 mutation list] [ Abstract] [PDF] [CORRECTIONS] Protein Science, 12, 2121 (2003). [DMONMER Server] [DMUTANT Server]

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

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

46.  Zhou, Y. and Linhananta, A., 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]

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

44.  Zhou, Y., Karplus, M., Ball, K. D. and Berry, R. S., 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]

43.  Zhou, Y., 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]

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

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

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

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

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

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

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

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

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

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

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

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

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

27.  Costa, L. A., Zhou, Y., Hall, C. K., and Carr, S., 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.  Zhou, Y. and Stell, G., Criticality of charged systems: II. The binary mixture of hard spheres and ions., J. Chem. Phys. 102, 5796 (1995).

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

24.  Zhou, Y. and Stell, G., 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).

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

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

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

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

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

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

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

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

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

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

12.  Zhou, Y., Friedman, H. L., and Stell, G., 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.  Zhou, Y. and Stell, G., Analytical approach to molecular liquids: II. Solvation of ions in molecular fluids., J. Chem. Phys. 91, 4869 (1989).

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

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

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

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

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

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

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

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