All Stories

  1. Predicting functional long non-coding RNAs validated by low throughput experiments

    Article • RNA Biology, July 2019, Taylor & Francis

    Professor Yaoqi Zhou

  2. Different effects of cholesterol on membrane permeation of arginine and tryptophan revealed by bias-exchange metadynamics simulations

    Article • The Journal of Chemical Physics, February 2019, American Institute of Physics

    Professor Yaoqi Zhou

  3. Self-derived structure-disrupting peptides targeting methionine aminopeptidase in pathogenic bacteria: a new strategy to generate antimicrobial peptides

    Article • The FASEB Journal, February 2019, Federation of American Societies For Experimental Biology (FASEB)

    Professor Yaoqi Zhou, Professor Michael P Jennings, Dr Sohinee Sarkar, Dr Kate L Seib, Qizhuang Ye

  4. EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments

    Article • Nucleic Acids Research, July 2017, Oxford University Press (OUP)

    Professor Yaoqi Zhou

  5. Investigating DNA-, RNA-, and protein-based features as a means to discriminate pathogenic synonymous variants

    Article • Human Mutation, July 2017, Wiley

    Professor Yaoqi Zhou

  6. Faculty of 1000 evaluation for Widespread position-specific conservation of synonymous rare codons within coding sequences.

    Article • June 2017, Faculty of 1000, Ltd.

    Professor Yaoqi Zhou

  7. Faculty of 1000 evaluation for A high-throughput approach to profile RNA structure.

    Article • May 2017, Faculty of 1000, Ltd.

    Professor Yaoqi Zhou

  8. Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI

    Article • Human Mutation, May 2017, Wiley

    Dr MARIA CHIARA SCAINI, Professor Yaoqi Zhou, Mr Abhishek Niroula

  9. regSNPs-splicing: a tool for prioritizing synonymous single-nucleotide substitution

    Article • Human Genetics, April 2017, Springer Science + Business Media

    Professor Yaoqi Zhou

  10. DisBind: A database of classified functional binding sites in disordered and structured regions of intrinsically disordered proteins

    Article • BMC Bioinformatics, April 2017, Springer Science + Business Media

    Professor Yaoqi Zhou

  11. Real-time reliable determination of binding kinetics of DNA hybridization using a multi-channel graphene biosensor

    Article • Nature Communications, March 2017, Nature

    Professor Yaoqi Zhou

  12. Systems-level understanding of ethanol-induced stresses and adaptation in E. coli

    Article • Scientific Reports, March 2017, Nature

    Professor Yaoqi Zhou

  13. SPOT-ligand 2: improving structure-based virtual screening by binding-homology search on an expanded structural template library

    Article • Bioinformatics, January 2017, Oxford University Press (OUP)

    Professor Yaoqi Zhou

  14. Prediction of Protein Secondary Structure

    Article • January 2017, Springer Science + Business Media

    Professor Yaoqi Zhou

  15. Sixty-five years of the long march in protein secondary structure prediction: the final stretch?

    Article • Briefings in Bioinformatics, December 2016, Oxford University Press (OUP)

    Professor Yaoqi Zhou

  16. Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks

    Article • Bioinformatics, December 2016, Oxford University Press (OUP)

    Professor Yaoqi Zhou

  17. Genome-scale characterization of RNA tertiary structures and their functional impact by RNA solvent accessibility prediction

    Article • RNA, November 2016, Cold Spring Harbor Laboratory Press

    Professor Yaoqi Zhou

  18. SPIDER2: A Package to Predict Secondary Structure, Accessible Surface Area, and Main-Chain Torsional Angles by Deep Neural Networks

    Article • October 2016, Springer Science + Business Media

    Professor Yaoqi Zhou

  19. Fast and Accurate Accessible Surface Area Prediction Without a Sequence Profile

    Article • October 2016, Springer Science + Business Media

    Professor Yaoqi Zhou

  20. Intrinsic Disorder and Semi-disorder Prediction by SPINE-D

    Article • October 2016, Springer Science + Business Media

    Professor Yaoqi Zhou

  21. Sequence-Based Prediction of Protein–Carbohydrate Binding Sites Using Support Vector Machines

    Article • Journal of Chemical Information and Modeling, October 2016, American Chemical Society (ACS)

    Professor Yaoqi Zhou

  22. LRFragLib: an effective algorithm to identify fragments for de novo protein structure prediction

    Article • Bioinformatics, October 2016, Oxford University Press (OUP)

    Professor Yaoqi Zhou

  23. ExonImpact: Prioritizing Pathogenic Alternative Splicing Events

    Article • Human Mutation, October 2016, Wiley

    Professor Yaoqi Zhou

  24. Predicting the errors of predicted local backbone angles and non-local solvent- accessibilities of proteins by deep neural networks

    Article • Bioinformatics, August 2016, Oxford University Press (OUP)

    Professor Yaoqi Zhou

  25. Infectivity of Plasmodium falciparum in Malaria-Naive Individuals Is Related to Knob Expression and Cytoadherence of the Parasite

    Article • Infection and Immunity, July 2016, ASM Journals

    Professor Yaoqi Zhou

  26. Faculty of 1000 evaluation for Contact Statistics Highlight Distinct Organizing Principles of Proteins and RNA.

    Article • June 2016, Faculty of 1000, Ltd.

