Yaoqi Zhou - Publications

State University of New York, Buffalo, Buffalo, NY, United States 
General Biophysics, Bioinformatics Biology

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Year Citation  Score
2019 Zhou B, Yang Y, Zhan J, Dou X, Wang J, Zhou Y. Predicting functional long non-coding RNAs validated by low throughput experiments. Rna Biology. 1-10. PMID 31345106 DOI: 10.1080/15476286.2019.1644590  1
2019 Clark WT, Kasak L, Bakolitsa C, Hu Z, Andreoletti G, Babbi G, Bromberg Y, Casadio R, Dunbrack R, Folkman L, Ford CT, Jones D, Katsonis P, Kundu K, Lichtarge O, ... ... Zhou Y, et al. Assessment of predicted enzymatic activity of alpha-N-acetylglucosaminidase (NAGLU) variants of unknown significance for CAGI 2016. Human Mutation. PMID 31342580 DOI: 10.1002/humu.23875  0.52
2019 Savojardo C, Petrosino M, Babbi G, Bovo S, Corbi-Verge C, Casadio R, Fariselli P, Folkman L, Garg A, Karimi M, Katsonis P, Kim PM, Lichtarge O, Martelli PL, Pasquo A, ... ... Zhou Y, et al. Evaluating the predictions of the protein stability change upon single amino acid substitutions for the FXN CAGI5 challenge. Human Mutation. PMID 31209948 DOI: 10.1002/humu.23843  0.52
2019 Pejaver V, Babbi G, Casadio R, Folkman L, Katsonis P, Kundu K, Lichtarge O, Martelli PL, Miller M, Moult J, Pal LR, Savojardo C, Yin Y, Zhou Y, Radivojac P, et al. Assessment of methods for predicting the effects of PTEN and TPMT protein variants. Human Mutation. PMID 31184403 DOI: 10.1002/humu.23838  0.52
2019 Zhou B, Zhao H, Yu J, Guo C, Dou X, Song F, Hu G, Cao Z, Qu Y, Yang Y, Zhou Y, Wang J. Experimentally Validated Plant lncRNAs in EVLncRNAs Database. Methods in Molecular Biology (Clifton, N.J.). 1933: 431-437. PMID 30945202 DOI: 10.1007/978-1-4939-9045-0_27  1
2019 Taherzadeh G, Dehzangi A, Golchin M, Zhou Y, Campbell MP. SPRINT-Gly: Predicting N- and O-linked glycosylation sites of human and mouse proteins by using sequence and predicted structural properties. Bioinformatics (Oxford, England). PMID 30903686 DOI: 10.1093/bioinformatics/btz215  0.84
2019 Cao Z, Zhang X, Wang C, Liu L, Zhao L, Wang J, Zhou Y. Different effects of cholesterol on membrane permeation of arginine and tryptophan revealed by bias-exchange metadynamics simulations. The Journal of Chemical Physics. 150: 084106. PMID 30823753 DOI: 10.1063/1.5082351  1
2019 Litfin T, Yang Y, Zhou Y. SPOT-peptide: Template-based prediction of peptide-binding proteins and peptide-binding sites. Journal of Chemical Information and Modeling. PMID 30698427 DOI: 10.1021/acs.jcim.8b00777  1
2018 Hanson J, Paliwal K, Litfin T, Yang Y, Zhou Y. Improving Prediction of Protein Secondary Structure, Backbone Angles, Solvent Accessibility, and Contact Numbers by Using Predicted Contact Maps and an Ensemble of Recurrent and Residual Convolutional Neural Networks. Bioinformatics (Oxford, England). PMID 30535134 DOI: 10.1093/bioinformatics/bty1006  1
2018 Bajzikova M, Kovarova J, Coelho AR, Boukalova S, Oh S, Rohlenova K, Svec D, Hubackova S, Endaya B, Judasova K, Bezawork-Geleta A, Kluckova K, Chatre L, Zobalova R, Novakova A, ... ... Zhou Y, et al. Reactivation of Dihydroorotate Dehydrogenase-Driven Pyrimidine Biosynthesis Restores Tumor Growth of Respiration-Deficient Cancer Cells. Cell Metabolism. PMID 30449682 DOI: 10.1016/j.cmet.2018.10.014  0.6
2018 Hanson J, Paliwal K, Zhou Y. Accurate Single-Sequence Prediction of Protein Intrinsic Disorder by an Ensemble of Deep Recurrent and Convolutional Architectures. Journal of Chemical Information and Modeling. PMID 30395465 DOI: 10.1021/acs.jcim.8b00636  0.68
2018 Heffernan R, Paliwal K, Lyons J, Singh J, Yang Y, Zhou Y. Single-sequence-based prediction of protein secondary structures and solvent accessibility by deep whole-sequence learning. Journal of Computational Chemistry. PMID 30368831 DOI: 10.1002/jcc.25534  1
2018 Zhan J, Jia H, Semchenko EA, Bian Y, Zhou AM, Li Z, Yang Y, Wang J, Sarkar S, Totsika M, Blanchard H, Jen FE, Ye Q, Haselhorst T, Jennings MP, ... ... Zhou Y, et al. Self-derived structure-disrupting peptides targeting methionine aminopeptidase in pathogenic bacteria: a new strategy to generate antimicrobial peptides. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. fj201700613RR. PMID 30260702 DOI: 10.1096/fj.201700613RR  1
