| Year |
Citation |
Score |
| 2023 |
Zhou Y, Litfin T, Zhan J. 3 = 1 + 2: how the divide conquered de novo protein structure prediction and what is next? National Science Review. 10: nwad259. PMID 38033736 DOI: 10.1093/nsr/nwad259 |
0.352 |
|
| 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, ... ... Zhou 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 |
0.52 |
|
| 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 |
0.594 |
|
| 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 |
0.529 |
|
| 2022 |
Singh J, Paliwal K, Litfin T, Singh J, Zhou Y. Predicting RNA distance-based contact maps by integrated deep learning on physics-inferred secondary structure and evolutionary-derived mutational coupling. Bioinformatics (Oxford, England). PMID 35751593 DOI: 10.1093/bioinformatics/btac421 |
0.35 |
|
| 2022 |
Singh J, Paliwal K, Litfin T, Singh J, Zhou Y. Reaching alignment-profile-based accuracy in predicting protein secondary and tertiary structural properties without alignment. Scientific Reports. 12: 7607. PMID 35534620 DOI: 10.1038/s41598-022-11684-w |
0.324 |
|
| 2022 |
Singh J, Litfin T, Singh J, Paliwal K, Zhou Y. SPOT-Contact-LM: Improving Single-Sequence-Based Prediction of Protein Contact Map using a Transformer Language Model. Bioinformatics (Oxford, England). PMID 35104320 DOI: 10.1093/bioinformatics/btac053 |
0.308 |
|
| 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 |
0.581 |
|
| 2021 |
Singh J, Litfin T, Paliwal K, Singh J, Hanumanthappa AK, Zhou Y. SPOT-1D-Single: Improving the Single-Sequence-Based Prediction of Protein Secondary Structure, Backbone Angles, Solvent Accessibility and Half-Sphere Exposures using a Large Training Set and Ensembled Deep Learning. Bioinformatics (Oxford, England). PMID 33983382 DOI: 10.1093/bioinformatics/btab316 |
0.356 |
|
| 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, ... ... Zhou 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 |
0.526 |
|
| 2020 |
Zhao B, Katuwawala A, Oldfield CJ, Dunker AK, Faraggi E, Gsponer J, Kloczkowski A, Malhis N, Mirdita M, Obradovic Z, Söding J, Steinegger M, Zhou Y, Kurgan L. DescribePROT: database of amino acid-level protein structure and function predictions. Nucleic Acids Research. PMID 33119734 DOI: 10.1093/nar/gkaa931 |
0.369 |
|
| 2020 |
Hanumanthappa AK, Singh J, Paliwal K, Singh J, Zhou Y. Single-sequence and profile-based prediction of RNA solvent accessibility using dilated convolutional neural network. Bioinformatics (Oxford, England). PMID 33106872 DOI: 10.1093/bioinformatics/btaa652 |
0.301 |
|
| 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 |
0.545 |
|
| 2020 |
Hanson J, Paliwal KK, Litfin T, Zhou Y. SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning. Genomics, Proteomics & Bioinformatics. PMID 32173600 DOI: 10.1016/j.gpb.2019.01.004 |
0.327 |
|
| 2019 |
Abrahams JL, Taherzadeh G, Jarvas G, Guttman A, Zhou Y, Campbell MP. Recent advances in glycoinformatic platforms for glycomics and glycoproteomics. Current Opinion in Structural Biology. 62: 56-69. PMID 31874386 DOI: 10.1016/J.Sbi.2019.11.009 |
0.357 |
|
| 2019 |
Zhang Z, Xiong P, Zhang T, Wang J, Zhan J, Zhou Y. Accurate inference of the full base-pairing structure of RNA by deep mutational scanning and covariation-induced deviation of activity. Nucleic Acids Research. PMID 31872260 DOI: 10.1093/Nar/Gkz1192 |
0.364 |
|
| 2019 |
Barik A, Katuwawala A, Hanson J, Paliwal K, Zhou Y, Kurgan L. DEPICTER: intrinsic disorder and disorder function prediction server. Journal of Molecular Biology. PMID 31870849 DOI: 10.1016/J.Jmb.2019.12.030 |
0.378 |
|
| 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 |
0.618 |
|
| 2019 |
Lin H, Hargreaves KA, Li R, Reiter JL, Wang Y, Mort M, Cooper DN, Zhou Y, Zhang C, Eadon MT, Dolan ME, Ipe J, Skaar TC, Liu Y. RegSNPs-intron: a computational framework for predicting pathogenic impact of intronic single nucleotide variants. Genome Biology. 20: 254. PMID 31779641 DOI: 10.1186/S13059-019-1847-4 |
0.375 |
|
| 2019 |
Singh J, Hanson J, Paliwal K, Zhou Y. RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning. Nature Communications. 10: 5407. PMID 31776342 DOI: 10.1038/S41467-019-13395-9 |
0.392 |
|
| 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 |
0.551 |
|
| 2019 |
Hanson J, Litfin T, Paliwal K, Zhou Y. Identifying Molecular Recognition Features in Intrinsically Disordered Regions of Proteins by Transfer Learning. Bioinformatics (Oxford, England). PMID 31504193 DOI: 10.1093/Bioinformatics/Btz691 |
0.363 |
|
| 2019 |