    Professor Yaoqi Zhou

  27. Optimal secretion of alkali-tolerant xylanase in Bacillus subtilis by signal peptide screening

    Article • Applied Microbiology and Biotechnology, May 2016, Springer Science + Business Media

    Professor Yaoqi Zhou

  28. Investigation the Possibility of Using Peptides with a Helical Repeating Pattern of Hydro-Phobic and Hydrophilic Residues to Inhibit IL-10

    Article • PLoS ONE, April 2016, PLOS

    Professor Yaoqi Zhou

  29. SPOT-Ligand: Fast and effective structure-based virtual screening by binding homology search according to ligand and receptor similarity

    Article • Journal of Computational Chemistry, April 2016, Wiley

    Professor Yaoqi Zhou

  30. EASE-MM: Sequence-Based Prediction of Mutation-Induced Stability Changes with Feature-Based Multiple Models

    Article • Journal of Molecular Biology, March 2016, Elsevier

    Professor Yaoqi Zhou

  31. sDFIRE: Sequence-specific statistical energy function for protein structure prediction by decoy selections

    Article • Journal of Computational Chemistry, February 2016, Wiley

    Professor Yaoqi Zhou

  32. Sequence-based prediction of protein-peptide binding sites using support vector machine

    Article • Journal of Computational Chemistry, February 2016, Wiley

    Professor Yaoqi Zhou

  33. Natural protein sequences are more intrinsically disordered than random sequences

    Article • Cellular and Molecular Life Sciences, January 2016, Springer Science + Business Media

    Professor Yaoqi Zhou

  34. Effective protein conformational sampling based on predicted torsion angles

    Article • Journal of Computational Chemistry, December 2015, Wiley

    Professor Yaoqi Zhou

  35. A heuristic for the time constrained asymmetric linear sum assignment problem

    Article • Journal of Combinatorial Optimization, December 2015, Springer Science + Business Media

    Professor Yaoqi Zhou

  36. Faculty of 1000 evaluation for Designed protein reveals structural determinants of extreme kinetic stability.

    Article • December 2015, Faculty of 1000, Ltd.

    Professor Yaoqi Zhou

  37. Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins

    Article • Bioinformatics, November 2015, Oxford University Press (OUP)

    Professor Yaoqi Zhou

  38. Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic

    Article • Bioinformatics, October 2015, Oxford University Press (OUP)

    Professor Yaoqi Zhou

  39. Advancing the Accuracy of Protein Fold Recognition by Utilizing Profiles From Hidden Markov Models

    Article • IEEE Transactions on NanoBioscience, October 2015, Institute of Electrical & Electronics Engineers (IEEE)

    Professor Yaoqi Zhou

  40. Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning

    Article • Scientific Reports, June 2015, Nature

    Professor Yaoqi Zhou

  41. DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels

    Article • Bioinformatics, January 2015, Oxford University Press (OUP)

    Professor Yaoqi Zhou

  42. Accurate single-sequence prediction of solvent accessible surface area using local and global features

    Article • Proteins Structure Function and Bioinformatics, September 2014, Wiley

    Professor Yaoqi Zhou

  43. Carbohydrate-binding protein identification by coupling structural similarity searching with binding affinity prediction

    Article • Journal of Computational Chemistry, September 2014, Wiley

    Professor Yaoqi Zhou

  44. Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network

    Article • Journal of Computational Chemistry, September 2014, Wiley

    Professor Yaoqi Zhou

  45. Direct prediction of profiles of sequences compatible with a protein structure by neural networks with fragment-based local and energy-based nonlocal profiles

    Article • Proteins Structure Function and Bioinformatics, June 2014, Wiley

    Professor Yaoqi Zhou

  46. Predicting DNA-Binding Proteins and Binding Residues by Complex Structure Prediction and Application to Human Proteome

    Article • PLoS ONE, May 2014, PLOS

    Professor Yaoqi Zhou

  47. Faculty Opinions recommendation of An antifreeze protein folds with an interior network of more than 400 semi-clathrate waters.

    Article • March 2014, F1000Research

    Professor Yaoqi Zhou

  48. Impact of human pathogenic micro-insertions and micro-deletions on post-transcriptional regulation

    Article • Human Molecular Genetics, January 2014, Oxford University Press (OUP)

    Professor Yaoqi Zhou

  49. SPOT-Seq-RNA: Predicting Protein–RNA Complex Structure and RNA-Binding Function by Fold Recognition and Binding Affinity Prediction

    Article • January 2014, Springer Science + Business Media

    Professor Yaoqi Zhou

  50. Correction for Zhou et al., Structural insights into the histone H1-nucleosome complex

    Article • Proceedings of the National Academy of Sciences, December 2013, Proceedings of the National Academy of Sciences