2018 Tiralongo J, Cooper O, Litfin T, Yang Y, King R, Zhan J, Zhao H, Bovin N, Day CJ, Zhou Y. YesU from Bacillus subtilis preferentially binds fucosylated glycans. Scientific Reports. 8: 13139. PMID 30177739 DOI: 10.1038/s41598-018-31241-8  1
2018 Singh J, Hanson J, Heffernan R, Paliwal K, Yang Y, Zhou Y. Detecting Proline and Non-Proline Cis-Isomers In Protein Structures from Sequences Using Deep Residual Ensemble Learning. Journal of Chemical Information and Modeling. PMID 30118602 DOI: 10.1021/acs.jcim.8b00442  1
2018 Zhao H, Taherzadeh G, Zhou Y, Yang Y. Computational Prediction of Carbohydrate-Binding Proteins and Binding Sites. Current Protocols in Protein Science. e75. PMID 30106511 DOI: 10.1002/cpps.75  1
2018 Hanson J, Paliwal K, Litfin T, Yang Y, Zhou Y. Accurate Prediction of Protein Contact Maps by Coupling Residual Two-Dimensional Bidirectional Long Short-Term Memory with Convolutional Neural Networks. Bioinformatics (Oxford, England). PMID 29931279 DOI: 10.1093/bioinformatics/bty481  1
2018 Zhao L, Cao Z, Bian Y, Hu G, Wang J, Zhou Y. Molecular Dynamics Simulations of Human Antimicrobial Peptide LL-37 in Model POPC and POPG Lipid Bilayers. International Journal of Molecular Sciences. 19. PMID 29652823 DOI: 10.3390/ijms19041186  1
2018 Atack JM, Yang Y, Seib KL, Zhou Y, Jennings MP. A survey of Type III restriction-modification systems reveals numerous, novel epigenetic regulators controlling phase-variable regulons; phasevarions. Nucleic Acids Research. PMID 29554328 DOI: 10.1093/nar/gky192  1
2018 Cao Z, Bian Y, Hu G, Zhao L, Kong Z, Yang Y, Wang J, Zhou Y. Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids. International Journal of Molecular Sciences. 19. PMID 29547563 DOI: 10.3390/ijms19030885  1
2018 O'Connell J, Li Z, Hanson J, Heffernan R, Lyons J, Paliwal K, Dehzangi A, Yang Y, Zhou Y. SPIN2: Predicting sequence profiles from protein structures using deep neural networks. Proteins. PMID 29508448 DOI: 10.1002/prot.25489  1
2018 Gao J, Yang Y, Zhou Y. Grid-based prediction of torsion angle probabilities of protein backbone and its application to discrimination of protein intrinsic disorder regions and selection of model structures. Bmc Bioinformatics. 19: 29. PMID 29390958 DOI: 10.1186/s12859-018-2031-7  1
2018 Khorramdelazad M, Bar I, Whatmore P, Smetham G, Bhaaskaria V, Yang Y, Bai SH, Mantri N, Zhou Y, Ford R. Transcriptome profiling of lentil (Lens culinaris) through the first 24 hours of Ascochyta lentis infection reveals key defence response genes. Bmc Genomics. 19: 108. PMID 29385986 DOI: 10.1186/s12864-018-4488-1  1
2017 Guruge I, Taherzadeh G, Zhan J, Zhou Y, Yang Y. B-factor profile prediction for RNA flexibility using support vector machines. Journal of Computational Chemistry. PMID 29164646 DOI: 10.1002/jcc.25124  1
2017 Zhao H, Yang Y, Lu Y, Mort M, Cooper DN, Zuo Z, Zhou Y. Quantitative mapping of genetic similarity in human heritable diseases by shared mutations. Human Mutation. PMID 29044887 DOI: 10.1002/humu.23358  1
2017 Taherzadeh G, Zhou Y, Liew AW, Yang Y. Structure-based prediction of protein-peptide binding regions using Random Forest. Bioinformatics (Oxford, England). PMID 29028926 DOI: 10.1093/bioinformatics/btx614  1
2017 Zhou B, Zhao H, Yu J, Guo C, Dou X, Song F, Hu G, Cao Z, Qu Y, Yang Y, Zhou Y, Wang J. EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments. Nucleic Acids Research. PMID 28985416 DOI: 10.1093/nar/gkx677  1
2017 Jegousse C, Yang Y, Zhan J, Wang J, Zhou Y. Structural signatures of thermal adaptation of bacterial ribosomal RNA, transfer RNA, and messenger RNA. Plos One. 12: e0184722. PMID 28910383 DOI: 10.1371/journal.pone.0184722  1
2017 Brown P, Zhou Y. Biomedical literature: Testers wanted for article search tool. Nature. 549: 31. PMID 28880292 DOI: 10.1038/549031c  0.52
2017 Livingstone M, Folkman L, Yang Y, Zhang P, Mort M, Cooper DN, Liu Y, Stantic B, Zhou Y. Investigating DNA, RNA and protein-based features as a means to discriminate pathogenic synonymous variants. Human Mutation. PMID 28649752 DOI: 10.1002/humu.23283  1
2017 Carraro M, Minervini G, Giollo M, Bromberg Y, Capriotti E, Casadio R, Dunbrack R, Elefanti L, Fariselli P, Ferrari C, Gough J, Katsonis P, Leonardi E, Lichtarge O, Menin C, ... ... Zhou Y, et al. Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI. Human Mutation. PMID 28440912 DOI: 10.1002/humu.23235  1
