| Year |
Citation |
Score |
| 2024 |
Yuan Q, Tian C, Song Y, Ou P, Zhu M, Zhao H, Yang Y. GPSFun: geometry-aware protein sequence function predictions with language models. Nucleic Acids Research. PMID 38738636 DOI: 10.1093/nar/gkae381 |
0.379 |
|
| 2024 |
Yuan Q, Tian C, Yang Y. Genome-scale annotation of protein binding sites via language model and geometric deep learning. Elife. 13. PMID 38630609 DOI: 10.7554/eLife.93695 |
0.405 |
|
| 2023 |
Zhou B, Ji B, Shen C, Zhang X, Yu X, Huang P, Yu R, Zhang H, Dou X, Chen Q, Zeng Q, Wang X, Cao Z, Hu G, Xu S, ... ... Yang Y, et al. EVLncRNAs 3.0: an updated comprehensive database for manually curated functional long non-coding RNAs validated by low-throughput experiments. Nucleic Acids Research. PMID 37953349 DOI: 10.1093/nar/gkad1057 |
0.508 |
|
| 2023 |
Wang J, Chen S, Yuan Q, Chen J, Li D, Wang L, Yang Y. Predicting the effects of mutations on protein solubility using graph convolution network and protein language model representation. Journal of Computational Chemistry. PMID 37933773 DOI: 10.1002/jcc.27249 |
0.354 |
|
| 2023 |
Song Y, Yuan Q, Zhao H, Yang Y. Accurately identifying nucleic-acid-binding sites through geometric graph learning on language model predicted structures. Briefings in Bioinformatics. 24. PMID 37824738 DOI: 10.1093/bib/bbad360 |
0.428 |
|
| 2023 |
Song Y, Yuan Q, Chen S, Chen K, Zhou Y, Yang Y. Fast and accurate protein intrinsic disorder prediction by using a pretrained language model. Briefings in Bioinformatics. PMID 37204193 DOI: 10.1093/bib/bbad173 |
0.575 |
|
| 2023 |
Yuan Q, Xie J, Xie J, Zhao H, Yang Y. Fast and accurate protein function prediction from sequence through pretrained language model and homology-based label diffusion. Briefings in Bioinformatics. PMID 36964722 DOI: 10.1093/bib/bbad117 |
0.382 |
|
| 2022 |
Zhou B, Ding M, Feng J, Ji B, Huang P, Zhang J, Yu X, Cao Z, Yang Y, Zhou Y, Wang J. EVlncRNA-Dpred: improved prediction of experimentally validated lncRNAs by deep learning. Briefings in Bioinformatics. PMID 36573492 DOI: 10.1093/bib/bbac583 |
0.517 |
|
| 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 |
0.356 |
|
| 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 |
0.403 |
|
| 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 |
0.336 |
|
| 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 |
0.57 |
|
| 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 |
0.388 |
|
| 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 |
0.514 |
|
| 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 |
0.525 |
|
| 2020 |
Ke Y, Rao J, Zhao H, Lu Y, Xiao N, Yang Y. Accurate Prediction of Genome-wide RNA Secondary Structure Profile Based on Extreme Gradient Boosting. Bioinformatics (Oxford, England). PMID 32467966 DOI: 10.1093/Bioinformatics/Btaa534 |
0.39 |
|
| 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 |
0.441 |
|
| 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 |
0.441 |
|
| 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 |
0.651 |
|
| 2019 |
Zheng S, Rao J, Zhang Z, Xu J, Yang Y. Predicting Retrosynthetic Reactions using Self-Corrected Transformer Neural Networks. Journal of Chemical Information and Modeling. PMID 31825611 DOI: 10.1021/Acs.Jcim.9B00949 |
0.323 |
|
| 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 |
0.462 |
|
| 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 |
0.531 |
|
| 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 |
0.632 |
|
| 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 |
0.657 |
|
| 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 |
0.573 |
|
| 2019 |
Mount SM, Avsec Ž, Carmel L, Casadio R, Çelik MH, Chen K, Cheng J, Cohen NE, Fairbrother WG, Fenesh T, Gagneur J, Gotea V, Holzer T, Lin CF, Martelli PL, ... ... Yang Y, et al. Assessing predictions of the impact of variants on splicing in CAGI5. Human Mutation. PMID 31301154 DOI: 10.1002/Humu.23869 |
0.399 |
|
| 2019 |
Chen K, Lu Y, Zhao H, Yang Y. Predicting the change of exon splicing caused by genetic variant using support vector regression. Human Mutation. PMID 31070294 DOI: 10.1002/Humu.23785 |
0.375 |
|
| 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 |
0.533 |
|
| 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 |
0.566 |
|
| 2019 |
Zheng S, Yan X, Yang Y, Xu J. Identifying Structure-Property Relationships through SMILES Syntax Analysis with Self-Attention Mechanism. Journal of Chemical Information and Modeling. PMID 30669836 DOI: 10.1021/Acs.Jcim.8B00803 |
0.361 |
|
| 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 |
0.653 |
|
| 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 |
0.663 |
|
| 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 |
0.518 |
|
| 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 |
0.596 |
|
| 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 |
0.63 |
|
| 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 |
0.665 |
|
| 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 |
0.616 |
|
| 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 |
0.639 |
|
| 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 |
0.504 |
|
| 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 |
0.506 |
|
| 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 |
0.588 |
|
| 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 |
0.608 |
|
| 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 |
0.477 |
|