    Professor Yaoqi Zhou

  51. LEAP: Highly accurate prediction of protein loop conformations by integrating coarse‐grained sampling and optimized energy scores with all‐atom refinement of backbone and side chains

    Article • Journal of Computational Chemistry, December 2013, Wiley

    Professor Yaoqi Zhou

  52. The Role of Semidisorder in Temperature Adaptation of Bacterial FlgM Proteins

    Article • Biophysical Journal, December 2013, Elsevier

    Professor Yaoqi Zhou

  53. Prediction and validation of the unexplored RNA‐binding protein atlas of the human proteome

    Article • Proteins Structure Function and Bioinformatics, November 2013, Wiley

    Professor Yaoqi Zhou

  54. Structural insights into the histone H1-nucleosome complex

    Article • Proceedings of the National Academy of Sciences, November 2013, Proceedings of the National Academy of Sciences

    Professor Yaoqi Zhou

  55. Intrinsically Semi-disordered State and Its Role in Induced Folding and Protein Aggregation

    Article • Cell Biochemistry and Biophysics, May 2013, Springer Science + Business Media

    Professor Yaoqi Zhou

  56. Energy Functions in De Novo Protein Design: Current Challenges and Future Prospects

    Article • Annual Review of Biophysics, May 2013, Annual Reviews

    Professor Yaoqi Zhou

  57. DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels

    Article • Genome Biology, March 2013, Springer Science + Business Media

    Professor Yaoqi Zhou

  58. Prediction of RNA binding proteins comes of age from low resolution to high resolution

    Article • Molecular BioSystems, January 2013, Royal Society of Chemistry

    Professor Yaoqi Zhou

  59. BEST: Improved Prediction of B-Cell Epitopes from Antigen Sequences

    Article • PLoS ONE, June 2012, PLOS

    Professor Yaoqi Zhou

  60. A new size‐independent score for pairwise protein structure alignment and its application to structure classification and nucleic‐acid binding prediction

    Article • Proteins Structure Function and Bioinformatics, May 2012, Wiley

    Professor Yaoqi Zhou

  61. Template‐based structure prediction and classification of transcription factors in Arabidopsis thaliana

    Article • Protein Science, May 2012, Wiley

    Professor Yaoqi Zhou

  62. SPINE-D: Accurate Prediction of Short and Long Disordered Regions by a Single Neural-Network Based Method

    Article • Journal of Biomolecular Structure and Dynamics, February 2012, Taylor & Francis

    Professor Yaoqi Zhou

  63. SPINE X: Improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles

    Article • Journal of Computational Chemistry, November 2011, Wiley

    Professor Yaoqi Zhou

  64. Highly accurate and high-resolution function prediction of RNA binding proteins by fold recognition and binding affinity prediction

    Article • RNA Biology, November 2011, Taylor & Francis

    Professor Yaoqi Zhou

  65. Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology

    Article • Journal of Molecular Biology, November 2011, Elsevier

    Professor Yaoqi Zhou, Dr. Alexandre M.J.J. Bonvin, Professor Martin Zacharias

  66. Editorial [Hot Topic: Machine Learning Models in Protein Bioinformatics (Guest Editors: Lukasz Kurgan & Yaoqi Zhou)]

    Article • Current Protein and Peptide Science, September 2011, Bentham Science Publishers

    Professor Yaoqi Zhou

  67. Small Open Reading Frames: Current Prediction Techniques and Future Prospect

    Article • Current Protein and Peptide Science, September 2011, Bentham Science Publishers

    Professor Yaoqi Zhou

  68. In-silico prediction of disorder content using hybrid sequence representation

    Article • BMC Bioinformatics, June 2011, Springer Science + Business Media

    Professor Yaoqi Zhou

  69. Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates

    Article • Bioinformatics, June 2011, Oxford University Press (OUP)

    Professor Yaoqi Zhou

  70. A data processing software package for passive seismic monitoring of hydraulic fracturing

    Article • June 2011, Institute of Electrical & Electronics Engineers (IEEE)

    Professor Yaoqi Zhou

  71. Characterizing the Existing and Potential Structural Space of Proteins by Large-Scale Multiple Loop Permutations

    Article • Journal of Molecular Biology, May 2011, Elsevier

    Professor Yaoqi Zhou

  72. Protein side chain modeling with orientation‐dependent atomic force fields derived by series expansions

    Article • Journal of Computational Chemistry, March 2011, Wiley

    Professor Yaoqi Zhou

  73. Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets

    Article • Nucleic Acids Research, December 2010, Oxford University Press (OUP)

    Professor Yaoqi Zhou

  74. Fluctuations of backbone torsion angles obtained from NMR‐determined structures and their prediction

    Article • Proteins Structure Function and Bioinformatics, November 2010, Wiley

    Professor Yaoqi Zhou

  75. Prediction of One‐Dimensional Structural Properties Of Proteins by Integrated Neural Networks

    Article • September 2010, Wiley

    Professor Yaoqi Zhou

  76. Trends in template/fragment-free protein structure prediction

    Article • Theoretical Chemistry Accounts, September 2010, Springer Science + Business Media