2017 Heffernan R, Yang Y, Paliwal K, Zhou Y. Capturing Non-Local Interactions by Long Short Term Memory Bidirectional Recurrent Neural Networks for Improving Prediction of Protein Secondary Structure, Backbone Angles, Contact Numbers, and Solvent Accessibility. Bioinformatics (Oxford, England). PMID 28430949 DOI: 10.1093/bioinformatics/btx218  1
2017 Zhang X, Li M, Lin H, Rao X, Feng W, Yang Y, Mort M, Cooper DN, Wang Y, Wang Y, Wells C, Zhou Y, Liu Y. regSNPs-splicing: a tool for prioritizing synonymous single-nucleotide substitution. Human Genetics. PMID 28391525 DOI: 10.1007/s00439-017-1783-x  1
2017 Yu JF, Dou XH, Sha YJ, Wang CL, Wang HB, Chen YT, Zhang F, Zhou Y, Wang JH. DisBind: A database of classified functional binding sites in disordered and structured regions of intrinsically disordered proteins. Bmc Bioinformatics. 18: 206. PMID 28381244 DOI: 10.1186/s12859-017-1620-1  0.64
2017 Xu S, Zhan J, Man B, Jiang S, Yue W, Gao S, Guo C, Liu H, Li Z, Wang J, Zhou Y. Real-time reliable determination of binding kinetics of DNA hybridization using a multi-channel graphene biosensor. Nature Communications. 8: 14902. PMID 28322227 DOI: 10.1038/ncomms14902  1
2017 Cao H, Wei D, Yang Y, Shang Y, Li G, Zhou Y, Ma Q, Xu Y. Systems-level understanding of ethanol-induced stresses and adaptation in E. coli. Scientific Reports. 7: 44150. PMID 28300180 DOI: 10.1038/srep44150  1
2017 Litfin T, Zhou Y, Yang Y. SPOT-Ligand 2: Improving structure-based virtual screening by binding-homology search on an expanded structural template library. Bioinformatics (Oxford, England). PMID 28057679 DOI: 10.1093/bioinformatics/btw829  1
2017 Zhang T, Faraggi E, Li Z, Zhou Y. Intrinsic Disorder and Semi-disorder Prediction by SPINE-D. Methods in Molecular Biology (Clifton, N.J.). 1484: 159-174. PMID 27787826 DOI: 10.1007/978-1-4939-6406-2_12  0.68
2017 Faraggi E, Kouza M, Zhou Y, Kloczkowski A. Fast and Accurate Accessible Surface Area Prediction Without a Sequence Profile. Methods in Molecular Biology (Clifton, N.J.). 1484: 127-136. PMID 27787824 DOI: 10.1007/978-1-4939-6406-2_10  0.64
2017 Yang Y, Heffernan R, Paliwal K, Lyons J, Dehzangi A, Sharma A, Wang J, Sattar A, Zhou Y. SPIDER2: A Package to Predict Secondary Structure, Accessible Surface Area, and Main-Chain Torsional Angles by Deep Neural Networks. Methods in Molecular Biology (Clifton, N.J.). 1484: 55-63. PMID 27787820 DOI: 10.1007/978-1-4939-6406-2_6  1
2016 Yang Y, Gao J, Wang J, Heffernan R, Hanson J, Paliwal K, Zhou Y. Sixty-five years of the long march in protein secondary structure prediction: the final stretch? Briefings in Bioinformatics. PMID 28040746 DOI: 10.1093/bib/bbw129  1
2016 Hanson J, Yang Y, Paliwal K, Zhou Y. Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks. Bioinformatics (Oxford, England). PMID 28011771 DOI: 10.1093/bioinformatics/btw678  1
2016 Yang Y, Li X, Zhao H, Zhan J, Wang J, Zhou Y. Genome-scale characterization of RNA tertiary structures and their functional impact by RNA solvent accessibility prediction. Rna (New York, N.Y.). PMID 27807179 DOI: 10.1261/rna.057364.116  1
2016 Wang T, Yang Y, Zhou Y, Gong H. LRFragLib: an effective algorithm to identify fragments for de novo protein structure prediction. Bioinformatics (Oxford, England). PMID 27797773 DOI: 10.1093/bioinformatics/btw668  1
2016 Taherzadeh G, Zhou Y, Liew AW, Yang Y. Sequence-based Prediction of Protein-Carbohydrate Binding Sites Using Support Vector Machines. Journal of Chemical Information and Modeling. PMID 27623166 DOI: 10.1021/acs.jcim.6b00320  1
2016 Li M, Feng W, Zhang X, Yang Y, Wang K, Mort M, Cooper DN, Wang Y, Zhou Y, Liu Y. ExonImpact: Prioritizing Pathogenic Alternative Splicing Events. Human Mutation. PMID 27604408 DOI: 10.1002/humu.23111  1
2016 Gao J, Yang Y, Zhou Y. Predicting the errors of predicted local backbone angles and nonlocal solvent-accessibilities of proteins by deep neural networks. Bioinformatics (Oxford, England). PMID 27551104 DOI: 10.1093/bioinformatics/btw549  1
2016 Stanisic DI, Gerrard J, Fink J, Griffin PM, Liu XQ, Sundac L, Sekuloski S, Rodriguez IB, Pingnet J, Yang Y, Zhou Y, Trenholme KR, Wang CY, Hackett H, Chan JA, et al. Infectivity of Plasmodium falciparum in malaria-naïve individuals is related to knob expression and cytoadherence of the parasite. Infection and Immunity. PMID 27382019 DOI: 10.1128/IAI.00414-16  0.32