Hadley B, Litfin T, Day CJ, Haselhorst T, Zhou Y, Tiralongo J. Nucleotide Sugar Transporter SLC35 Family Structure and Function. Computational and Structural Biotechnology Journal. 17: 1123-1134. PMID 31462968 DOI: 10.1016/J.Csbj.2019.08.002 |
0.317 |
|
| 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 |
0.607 |
|
| 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 |
0.58 |
|
| 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 |
0.583 |
|
| 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 |
0.397 |
|
| 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 |
0.381 |
|
| 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 |
0.548 |
|
| 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 |
0.371 |
|
| 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 |
0.577 |
|
| 2019 |
Wang T, Qiao Y, Ding W, Mao W, Zhou Y, Gong H. Improved fragment sampling for ab initio protein structure prediction using deep neural networks Nature Machine Intelligence. 1: 347-355. DOI: 10.1038/S42256-019-0075-7 |
0.443 |
|
| 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 |
0.654 |
|
| 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 |
0.387 |
|
| 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 |
0.664 |
|
| 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 |
0.536 |
|
| 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 |
0.604 |
|
| 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 |
0.636 |
|
| 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 |
0.664 |
|
| 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 |
0.624 |
|
| 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 |
0.642 |
|
| 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 |
0.528 |
|
| 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 |
0.537 |
|
| 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 |
0.598 |
|
| 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 |
0.618 |
|
| 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 |
0.502 |
|
| 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 |
0.593 |
|
| 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 |
0.516 |
|
| 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 |
0.615 |
|
| 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 |
0.569 |
|
| 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 |
0.567 |
|
| 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 |
0.621 |
|
| 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 |
0.692 |
|
| 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 |
0.612 |
|
| 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 |
0.648 |
|
| 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 |
0.335 |
|
| 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 |
0.511 |
|
| 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 |
0.588 |
|
| 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 |
0.327 |
|
| 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 |
0.408 |
|
| 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 |
0.636 |
|
| 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 |
0.579 |
|
| 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 |
0.62 |
|
| 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 |
0.635 |
|
| 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 |
0.587 |
|
| 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 |
0.622 |
|
| 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 |
0.487 |
|
| 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 |
0.524 |
|
| 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 |
0.506 |
|
| 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 |
0.579 |
|
| 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 |
0.642 |
|
| 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 |
0.646 |
|
| 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 |
0.455 |
|
| 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 |
0.602 |
|
| 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 |
0.637 |
|
| 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 |
0.652 |
|
| 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 |
0.64 |
|
| 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 |
0.611 |
|
| 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 |
0.648 |
|
| 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 |
0.585 |
|
| 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 |
0.534 |
|
| 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 |
0.659 |
|
| 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 |
0.627 |
|
| 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 |
0.434 |
|
| 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 |
0.639 |