    Professor Yaoqi Zhou

  77. Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function

    Article • Bioinformatics, June 2010, Oxford University Press (OUP)

    Professor Yaoqi Zhou

  78. Improving computational protein design by using structure‐derived sequence profile

    Article • Proteins Structure Function and Bioinformatics, May 2010, Wiley

    Professor Yaoqi Zhou

  79. Predicting Continuous Local Structure and the Effect of Its Substitution for Secondary Structure in Fragment-Free Protein Structure Prediction

    Article • Structure, November 2009, Elsevier

    Professor Yaoqi Zhou

  80. An all‐atom knowledge‐based energy function for protein‐DNA threading, docking decoy discrimination, and prediction of transcription‐factor binding profiles

    Article • Proteins Structure Function and Bioinformatics, March 2009, Wiley

    Professor Yaoqi Zhou

  81. Refining near‐native protein–protein docking decoys by local resampling and energy minimization

    Article • Proteins Structure Function and Bioinformatics, January 2009, Wiley

    Professor Yaoqi Zhou

  82. Predicting residue–residue contact maps by a two‐layer, integrated neural‐network method

    Article • Proteins Structure Function and Bioinformatics, January 2009, Wiley

    Professor Yaoqi Zhou

  83. Exploring the Molecular Design of Protein Interaction Sites with Molecular Dynamics Simulations and Free Energy Calculations

    Article • Biochemistry, December 2008, American Chemical Society (ACS)

    Professor Yaoqi Zhou

  84. Consensus scoring for enriching near‐native structures from protein–protein docking decoys

    Article • Proteins Structure Function and Bioinformatics, October 2008, Wiley

    Professor Yaoqi Zhou

  85. Improving the prediction accuracy of residue solvent accessibility and real‐value backbone torsion angles of proteins by guided‐learning through a two‐layer neural network

    Article • Proteins Structure Function and Bioinformatics, August 2008, Wiley

    Professor Yaoqi Zhou

  86. Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all‐atom statistical energy functions

    Article • Protein Science, July 2008, Wiley

    Professor Yaoqi Zhou

  87. Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations

    Article • The Journal of Chemical Physics, June 2008, American Institute of Physics

    Professor Yaoqi Zhou

  88. Folding mechanisms of individual β-hairpins in a Gō model of Pin1 WW domain by all-atom molecular dynamics simulations

    Article • The Journal of Chemical Physics, June 2008, American Institute of Physics

    Professor Yaoqi Zhou

  89. SP5: Improving Protein Fold Recognition by Using Torsion Angle Profiles and Profile-Based Gap Penalty Model

    Article • PLoS ONE, June 2008, PLOS

    Professor Yaoqi Zhou

  90. Specific interactions for ab initio folding of protein terminal regions with secondary structures

    Article • Proteins Structure Function and Bioinformatics, February 2008, Wiley

    Professor Yaoqi Zhou

  91. Real‐value prediction of backbone torsion angles

    Article • Proteins Structure Function and Bioinformatics, January 2008, Wiley

    Professor Yaoqi Zhou

  92. Assessing secondary structure assignment of protein structures by using pairwise sequence‐alignment benchmarks

    Article • Proteins Structure Function and Bioinformatics, October 2007, Wiley

    Professor Yaoqi Zhou

  93. Temperature-Dependent Folding Pathways of Pin1 WW Domain: An All-Atom Molecular Dynamics Simulation of a Gō Model

    Article • Biophysical Journal, September 2007, Elsevier

    Professor Yaoqi Zhou

  94. A simple reference state makes a significant improvement in near‐native selections from structurally refined docking decoys

    Article • Proteins Structure Function and Bioinformatics, July 2007, Wiley

    Professor Yaoqi Zhou

  95. The helix–coil transition revisited

    Article • Proteins Structure Function and Bioinformatics, June 2007, Wiley

    Professor Yaoqi Zhou

  96. Fold recognition by concurrent use of solvent accessibility and residue depth

    Article • Proteins Structure Function and Bioinformatics, May 2007, Wiley

    Professor Yaoqi Zhou

  97. DDOMAIN: Dividing structures into domains using a normalized domain–domain interaction profile

    Article • Protein Science, May 2007, Wiley

    Professor Yaoqi Zhou

  98. Real‐SPINE: An integrated system of neural networks for real‐value prediction of protein structural properties

    Article • Proteins Structure Function and Bioinformatics, March 2007, Wiley

    Professor Yaoqi Zhou

  99. Achieving 80% ten‐fold cross‐validated accuracy for secondary structure prediction by large‐scale training

    Article • Proteins Structure Function and Bioinformatics, February 2007, Wiley

    Professor Yaoqi Zhou

  100. Perineural clonidine reduces p38 mitogen-activated protein kinase activation in sensory neurons

    Article • Neuroreport, August 2006, Wolters Kluwer Health

    Professor Yaoqi Zhou

  101. Protein binding site prediction using an empirical scoring function

    Article • Nucleic Acids Research, July 2006, Oxford University Press (OUP)

    Professor Yaoqi Zhou

  102. Fast and Accurate Method for Identifying High-Quality Protein-Interaction Modules by Clique Merging and Its Application to Yeast