2016 Zhang W, Yang M, Yang Y, Zhan J, Zhou Y, Zhao X. Optimal secretion of alkali-tolerant xylanase in Bacillus subtilis by signal peptide screening. Applied Microbiology and Biotechnology. PMID 27225471 DOI: 10.1007/s00253-016-7615-4  1
2016 Ni G, Chen S, Yang Y, Cummins SF, Zhan J, Li Z, Zhu B, Mounsey K, Walton S, Wei MQ, Wang Y, Zhou Y, Wang T, Liu X. Investigation the Possibility of Using Peptides with a Helical Repeating Pattern of Hydro-Phobic and Hydrophilic Residues to Inhibit IL-10. Plos One. 11: e0153939. PMID 27100390 DOI: 10.1371/journal.pone.0153939  1
2016 Yang Y, Zhan J, Zhou Y. SPOT-Ligand: Fast and effective structure-based virtual screening by binding homology search according to ligand and receptor similarity. Journal of Computational Chemistry. PMID 27074979 DOI: 10.1002/jcc.24380  1
2016 Hoque MT, Yang Y, Mishra A, Zhou Y. sDFIRE: Sequence-specific statistical energy function for protein structure prediction by decoy selections. Journal of Computational Chemistry. PMID 26849026 DOI: 10.1002/jcc.24298  1
2016 Taherzadeh G, Yang Y, Zhang T, Liew AW, Zhou Y. Sequence-based prediction of protein-peptide binding sites using support vector machine. Journal of Computational Chemistry. PMID 26833816 DOI: 10.1002/jcc.24314  1
2016 Folkman L, Stantic B, Sattar A, Zhou Y. EASE-MM: Sequence-Based Prediction of Mutation-Induced Stability Changes with Feature-Based Multiple Models. Journal of Molecular Biology. PMID 26804571 DOI: 10.1016/j.jmb.2016.01.012  0.52
2016 Yu JF, Cao Z, Yang Y, Wang CL, Su ZD, Zhao YW, Wang JH, Zhou Y. Natural protein sequences are more intrinsically disordered than random sequences. Cellular and Molecular Life Sciences : Cmls. PMID 26801222 DOI: 10.1007/s00018-016-2138-9  1
2015 Yang Y, Zhou Y. Effective protein conformational sampling based on predicted torsion angles. Journal of Computational Chemistry. PMID 26696379 DOI: 10.1002/jcc.24285  1
2015 Heffernan R, Dehzangi A, Lyons J, Paliwal K, Sharma A, Wang J, Sattar A, Zhou Y, Yang Y. Highly Accurate Sequence-based Prediction of Half-Sphere Expo-sures of Amino Acid Residues in Proteins. Bioinformatics (Oxford, England). PMID 26568622 DOI: 10.1093/bioinformatics/btv665  1
2015 Brown P, Pullan W, Yang Y, Zhou Y. Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic. Bioinformatics (Oxford, England). PMID 26454279 DOI: 10.1093/bioinformatics/btv580  1
2015 Lyons J, Dehzangi A, Heffernan R, Yang Y, Zhou Y, Sharma A, Paliwal K. Advancing the Accuracy of Protein Fold Recognition by Utilizing Profiles from Hidden Markov Models. Ieee Transactions On Nanobioscience. PMID 26208362 DOI: 10.1109/TNB.2015.2457906  1
2015 Heffernan R, Paliwal K, Lyons J, Dehzangi A, Sharma A, Wang J, Sattar A, Yang Y, Zhou Y. Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning. Scientific Reports. 5: 11476. PMID 26098304 DOI: 10.1038/srep11476  1
2015 Folkman L, Yang Y, Li Z, Stantic B, Sattar A, Mort M, Cooper DN, Liu Y, Zhou Y. DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels. Bioinformatics (Oxford, England). 31: 1599-606. PMID 25573915 DOI: 10.1093/bioinformatics/btu862  1
2014 Zhao H, Yang Y, von Itzstein M, Zhou Y. Carbohydrate-binding protein identification by coupling structural similarity searching with binding affinity prediction. Journal of Computational Chemistry. 35: 2177-83. PMID 25220682 DOI: 10.1002/jcc.23730  1
2014 Lyons J, Dehzangi A, Heffernan R, Sharma A, Paliwal K, Sattar A, Zhou Y, Yang Y. Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network. Journal of Computational Chemistry. 35: 2040-6. PMID 25212657 DOI: 10.1002/jcc.23718  1
2014 Faraggi E, Zhou Y, Kloczkowski A. Accurate single-sequence prediction of solvent accessible surface area using local and global features. Proteins. 82: 3170-6. PMID 25204636 DOI: 10.1002/prot.24682  1
2014 Li Z, Yang Y, Faraggi E, Zhan J, Zhou Y. Direct prediction of profiles of sequences compatible with a protein structure by neural networks with fragment-based local and energy-based nonlocal profiles. Proteins. 82: 2565-73. PMID 24898915 DOI: 10.1002/prot.24620  1
2014 Zhao H, Wang J, Zhou Y, Yang Y. Predicting DNA-binding proteins and binding residues by complex structure prediction and application to human proteome. Plos One. 9: e96694. PMID 24792350 DOI: 10.1371/journal.pone.0096694  1