| 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 |
0.582 |
|
| 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 |
0.493 |
|
| 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 |
0.607 |
|
| 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 |
0.559 |
|
| 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 |
0.557 |
|
| 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 |
0.615 |
|
| 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 |
0.565 |
|
| 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 |
0.604 |
|
| 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 |
0.644 |
|
| 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 |
0.487 |
|
| 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 |
0.581 |
|
| 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 |
0.634 |
|
| 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 |
0.665 |
|
| 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 |
0.566 |
|
| 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 |
0.618 |
|
| 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 |
0.641 |
|
| 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 |
0.63 |
|
| 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 |
0.571 |
|
| 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 |
0.613 |
|
| 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 |
0.46 |
|
| 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 |
0.5 |
|
| 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 |
0.483 |
|
| 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 |
0.568 |
|
| 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 |
0.628 |
|
| 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 |
0.643 |
|
| 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 |
0.587 |
|
| 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 |
0.626 |
|
| 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 |
0.646 |
|
| 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 |
0.631 |
|
| 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 |
0.446 |
|
| 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 |
0.602 |
|
| 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 |
0.645 |
|
| 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 |
0.573 |
|
| 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 |
0.511 |
|
| 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 |
0.658 |
|
| 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 |
0.624 |
|
| 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 |
0.634 |
|
| 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 |
0.638 |
|
| 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 |
0.611 |
|
| 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 |
0.646 |
|
| 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 |
0.491 |
|
| 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 |
0.57 |
|
| 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 |
0.508 |
|
| 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 |
0.658 |
|
| 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 |
0.544 |
|
| 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 |
0.607 |
|
| 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 |
0.576 |
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| 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 |
0.645 |
|
| 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 |
0.657 |
|
| 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 |
0.592 |
|
| 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 |
0.646 |
|
| 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 |
0.626 |
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| 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 |
0.658 |
|
| 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 |
0.614 |
|
| 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 |
0.606 |
|
| 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 |
0.624 |
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| 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 |
0.649 |
|
| 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 |
0.724 |
|
| 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 |
0.574 |
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| 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 |
0.615 |
|
| 2006 |
Yang Y, Liu H. Genetic algorithms for protein conformation sampling and optimization in a discrete backbone dihedral angle space. Journal of Computational Chemistry. 27: 1593-602. PMID 16868993 DOI: 10.1002/Jcc.20463 |
0.344 |
|
| 2005 |
Cheng S, Yang Y, Wang W, Liu H. Transition state ensemble for the folding of B domain of protein A: a comparison of distributed molecular dynamics simulations with experiments. The Journal of Physical Chemistry. B. 109: 23645-54. PMID 16375343 DOI: 10.1021/Jp0517798 |
0.382 |
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| 2005 |
Ding H, Yang Y, Zhang J, Wu J, Liu H, Shi Y. Structural basis for SUMO-E2 interaction revealed by a complex model using docking approach in combination with NMR data. Proteins. 61: 1050-8. PMID 16224784 DOI: 10.1002/Prot.20695 |
0.357 |
|
| 2005 |
Zhou H, Xu Y, Yang Y, Huang A, Wu J, Shi Y. Solution structure of AF-6 PDZ domain and its interaction with the C-terminal peptides from Neurexin and Bcr. The Journal of Biological Chemistry. 280: 13841-7. PMID 15684424 DOI: 10.1074/Jbc.M411065200 |
0.301 |
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