    Article • Journal of Proteome Research, March 2006, American Chemical Society (ACS)

    Professor Yaoqi Zhou

  103. QBES: Predicting real values of solvent accessibility from sequences by efficient, constrained energy optimization

    Article • Proteins Structure Function and Bioinformatics, March 2006, Wiley

    Professor Yaoqi Zhou

  104. Cooperativity inScapharca dimeric hemoglobin: Simulation of binding intermediates and elucidation of the role of interfacial water

    Article • RENDICONTI LINCEI, March 2006, Springer Science + Business Media

    Professor Yaoqi Zhou

  105. Uneven size distribution of mammalian genes in the number of tissues expressed and in the number of co-expressed genes

    Article • Human Molecular Genetics, March 2006, Oxford University Press (OUP)

    Professor Yaoqi Zhou

  106. What is a Desirable Statistical Energy Function for Proteins and How Can It Be Obtained?

    Article • Cell Biochemistry and Biophysics, January 2006, Springer Science + Business Media

    Professor Yaoqi Zhou

  107. Relevance judgment: What do information users consider beyond topicality?

    Article • Journal of the American Society for Information Science and Technology, January 2006, Wiley

    Professor Yaoqi Zhou

  108. FOLD HELICAL PROTEINS BY ENERGY MINIMIZATION IN DIHEDRAL SPACE AND A DFIRE-BASED STATISTICAL ENERGY FUNCTION

    Article • Journal of Bioinformatics and Computational Biology, October 2005, World Scientific Pub Co Pte Lt

    Professor Yaoqi Zhou

  109. Design and Folding of a Multidomain Protein

    Article • Biochemistry, August 2005, American Chemical Society (ACS)

    Professor Yaoqi Zhou

  110. SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures

    Article • Bioinformatics, July 2005, Oxford University Press (OUP)

    Professor Yaoqi Zhou

  111. Protein flexibility prediction by an all‐atom mean‐field statistical theory

    Article • Protein Science, July 2005, Wiley

    Professor Yaoqi Zhou

  112. 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

    Article • Nucleic Acids Research, July 2005, Oxford University Press (OUP)

    Professor Yaoqi Zhou

  113. Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function

    Article • Proteins Structure Function and Bioinformatics, June 2005, Wiley

    Professor Yaoqi Zhou

  114. SCUD: Fast structure clustering of decoys using reference state to remove overall rotation

    Article • Journal of Computational Chemistry, June 2005, Wiley

    Professor Yaoqi Zhou

  115. A Knowledge-Based Energy Function for Protein−Ligand, Protein−Protein, and Protein−DNA Complexes

    Article • Journal of Medicinal Chemistry, February 2005, American Chemical Society (ACS)

    Professor Yaoqi Zhou

  116. Domain Graph of Arabidopsis Proteome by Comparative Analysis

    Article • Journal of Proteome Research, February 2005, American Chemical Society (ACS)

    Professor Yaoqi Zhou

  117. SPARKS 2 and SP3 servers in CASP6

    Article • Proteins Structure Function and Bioinformatics, January 2005, Wiley

    Professor Yaoqi Zhou

  118. Fold recognition by combining sequence profiles derived from evolution and from depth‐dependent structural alignment of fragments

    Article • Proteins Structure Function and Bioinformatics, November 2004, Wiley

    Professor Yaoqi Zhou

  119. The Dependence of All-Atom Statistical Potentials on Structural Training Database

    Article • Biophysical Journal, June 2004, Elsevier

    Professor Yaoqi Zhou

  120. Critical nucleation size in the folding of small apparently two‐state proteins

    Article • Protein Science, May 2004, Wiley

    Professor Yaoqi Zhou

  121. A physical reference state unifies the structure‐derived potential of mean force for protein folding and binding

    Article • Proteins Structure Function and Bioinformatics, April 2004, Wiley

    Professor Yaoqi Zhou

  122. Single‐body residue‐level knowledge‐based energy score combined with sequence‐profile and secondary structure information for fold recognition

    Article • Proteins Structure Function and Bioinformatics, April 2004, Wiley

    Professor Yaoqi Zhou

  123. Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential

    Article • Protein Science, February 2004, Wiley

    Professor Yaoqi Zhou

  124. An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state

    Article • Protein Science, February 2004, Wiley

    Professor Yaoqi Zhou

  125. Assembly and Kinetic Folding Pathways of a Tetrameric β-Sheet Complex: Molecular Dynamics Simulations on Simplified Off-Lattice Protein Models

    Article • Biophysical Journal, January 2004, Elsevier

    Professor Yaoqi Zhou

  126. Thermodynamics and stability of a  -sheet complex: Molecular dynamics simulations on simplified off-lattice protein models

    Article • Protein Science, January 2004, Wiley

    Professor Yaoqi Zhou

  127. Quantifying the effect of burial of amino acid residues on protein stability

    Article • Proteins Structure Function and Bioinformatics, December 2003, Wiley

    Professor Yaoqi Zhou

  128. CORRECTION

    Article • Protein Science, September 2003, Wiley

    Professor Yaoqi Zhou

  129. Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden‐Markov‐model‐based method