2014 Yang Y, Zhao H, Wang J, Zhou Y. SPOT-Seq-RNA: predicting protein-RNA complex structure and RNA-binding function by fold recognition and binding affinity prediction. Methods in Molecular Biology (Clifton, N.J.). 1137: 119-30. PMID 24573478 DOI: 10.1007/978-1-4939-0366-5_9  1
2014 Zhang X, Lin H, Zhao H, Hao Y, Mort M, Cooper DN, Zhou Y, Liu Y. Impact of human pathogenic micro-insertions and micro-deletions on post-transcriptional regulation. Human Molecular Genetics. 23: 3024-34. PMID 24436305 DOI: 10.1093/hmg/ddu019  1
2014 Liang S, Zhang C, Zhou Y. 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. Journal of Computational Chemistry. 35: 335-41. PMID 24327406 DOI: 10.1002/jcc.23509  0.88
2014 Zhao H, Yang Y, Janga SC, Kao CC, Zhou Y. Prediction and validation of the unexplored RNA-binding protein atlas of the human proteome. Proteins. 82: 640-7. PMID 24123256 DOI: 10.1002/prot.24441  1
2013 Wang J, Yang Y, Cao Z, Li Z, Zhao H, Zhou Y. The role of semidisorder in temperature adaptation of bacterial FlgM proteins. Biophysical Journal. 105: 2598-605. PMID 24314090 DOI: 10.1016/j.bpj.2013.10.026  1
2013 Zhou BR, Feng H, Kato H, Dai L, Yang Y, Zhou Y, Bai Y. Structural insights into the histone H1-nucleosome complex. Proceedings of the National Academy of Sciences of the United States of America. 110: 19390-5. PMID 24218562 DOI: 10.1073/pnas.1314905110  1
2013 Zhao H, Yang Y, Zhou Y. Prediction of RNA binding proteins comes of age from low resolution to high resolution. Molecular Biosystems. 9: 2417-25. PMID 23872922 DOI: 10.1039/c3mb70167k  1
2013 Zhang T, Faraggi E, Li Z, Zhou Y. Intrinsically semi-disordered state and its role in induced folding and protein aggregation. Cell Biochemistry and Biophysics. 67: 1193-205. PMID 23723000 DOI: 10.1007/s12013-013-9638-0  1
2013 Zhao H, Yang Y, Lin H, Zhang X, Mort M, Cooper DN, Liu Y, Zhou Y. DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels. Genome Biology. 14: R23. PMID 23497682 DOI: 10.1186/gb-2013-14-3-r23  1
2013 Li Z, Yang Y, Zhan J, Dai L, Zhou Y. Energy functions in de novo protein design: current challenges and future prospects. Annual Review of Biophysics. 42: 315-35. PMID 23451890 DOI: 10.1146/annurev-biophys-083012-130315  1
2012 Gao J, Faraggi E, Zhou Y, Ruan J, Kurgan L. BEST: improved prediction of B-cell epitopes from antigen sequences. Plos One. 7: e40104. PMID 22761950 DOI: 10.1371/journal.pone.0040104  1
2012 Lu T, Yang Y, Yao B, Liu S, Zhou Y, Zhang C. Template-based structure prediction and classification of transcription factors in Arabidopsis thaliana. Protein Science : a Publication of the Protein Society. 21: 828-38. PMID 22549903 DOI: 10.1002/pro.2066  1
2012 Yang Y, Zhan J, Zhao H, Zhou Y. A new size-independent score for pairwise protein structure alignment and its application to structure classification and nucleic-acid binding prediction. Proteins. 80: 2080-8. PMID 22522696 DOI: 10.1002/prot.24100  1
2012 Zhang T, Faraggi E, Xue B, Dunker AK, Uversky VN, Zhou Y. SPINE-D: accurate prediction of short and long disordered regions by a single neural-network based method. Journal of Biomolecular Structure & Dynamics. 29: 799-813. PMID 22208280 DOI: 10.1080/073911012010525022  1
2012 Faraggi E, Zhang T, Yang Y, Kurgan L, Zhou Y. SPINE X: improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles. Journal of Computational Chemistry. 33: 259-67. PMID 22045506 DOI: 10.1002/jcc.21968  1
2011 Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, ... ... Zhou Y, et al. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. Journal of Molecular Biology. 414: 289-302. PMID 22001016 DOI: 10.1016/j.jmb.2011.09.031  1
2011 Zhao H, Yang Y, Zhou Y. Highly accurate and high-resolution function prediction of RNA binding proteins by fold recognition and binding affinity prediction. Rna Biology. 8: 988-96. PMID 21955494 DOI: 10.4161/rna.8.6.17813  1
2011 Kurgan L, Zhou Y. Machine learning models in protein bioinformatics. Current Protein & Peptide Science. 12: 455. PMID 21787309  0.48
2011 Cheng H, Chan WS, Li Z, Wang D, Liu S, Zhou Y. Small open reading frames: current prediction techniques and future prospect. Current Protein & Peptide Science. 12: 503-7. PMID 21787300  0.88
