Yuedong Yang - Publications

Affiliations: 
Griffith University 
Area:
protein structure prediction; protein interaction; virtual screening

90 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Wang P, Zheng S, Jiang Y, Li C, Liu J, Wen C, Patronov A, Qian D, Chen H, Yang Y. Structure-Aware Multimodal Deep Learning for Drug-Protein Interaction Prediction. Journal of Chemical Information and Modeling. PMID 35200015 DOI: 10.1021/acs.jcim.2c00060  0.367
2022 Yuan Q, Chen S, Rao J, Zheng S, Zhao H, Yang Y. AlphaFold2-aware protein-DNA binding site prediction using graph transformer. Briefings in Bioinformatics. PMID 35039821 DOI: 10.1093/bib/bbab564  0.404
2021 Sun Z, Zheng S, Zhao H, Niu Z, Lu Y, Pan Y, Yang Y. To improve the predictions of binding residues with DNA, RNA, carbohydrate, and peptide via multi-task deep neural networks. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 34637380 DOI: 10.1109/TCBB.2021.3118916  0.303
2021 Yuan Q, Chen J, Zhao H, Zhou Y, Yang Y. Structure-aware protein-protein interaction site prediction using deep graph convolutional network. Bioinformatics (Oxford, England). PMID 34498061 DOI: 10.1093/bioinformatics/btab643  0.568
2021 Chen J, Zheng S, Zhao H, Yang Y. Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map. Journal of Cheminformatics. 13: 7. PMID 33557952 DOI: 10.1186/s13321-021-00488-1  0.367
2020 Zhou B, Ji B, Liu K, Hu G, Wang F, Chen Q, Yu R, Huang P, Ren J, Guo C, Zhao H, Zhang H, Zhao D, Li Z, Zeng Q, ... ... Yang Y, et al. EVLncRNAs 2.0: an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments. Nucleic Acids Research. PMID 33221906 DOI: 10.1093/nar/gkaa1076  0.552
2020 Tan A, Blakeway LV, Taha, Yang Y, Zhou Y, Atack JM, Peak IR, Seib KL. Moraxella catarrhalis phase-variable loci show differences in expression during conditions relevant to disease. Plos One. 15: e0234306. PMID 32555615 DOI: 10.1371/Journal.Pone.0234306  0.492
2020 Lv X, Chen J, Lu Y, Chen Z, Xiao N, Yang Y. Accurately predicting mutation-caused stability changes from protein sequences using Extreme Gradient Boosting. Journal of Chemical Information and Modeling. PMID 32203653 DOI: 10.1021/Acs.Jcim.0C00064  0.352
2020 Zheng S, Li Y, Chen S, Xu J, Yang Y. Predicting drug–protein interaction using quasi-visual question answering system Nature Machine Intelligence. 2: 134-140. DOI: 10.1038/S42256-020-0152-Y  0.333
2019 Cai Y, Li X, Sun Z, Lu Y, Zhao H, Hanson J, Paliwal K, Litfin T, Zhou Y, Yang Y. SPOT-Fold: Fragment-Free Protein Structure Prediction Guided by Predicted Backbone Structure and Contact Map. Journal of Computational Chemistry. PMID 31845383 DOI: 10.1002/Jcc.26132  0.602
2019 Chen S, Sun Z, Lin L, Liu Z, Liu X, Chong Y, Lu Y, Zhao H, Yang Y. To Improve Protein Sequence Profile Prediction through Image Captioning on Pairwise Residue Distance Map. Journal of Chemical Information and Modeling. PMID 31800243 DOI: 10.1021/Acs.Jcim.9B00438  0.402
2019 Zhang T, Hu G, Yang Y, Wang J, Zhou Y. All-Atom Knowledge-Based Potential for RNA Structure Discrimination Based on the Distance-Scaled Finite Ideal-Gas Reference State. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 31638408 DOI: 10.1089/Cmb.2019.0251  0.461
2019 Chen P, Ke Y, Lu Y, Du Y, Li J, Yan H, Zhao H, Zhou Y, Yang Y. DLIGAND2: an improved knowledge-based energy function for protein-ligand interactions using the distance-scaled, finite, ideal-gas reference state. Journal of Cheminformatics. 11: 52. PMID 31392430 DOI: 10.1186/S13321-019-0373-4  0.604
2019 Hanson J, Paliwal KK, Litfin T, Yang Y, Zhou Y. Getting to Know Your Neighbor: Protein Structure Prediction Comes of Age with Contextual Machine Learning. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 31390220 DOI: 10.1089/Cmb.2019.0193  0.615
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  0.543
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  0.501
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  0.523
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  0.608
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  0.622
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, 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  0.484
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  0.538
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  0.587
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  0.632
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  0.586
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  0.582
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  0.469
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  0.47
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  0.579
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  0.5
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  0.454
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  0.534
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  0.474
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  0.559
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  0.549
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  0.493
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  0.567
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, ... ... Yang 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  0.56
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  0.569
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  0.588
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  0.438
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  0.532
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  0.604
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  0.626
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  0.533
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  0.572
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  0.594
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  0.582
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  0.563
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  0.562
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  0.415
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  0.467
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  0.43
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  0.547
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  0.57
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  0.606
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  0.55
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  0.576
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  0.575
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  0.593
2015 Yu JF, Yang YD, Sun X, Wang JH. Sequence and Structure Analysis of Biological Molecules Based on Computational Methods. Biomed Research International. 2015: 565328. PMID 26236729 DOI: 10.1155/2015/565328  0.35
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  0.588
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  0.606
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  0.515
2015 Brown P, Yang Y, Zhou Y, Pullan W. A heuristic for the time constrained asymmetric linear sum assignment problem Journal of Combinatorial Optimization. 1-16. DOI: 10.1007/S10878-015-9979-2  0.501
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  0.614
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  0.574
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  0.59
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  0.583
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  0.556
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  0.598
2014 Zhou B, Feng H, Kato H, Dai L, Yang Y, Zhou Y, Bai Y. Erratum: Structural insights into the histone H1-nucleosome complex (Proceedings of the National Academy of Sciences of the United States of America (2013) 110:48 (19390-19395) DOI: 10.1073/pnas.1314905110) Proceedings of the National Academy of Sciences of the United States of America. 111. DOI: 10.1073/Pnas.1323266111  0.461
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  0.524
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  0.457
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  0.601
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  0.524
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  0.598
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  0.536
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  0.604
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  0.593
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, ... ... Yang 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  0.58
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  0.593
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  0.556
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  0.622
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  0.556
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  0.57
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  0.555
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  0.604
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  0.738
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  0.527
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  0.551
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