    Article • Protein Science, July 2003, Wiley

    Professor Yaoqi Zhou

  130. Temperature Dependence of the Distribution of the First Passage Time:  Results from Discontinuous Molecular Dynamics Simulations of an All-Atom Model of the Second β-Hairpin Fragment of Protein G

    Article • Journal of the American Chemical Society, April 2003, American Chemical Society (ACS)

    Professor Yaoqi Zhou

  131. Cooperativity in Scapharca Dimeric Hemoglobin: Simulation of Binding Intermediates and Elucidation of the Role of Interfacial Water

    Article • Journal of Molecular Biology, February 2003, Elsevier

    Professor Yaoqi Zhou

  132. The role of sidechain packing and native contact interactions in folding: Discontinuous molecular dynamics folding simulations of an all-atom Gō model of fragment B of Staphylococcal protein A

    Article • The Journal of Chemical Physics, November 2002, American Institute of Physics

    Professor Yaoqi Zhou

  133. Distance‐scaled, finite ideal‐gas reference state improves structure‐derived potentials of mean force for structure selection and stability prediction

    Article • Protein Science, November 2002, Wiley

    Professor Yaoqi Zhou

  134. Stability scale and atomic solvation parameters extracted from 1023 mutation experiments

    Article • Proteins Structure Function and Bioinformatics, October 2002, Wiley

    Professor Yaoqi Zhou

  135. Protein Folding Pathways and Kinetics: Molecular Dynamics Simulations of β-Strand Motifs

    Article • Biophysical Journal, August 2002, Elsevier

    Professor Yaoqi Zhou

  136. The dual role of a loop with low loop contact distance in folding and domain swapping

    Article • Protein Science, July 2002, Wiley

    Professor Yaoqi Zhou

  137. Role of hydrophilic and hydrophobic contacts in folding of the second β‐hairpin fragment of protein G: Molecular dynamics simulation studies of an all‐atom model

    Article • Proteins Structure Function and Bioinformatics, February 2002, Wiley

    Professor Yaoqi Zhou

  138. Folding Thermodynamics of Model Four-Strand Antiparallel β-Sheet Proteins

    Article • Biophysical Journal, February 2002, Elsevier

    Professor Yaoqi Zhou

  139. The distance fluctuation criterion for melting: Comparison of square-well and Morse potential models for clusters and homopolymers

    Article • The Journal of Chemical Physics, February 2002, American Institute of Physics

    Professor Yaoqi Zhou

  140. Thermodynamics of an All-Atom Off-Lattice Model of the Fragment B ofStaphylococcalProtein A:  Implication for the Origin of the Cooperativity of Protein Folding

    Article • The Journal of Physical Chemistry B, January 2002, American Chemical Society (ACS)

    Professor Yaoqi Zhou

  141. Folding Rate Prediction Using Total Contact Distance

    Article • Biophysical Journal, January 2002, Elsevier

    Professor Yaoqi Zhou

  142. Fast and accurate thermodynamics of square-well systems from umbrella-sampling simulations of hard-sphere systems

    Article • The Journal of Chemical Physics, October 2001, American Institute of Physics

    Professor Yaoqi Zhou

  143. Protein Motions at Zero-Total Angular Momentum: The Importance of Long-Range Correlations

    Article • Biophysical Journal, December 2000, Elsevier

    Professor Yaoqi Zhou

  144. Folding of a model three-helix bundle protein: a thermodynamic and kinetic analysis 1 1Edited by A. R. Fersht

    Article • Journal of Molecular Biology, November 1999, Elsevier

    Professor Yaoqi Zhou

  145. Interpreting the folding kinetics of helical proteins

    Article • Nature, September 1999, Springer Science + Business Media

    Professor Yaoqi Zhou

  146. Article • Nature, September 1999, Nature

    Professor Yaoqi Zhou

  147. The calorimetric criterion for a two‐state process revisited

    Article • Protein Science, January 1999, Wiley

    Professor Yaoqi Zhou

  148. Native proteins are surface-molten solids: application of the lindemann criterion for the solid versus liquid state

    Article • Journal of Molecular Biology, January 1999, Elsevier

    Professor Yaoqi Zhou

  149. Solute excluded-volume effects on the stability of globular proteins: A statistical thermodynamic theory

    Article • Biopolymers, December 1998, Wiley

    Professor Yaoqi Zhou

  150. Salt Effects on Protein Titration and Binding

    Article • The Journal of Physical Chemistry B, November 1998, American Chemical Society (ACS)

    Professor Yaoqi Zhou

  151. Folding thermodynamics of a model three-helix-bundle protein

    Article • Proceedings of the National Academy of Sciences, December 1997, Proceedings of the National Academy of Sciences

    Professor Yaoqi Zhou

  152. Equilibrium thermodynamics of homopolymers and clusters: Molecular dynamics and Monte Carlo simulations of systems with square-well interactions

    Article • The Journal of Chemical Physics, December 1997, American Institute of Physics