2011 Mizianty MJ, Zhang T, Xue B, Zhou Y, Dunker AK, Uversky VN, Kurgan L. In-silico prediction of disorder content using hybrid sequence representation. Bmc Bioinformatics. 12: 245. PMID 21682902 DOI: 10.1186/1471-2105-12-245  1
2011 Yang Y, Faraggi E, Zhao H, Zhou Y. 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. Bioinformatics (Oxford, England). 27: 2076-82. PMID 21666270 DOI: 10.1093/bioinformatics/btr350  1
2011 Zhou Y, Duan Y, Yang Y, Faraggi E, Lei H. Trends in template/fragment-free protein structure prediction. Theoretical Chemistry Accounts. 128: 3-16. PMID 21423322 DOI: 10.1007/s00214-010-0799-2  1
2011 Dai L, Zhou Y. Characterizing the existing and potential structural space of proteins by large-scale multiple loop permutations. Journal of Molecular Biology. 408: 585-95. PMID 21376059 DOI: 10.1016/j.jmb.2011.02.056  0.6
2011 Liang S, Zhou Y, Grishin N, Standley DM. Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions. Journal of Computational Chemistry. 32: 1680-6. PMID 21374632 DOI: 10.1002/jcc.21747  0.68
2011 Zhao H, Yang Y, Zhou Y. Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets. Nucleic Acids Research. 39: 3017-25. PMID 21183467 DOI: 10.1093/nar/gkq1266  1
2010 Zhang T, Faraggi E, Zhou Y. Fluctuations of backbone torsion angles obtained from NMR-determined structures and their prediction. Proteins. 78: 3353-62. PMID 20818661 DOI: 10.1002/prot.22842  1
2010 Dai L, Yang Y, Kim HR, Zhou Y. Improving computational protein design by using structure-derived sequence profile. Proteins. 78: 2338-48. PMID 20544969 DOI: 10.1002/prot.22746  1
2010 Zhao H, Yang Y, Zhou Y. Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function. Bioinformatics (Oxford, England). 26: 1857-63. PMID 20525822 DOI: 10.1093/bioinformatics/btq295  1
2009 Faraggi E, Yang Y, Zhang S, Zhou Y. Predicting continuous local structure and the effect of its substitution for secondary structure in fragment-free protein structure prediction. Structure (London, England : 1993). 17: 1515-27. PMID 19913486 DOI: 10.1016/j.str.2009.09.006  1
2009 Xu B, Yang Y, Liang H, Zhou Y. An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription-factor binding profiles. Proteins. 76: 718-30. PMID 19274740 DOI: 10.1002/prot.22384  1
2009 Liang S, Wang G, Zhou Y. Refining near-native protein-protein docking decoys by local resampling and energy minimization. Proteins. 76: 309-16. PMID 19156819 DOI: 10.1002/prot.22343  0.68
2009 Xue B, Faraggi E, Zhou Y. Predicting residue-residue contact maps by a two-layer, integrated neural-network method. Proteins. 76: 176-83. PMID 19137600 DOI: 10.1002/prot.22329  1
2009 Liang S, Li L, Hsu WL, Pilcher MN, Uversky V, Zhou Y, Dunker AK, Meroueh SO. Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculations. Biochemistry. 48: 399-414. PMID 19113835 DOI: 10.1021/bi8017043  0.68
2009 Liang S, Meroueh SO, Wang G, Qiu C, Zhou Y. Consensus scoring for enriching near-native structures from protein-protein docking decoys. Proteins. 75: 397-403. PMID 18831053 DOI: 10.1002/prot.22252  0.68
2009 Faraggi E, Xue B, Zhou Y. 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. Proteins. 74: 847-56. PMID 18704931 DOI: 10.1002/prot.22193  1
2008 Lei H, Wu C, Wang ZX, Zhou Y, Duan Y. Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations. The Journal of Chemical Physics. 128: 235105. PMID 18570534 DOI: 10.1063/1.2937135  0.68
2008 Luo Z, Ding J, Zhou Y. Folding mechanisms of individual beta-hairpins in a Go model of Pin1 WW domain by all-atom molecular dynamics simulations. The Journal of Chemical Physics. 128: 225103. PMID 18554060 DOI: 10.1063/1.2936832  0.92
2008 Zhang W, Liu S, Zhou Y. SP5: improving protein fold recognition by using torsion angle profiles and profile-based gap penalty model. Plos One. 3: e2325. PMID 18523556 DOI: 10.1371/journal.pone.0002325  0.88
2008 Yang Y, 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 : a Publication of the Protein Society. 17: 1212-9. PMID 18469178 DOI: 10.1110/ps.033480.107  1
2008 Yang Y, Zhou Y. Specific interactions for ab initio folding of protein terminal regions with secondary structures. Proteins. 72: 793-803. PMID 18260109 DOI: 10.1002/prot.21968  1
2008 Xue B, Dor O, Faraggi E, Zhou Y. Real-value prediction of backbone torsion angles. Proteins. 72: 427-33. PMID 18214956 DOI: 10.1002/prot.21940  1