|
| 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 |
0.642 |
|
| 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 |
0.61 |
|
| 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 |
0.351 |
|
| 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 |
0.456 |
|
| 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 |
0.645 |
|
| 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 |
0.517 |
|
| 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 |
0.593 |
|
| 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 |
0.531 |
|
| 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 |
0.657 |
|
| 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 |
0.352 |
|
| 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 |
0.561 |
|
| 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 |
0.62 |
|
| 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 |
0.377 |
|
| 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 |
0.586 |
|
| 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 |
0.652 |
|
| 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 |
0.366 |
|
| 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 |
0.658 |
|
| 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 |
0.607 |
|
| 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 |
0.645 |
|
| 2011 |
Kurgan L, Zhou Y. Machine learning models in protein bioinformatics. Current Protein & Peptide Science. 12: 455. PMID 21787309 DOI: 10.2174/138920311796957621 |
0.471 |
|
| 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 DOI: 10.2174/138920311796957667 |
0.336 |
|
| 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 |
0.345 |
|
| 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 |
0.633 |
|
| 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 |
0.659 |
|
| 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 |
0.437 |
|
| 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 |
0.366 |
|
| 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 |
0.615 |
|
| 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 |
0.438 |
|
| 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 |
0.617 |
|
| 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 |
0.631 |
|
| 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 |
0.648 |
|
| 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 |
0.776 |
|
| 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 |
0.443 |
|
| 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 |
0.386 |
|
| 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 |
0.397 |
|
| 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 |
0.425 |
|
| 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 |
0.396 |
|
| 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 |
0.392 |
|
| 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 |
0.38 |
|
| 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 |
0.598 |
|
| 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 |
0.633 |
|
| 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 |
0.417 |
|
| 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 |
0.416 |
|
| 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 |
0.429 |
|
| 2007 |
Chen Y, Zhou Y, Ding J. The helix-coil transition revisited. Proteins. 69: 58-68. PMID 17596846 DOI: 10.1002/Prot.21492 |
0.306 |
|
| 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 |
0.319 |
|
| 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 |
0.411 |
|
| 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 |
0.332 |
|
| 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 |
0.45 |
|
| 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 |
0.431 |
|
| 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 DOI: 10.1385/Cbb:46:2:165 |
0.343 |
|
| 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 |
0.455 |
|
| 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 |
0.327 |
|
| 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 |
0.429 |
|
| 2006 |
Zhou Y, Zhou H, Karplus M. Cooperativity inScapharca dimeric hemoglobin: Simulation of binding intermediates and elucidation of the role of interfacial water Rendiconti Lincei. 17: 192-211. DOI: 10.1007/BF02904509 |
0.325 |
|
| 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 DOI: 10.1142/S0219720005001430 |
0.377 |
|
| 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 |
0.349 |
|
| 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 |
0.377 |
|
| 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 |
0.398 |
|
| 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 |
0.345 |
|
| 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 |