    Professor Yaoqi Zhou

  153. Exact results for the effect of bond flexibility on the structure and the collapse transition of isolated square-well trimers

    Article • Molecular Physics, December 1996, Taylor & Francis

    Professor Yaoqi Zhou

  154. Exact results for the effect of bond flexibility on the structure and the collapse transition of isolated square-well trimers

    Article • Molecular Physics, December 1996, Taylor & Francis

    Professor Yaoqi Zhou

  155. First-Order Disorder-to-Order Transition in an Isolated Homopolymer Model

    Article • Physical Review Letters, September 1996, American Physical Society (APS)

    Professor Yaoqi Zhou

  156. Solute excluded‐volume effects on the stability of globular proteins: A statistical thermodynamic theory

    Article • Biopolymers, February 1996, Wiley

    Professor Yaoqi Zhou

  157. Phase Separation of Ionic Fluids:  An Extended Ebeling−Grigo Approach

    Article • The Journal of Physical Chemistry B, January 1996, American Chemical Society (ACS)

    Professor Yaoqi Zhou

  158. Exact results for isolated sticky chains

    Article • Molecular Physics, December 1995, Taylor & Francis

    Professor Yaoqi Zhou

  159. Linear dependence on chain length for the thermodynamic properties of tangent hard-sphere chains

    Article • Molecular Physics, December 1995, Taylor & Francis

    Professor Yaoqi Zhou

  160. Thermodynamic perturbation theory for fused hard-sphere and hard-disk chain fluids

    Article • The Journal of Chemical Physics, August 1995, American Institute of Physics

    Professor Yaoqi Zhou

  161. 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

    Article • The Journal of Chemical Physics, May 1995, American Institute of Physics

    Professor Yaoqi Zhou

  162. Fused hard-sphere chain molecules: Comparison between Monte Carlo simulation for the bulk pressure and generalized Flory theories

    Article • The Journal of Chemical Physics, April 1995, American Institute of Physics

    Professor Yaoqi Zhou

  163. Criticality of charged systems. I. The restricted primitive model

    Article • The Journal of Chemical Physics, April 1995, American Institute of Physics

    Professor Yaoqi Zhou

  164. Criticality of charged systems. II. The binary mixture of hard spheres and ions

    Article • The Journal of Chemical Physics, April 1995, American Institute of Physics

    Professor Yaoqi Zhou

  165. Analytical approach to molecular liquids. V. Symmetric dissociative dipolar dumbbells with the bonding length σ/3≤L≤σ/2 and related systems

    Article • The Journal of Chemical Physics, April 1993, American Institute of Physics

    Professor Yaoqi Zhou

  166. Microscopic modelling of association

    Article • Fluid Phase Equilibria, November 1992, Elsevier

    Professor Yaoqi Zhou

  167. Electron rearrangement and energy relaxation due to a core hole creation in molecules

    Article • The Journal of Physical Chemistry B, April 1992, American Chemical Society (ACS)

    Professor Yaoqi Zhou

  168. Chemical association in simple models of molecular and ionic fluids. III. The cavity function

    Article • The Journal of Chemical Physics, January 1992, American Institute of Physics

    Professor Yaoqi Zhou

  169. Chemical association in simple models of molecular and ionic fluids. II. Thermodynamic properties

    Article • The Journal of Chemical Physics, January 1992, American Institute of Physics

    Professor Yaoqi Zhou

  170. Outer-sphere electron-transfer reactions in model molecular solvents: the mean spherical approximation

    Article • Chemical Physics, April 1991, Elsevier

    Professor Yaoqi Zhou

  171. Ion solvation dynamics in an interaction-site model solvent

    Article • Chemical Physics, April 1991, Elsevier

    Professor Yaoqi Zhou

  172. Nonlocal integral-equation approximations. II. Lennard-Jones fluids

    Article • The Journal of Chemical Physics, May 1990, American Institute of Physics

    Professor Yaoqi Zhou

  173. Nonlocal integral-equation approximations. I. The zeroth order (hydrostatic) approximation with applications

    Article • The Journal of Chemical Physics, May 1990, American Institute of Physics

    Professor Yaoqi Zhou

  174. Fluids inside a pore—An integral equation approach

    Article • Molecular Physics, December 1989, Taylor & Francis

    Professor Yaoqi Zhou

  175. Analytical approach to molecular liquids. II. Solvation of ions in molecular fluids

    Article • The Journal of Chemical Physics, October 1989, American Institute of Physics

    Professor Yaoqi Zhou

  176. Analytical approach to molecular liquids. I. Site–site interaction model using an extended mean-spherical approximation

    Article • The Journal of Chemical Physics, October 1989, American Institute of Physics

    Professor Yaoqi Zhou

  177. Analytical approach to molecular liquids. III. The Born solvation free energy of two fixed ions in a dipolar solvent

    Article • The Journal of Chemical Physics, October 1989, American Institute of Physics

    Professor Yaoqi Zhou

  178. Analytical approach to molecular liquids. IV. Solvation dynamics and electron-transfer reactions

    Article • The Journal of Chemical Physics, October 1989, American Institute of Physics