2008 Zhang W, Dunker AK, Zhou Y. Assessing secondary structure assignment of protein structures by using pairwise sequence-alignment benchmarks. Proteins. 71: 61-7. PMID 17932927 DOI: 10.1002/prot.21654  1
2007 Liang S, Liu S, Zhang C, Zhou Y. A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys. Proteins. 69: 244-53. PMID 17623864 DOI: 10.1002/prot.21498  0.88
2007 Chen Y, Zhou Y, Ding J. The helix-coil transition revisited. Proteins. 69: 58-68. PMID 17596846 DOI: 10.1002/prot.21492  0.92
2007 Luo Z, Ding J, Zhou Y. Temperature-dependent folding pathways of Pin1 WW domain: an all-atom molecular dynamics simulation of a Gō model. Biophysical Journal. 93: 2152-61. PMID 17513360 DOI: 10.1529/biophysj.106.102095  0.92
2007 Liu S, Zhang C, Liang S, Zhou Y. Fold recognition by concurrent use of solvent accessibility and residue depth. Proteins. 68: 636-45. PMID 17510969 DOI: 10.1002/prot.21459  0.88
2007 Zhou H, Xue B, Zhou Y. DDOMAIN: Dividing structures into domains using a normalized domain-domain interaction profile. Protein Science : a Publication of the Protein Society. 16: 947-55. PMID 17456745 DOI: 10.1110/ps.062597307  1
2007 Dor O, Zhou Y. Real-SPINE: an integrated system of neural networks for real-value prediction of protein structural properties. Proteins. 68: 76-81. PMID 17397056 DOI: 10.1002/prot.21408  1
2007 Dor O, Zhou Y. Achieving 80% ten-fold cross-validated accuracy for secondary structure prediction by large-scale training. Proteins. 66: 838-45. PMID 17177203 DOI: 10.1002/prot.21298  1
2006 Zhou Y, Zhou H, Zhang C, Liu S. What is a desirable statistical energy function for proteins and how can it be obtained? Cell Biochemistry and Biophysics. 46: 165-74. PMID 17012757  1
2006 Liang S, Zhang C, Liu S, Zhou Y. Protein binding site prediction using an empirical scoring function. Nucleic Acids Research. 34: 3698-707. PMID 16893954 DOI: 10.1093/nar/gkl454  0.88
2006 Zhang C, Liu S, Zhou Y. Fast and accurate method for identifying high-quality protein-interaction modules by clique merging and its application to yeast. Journal of Proteome Research. 5: 801-7. PMID 16602686 DOI: 10.1021/pr050366g  0.88
2006 Liu S, Zhang C, Zhou Y. Uneven size distribution of mammalian genes in the number of tissues expressed and in the number of co-expressed genes. Human Molecular Genetics. 15: 1313-8. PMID 16537573 DOI: 10.1093/hmg/ddl051  0.88
2006 Xu Z, Zhang C, Liu S, Zhou Y. QBES: predicting real values of solvent accessibility from sequences by efficient, constrained energy optimization. Proteins. 63: 961-6. PMID 16514609 DOI: 10.1002/prot.20934  0.88
2005 Li H, Zhou Y. Fold helical proteins by energy minimization in dihedral space and a DFIRE-based statistical energy function. Journal of Bioinformatics and Computational Biology. 3: 1151-70. PMID 16278952  1
2005 Zhou H, Zhou Y. SPARKS 2 and SP3 servers in CASP6. Proteins. 61: 152-6. PMID 16187357 DOI: 10.1002/prot.20732  1
2005 Zhou Z, Feng H, Zhou H, Zhou Y, Bai Y. Design and folding of a multidomain protein. Biochemistry. 44: 12107-12. PMID 16142908 DOI: 10.1021/bi050785r  1
2005 Zhou H, Zhou Y. SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures. Bioinformatics (Oxford, England). 21: 3615-21. PMID 16020471 DOI: 10.1093/bioinformatics/bti582  1
2005 Pandey BP, Zhang C, Yuan X, Zi J, Zhou Y. Protein flexibility prediction by an all-atom mean-field statistical theory Protein Science. 14: 1772-1777. PMID 15987905 DOI: 10.1110/ps.041311005  1
2005 Zhang C, Liu S, Zhou Y. Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function. Proteins. 60: 314-8. PMID 15981255 DOI: 10.1002/prot.20576  0.88
2005 Zhou H, Zhang C, Liu S, 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. Nucleic Acids Research. 33: W193-7. PMID 15980453 DOI: 10.1093/nar/gki360  1
2005 Li H, Zhou Y. SCUD: fast structure clustering of decoys using reference state to remove overall rotation. Journal of Computational Chemistry. 26: 1189-92. PMID 15954080 DOI: 10.1002/jcc.20251  1
2005 Liu S, Zhang C, Zhou Y. Domain graph of Arabidopsis proteome by comparative analysis. Journal of Proteome Research. 4: 435-44. PMID 15822920 DOI: 10.1021/pr049805m  0.88
2005 Zhang C, Liu S, Zhu Q, Zhou Y. A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. Journal of Medicinal Chemistry. 48: 2325-35. PMID 15801826 DOI: 10.1021/jm049314d  0.88