0.487 |
|
| 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 |
0.314 |
|
| 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 |
0.307 |
|
| 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 |
0.567 |
|
| 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 |
0.389 |
|
| 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 |
0.386 |
|
| 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 |
0.454 |
|
| 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 |
0.414 |
|
| 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 |
0.371 |
|
| 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 |
0.4 |
|
| 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 |
0.385 |
|
| 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 |
0.356 |
|
| 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 |
0.307 |
|
| 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 |
0.434 |
|
| 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 |
0.469 |
|
| 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 |
0.344 |
|
| 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 |
0.342 |
|
| 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 |
0.364 |
|
| 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 |
0.363 |
|
| 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 |
0.349 |
|
| 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 |
0.326 |
|
| 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 |
0.408 |
|
| 2002 |
Linhananta A, Zhou Y. 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 Journal of Chemical Physics. 117: 8983-8995. DOI: 10.1063/1.1514574 |
0.329 |
|
| 2002 |
Zhou Y, Karplus M, Ball KD, Berry RS. The distance fluctuation criterion for melting: Comparison of square-well and Morse potential models for clusters and homopolymers Journal of Chemical Physics. 116: 2323-2329. DOI: 10.1063/1.1426419 |
0.412 |
|
| 2002 |
Zhou Y, Linhananta A. Thermodynamics of an all-atom off-lattice model of the fragment B of Staphylococcal protein A: Implication for the origin of the cooperativity of protein folding Journal of Physical Chemistry B. 106: 1481-1485. DOI: 10.1021/Jp013824R |
0.373 |
|
| 2001 |
Zhou Y, Cook M, Karplus M. Protein motions at zero-total angular momentum: the importance of long-range correlations. Biophysical Journal. 79: 2902-8. PMID 11106598 DOI: 10.1016/S0006-3495(00)76527-1 |
0.442 |
|
| 1999 |
Zhou Y, Karplus M. Folding of a model three-helix bundle protein: a thermodynamic and kinetic analysis. Journal of Molecular Biology. 293: 917-51. PMID 10543976 DOI: 10.1006/Jmbi.1999.2936 |
0.507 |
|
| 1999 |
Zhou Y, Karplus M. Interpreting the folding kinetics of helical proteins. Nature. 401: 400-3. PMID 10517642 DOI: 10.1038/43937 |
0.548 |
|
| 1999 |
Zhou Y, Hall CK, Karplus M. The calorimetric criterion for a two-state process revisited. Protein Science : a Publication of the Protein Society. 8: 1064-74. PMID 10338017 DOI: 10.1110/Ps.8.5.1064 |
0.444 |
|
| 1999 |
Zhou Y, Vitkup D, Karplus M. Native proteins are surface-molten solids: application of the Lindemann criterion for the solid versus liquid state. Journal of Molecular Biology. 285: 1371-5. PMID 9917381 DOI: 10.1006/Jmbi.1998.2374 |
0.728 |
|
| 1998 |
Zhou Y, Karplus M. Folding thermodynamics of a model three-helix-bundle protein. Proceedings of the National Academy of Sciences of the United States of America. 94: 14429-32. PMID 9405629 DOI: 10.1073/Pnas.94.26.14429 |
0.481 |
|
| 1998 |
Zhou Y. Salt Effects on Protein Titration and Binding The Journal of Physical Chemistry B. 102: 10615-10621. DOI: 10.1021/Jp982542X |
0.383 |
|
| 1998 |
Zhou Y, Hall CK. Solute excluded-volume effects on the stability of globular proteins: A statistical thermodynamic theory Biopolymers. 38: 273-284. DOI: 10.1002/(Sici)1097-0282(199602)38:2<273::Aid-Bip11>3.0.Co;2-G |
0.339 |
|
| 1997 |
Zhou Y, Karplus M, Wichert JM, Hall CK. Equilibrium thermodynamics of homopolymers and clusters: Molecular dynamics and Monte Carlo simulations of systems with square-well interactions The Journal of Chemical Physics. 107: 10691-10708. DOI: 10.1063/1.474186 |
0.429 |
|
| 1996 |
Zhou Y, Hall CK, Karplus M. First-Order Disorder-to-Order Transition in an Isolated Homopolymer Model. Physical Review Letters. 77: 2822-2825. PMID 10062054 DOI: 10.1103/Physrevlett.77.2822 |
0.417 |
|
| 1996 |
ZHOU Y, KARPLUS M. Exact results for the effect of bond flexibility on the structure and the collapse transition of isolated square-well trimers Molecular Physics. 89: 1707-1717. DOI: 10.1080/00268979609482568 |
0.426 |
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