    Professor Yaoqi Zhou

  179. Chemical association in simple models of molecular and ionic fluids

    Article • The Journal of Chemical Physics, September 1989, American Institute of Physics

    Professor Yaoqi Zhou

  180. The theory of semipermeable vesicles and membranes: An integral-equation approach. III. Vesicles with internal nonpermeating ions

    Article • The Journal of Chemical Physics, September 1989, American Institute of Physics

    Professor Yaoqi Zhou

  181. Fluids inside a pore—an integral-equation approach

    Article • Molecular Physics, March 1989, Taylor & Francis

    Professor Yaoqi Zhou

  182. Fluids inside a pore—an integral-equation approach

    Article • Molecular Physics, March 1989, Taylor & Francis

    Professor Yaoqi Zhou

  183. The theory of semipermeable vesicles and membranes: An integral-equation approach. II. Donnan equilibrium

    Article • The Journal of Chemical Physics, December 1988, American Institute of Physics

    Professor Yaoqi Zhou

  184. The theory of semipermeable vesicles and membranes: An integral-equation approach. I. General formalism and application to a hard-sphere mixture

    Article • The Journal of Chemical Physics, December 1988, American Institute of Physics

    Professor Yaoqi Zhou

  185. Equations of state for hard-sphere fluids

    Article • International Journal of Thermophysics, November 1988, Springer Science + Business Media

    Professor Yaoqi Zhou

  186. Note on standard free energy of transfer and partitioning of ionic species between two fluid phases

    Article • The Journal of Chemical Physics, September 1988, American Institute of Physics

    Professor Yaoqi Zhou

  187. The hard-sphere fluid: New exact results with applications

    Article • Journal of Statistical Physics, September 1988, Springer Science + Business Media

    Professor Yaoqi Zhou

  188. Faculty of 1000 evaluation for Evaluating template-based and template-free protein-protein complex structure prediction.

    Article • Faculty of 1000, Ltd.

    Professor Yaoqi Zhou

  189. Faculty of 1000 evaluation for Golden triangle for folding rates of globular proteins.

    Article • Faculty of 1000, Ltd.

    Professor Yaoqi Zhou

  190. Faculty of 1000 evaluation for Evolutionary optimization of protein folding.

    Article • Faculty of 1000, Ltd.

    Professor Yaoqi Zhou

  191. Faculty of 1000 evaluation for Buried and accessible surface area control intrinsic protein flexibility.

    Article • Faculty of 1000, Ltd.

    Professor Yaoqi Zhou

  192. Faculty of 1000 evaluation for Residue level quantification of protein stability in living cells.

    Article • Faculty of 1000, Ltd.

    Professor Yaoqi Zhou

  193. Faculty of 1000 evaluation for Quantitative modeling of transcription factor binding specificities using DNA shape.

    Article • Faculty of 1000, Ltd.

    Professor Yaoqi Zhou

  194. Faculty of 1000 evaluation for Single-molecule correlated chemical probing of RNA.

    Article • Faculty of 1000, Ltd.

    Professor Yaoqi Zhou

  195. Faculty of 1000 evaluation for Removing T-cell epitopes with computational protein design.

    Article • Faculty of 1000, Ltd.

    Professor Yaoqi Zhou

  196. Faculty of 1000 evaluation for Knowledge discovery by accuracy maximization.

    Article • Faculty of 1000, Ltd.

    Professor Yaoqi Zhou

  197. Faculty of 1000 evaluation for Specific RNA-Binding Antibodies with a Four-Amino-Acid Code.

    Article • Faculty of 1000, Ltd.

    Professor Yaoqi Zhou

  198. Faculty of 1000 evaluation for Protein-protein association rates captured in a single geometric parameter.

    Article • Faculty of 1000, Ltd.

    Professor Yaoqi Zhou

  199. Faculty of 1000 evaluation for Inactive conformation enhances binding function in physiological conditions.

    Article • Faculty of 1000, Ltd.

    Professor Yaoqi Zhou

  200. Faculty of 1000 evaluation for Blind prediction of charged ligand binding affinities in a model binding site.

    Article • Faculty of 1000, Ltd.

    Professor Yaoqi Zhou

  201. Faculty of 1000 evaluation for Proteins feel more than they see: Fine-tuning of binding affinity by properties of the non-interacting surface.

    Article • Faculty of 1000, Ltd.

    Professor Yaoqi Zhou

  202. Faculty of 1000 evaluation for The s2D Method: Simultaneous Sequence-Based Prediction of the Statistical Populations of Ordered and Disordered Regions in Proteins.

    Article • Faculty of 1000, Ltd.

    Professor Yaoqi Zhou

  203. Faculty of 1000 evaluation for The Contribution of Missense Mutations in Core and Rim Residues of Protein-Protein Interfaces to Human Disease.

    Article • Faculty of 1000, Ltd.

    Professor Yaoqi Zhou

  204. Protein Structure Prediction

    Article • Springer Science + Business Media

    Professor Yaoqi Zhou