2005 Zhou H, Zhou Y. Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins. 58: 321-8. PMID 15523666 DOI: 10.1002/prot.20308  1
2004 Zhang C, Liu S, Zhou H, Zhou Y. The dependence of all-atom statistical potentials on structural training database. Biophysical Journal. 86: 3349-58. PMID 15189839 DOI: 10.1529/biophysj.103.035998  1
2004 Liu S, Zhang C, Zhou H, Zhou Y. A physical reference state unifies the structure-derived potential of mean force for protein folding and binding. Proteins. 56: 93-101. PMID 15162489 DOI: 10.1002/prot.20019  1
2004 Zhou H, Zhou Y. Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition. Proteins. 55: 1005-13. PMID 15146497 DOI: 10.1002/prot.20007  1
2004 Bai Y, Zhou H, Zhou Y. Critical nucleation size in the folding of small apparently two-state proteins. Protein Science : a Publication of the Protein Society. 13: 1173-81. PMID 15075405 DOI: 10.1110/ps.03587604  1
2004 Zhang C, Liu S, Zhou H, 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 Science : a Publication of the Protein Society. 13: 400-11. PMID 14739325 DOI: 10.1110/ps.03348304  1
2004 Zhang C, Liu S, Zhou Y. Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential. Protein Science : a Publication of the Protein Society. 13: 391-9. PMID 14739324 DOI: 10.1110/ps.03411904  0.88
2004 Zhou H, Zhou Y. Quantifying the effect of burial of amino acid residues on protein stability. Proteins. 54: 315-22. PMID 14696193 DOI: 10.1002/prot.10584  1
2004 Jang H, Hall CK, Zhou Y. Assembly and kinetic folding pathways of a tetrameric beta-sheet complex: molecular dynamics simulations on simplified off-lattice protein models. Biophysical Journal. 86: 31-49. PMID 14695247 DOI: 10.1016/S0006-3495(04)74081-3  1
2004 Jang H, Hall CK, Zhou Y. Thermodynamics and stability of a beta-sheet complex: molecular dynamics simulations on simplified off-lattice protein models. Protein Science : a Publication of the Protein Society. 13: 40-53. PMID 14691220 DOI: 10.1110/ps.03162804  1
2003 Zhou H, Zhou Y. Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model-based method. Protein Science : a Publication of the Protein Society. 12: 1547-55. PMID 12824500 DOI: 10.1110/ps.0305103  1
2003 Zhou Y, Zhang C, Stell G, Wang J. 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 Journal of the American Chemical Society. 125: 6300-6305. PMID 12785863 DOI: 10.1021/ja029855x  1
2003 Zhou Y, Zhou H, Karplus M. Cooperativity in Scapharca dimeric hemoglobin: simulation of binding intermediates and elucidation of the role of interfacial water. Journal of Molecular Biology. 326: 593-606. PMID 12559925 DOI: 10.1016/S0022-2836(02)01329-3  1
2002 Zhou H, Zhou Y. Stability scale and atomic solvation parameters extracted from 1023 mutation experiments. Proteins. 49: 483-92. PMID 12402358 DOI: 10.1002/prot.10241  1
2002 Zhou H, Zhou Y. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Science : a Publication of the Protein Society. 11: 2714-26. PMID 12381853 DOI: 10.1110/ps.0217002  1
2002 Jang H, Hall CK, Zhou Y. Protein folding pathways and kinetics: molecular dynamics simulations of beta-strand motifs. Biophysical Journal. 83: 819-35. PMID 12124267 DOI: 10.1016/S0006-3495(02)75211-9  1
2002 Linhananta A, Zhou H, Zhou Y. The dual role of a loop with low loop contact distance in folding and domain swapping. Protein Science : a Publication of the Protein Society. 11: 1695-701. PMID 12070322 DOI: 10.1110/ps.0205002  1
2002 Zhou Y, Linhananta A. Role of hydrophilic and hydrophobic contacts in folding of the second beta-hairpin fragment of protein G: molecular dynamics simulation studies of an all-atom model. Proteins. 47: 154-62. PMID 11933062 DOI: 10.1002/prot.10065  1
2002 Jang H, Hall CK, Zhou Y. Folding thermodynamics of model four-strand antiparallel beta-sheet proteins. Biophysical Journal. 82: 646-59. PMID 11806908 DOI: 10.1016/S0006-3495(02)75428-3  1
2002 Zhou H, Zhou Y. Folding rate prediction using total contact distance. Biophysical Journal. 82: 458-63. PMID 11751332 DOI: 10.1016/S0006-3495(02)75410-6  1
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2018 Taherzadeh G, Yang Y, Xu H, Xue Y, Liew AW, Zhou Y. Predicting lysine-malonylation sites of proteins using sequence and predicted structural features. Journal of Computational Chemistry. PMID 29761520 DOI: 10.1002/jcc.25353  0.01
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