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Items: 1 to 20 of 148

1.

Assessment of methods for predicting the effects of PTEN and TPMT protein variants.

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, Bromberg Y.

Hum Mutat. 2019 Jun 11. doi: 10.1002/humu.23838. [Epub ahead of print]

PMID:
31184403
2.

Experimentally Validated Plant lncRNAs in EVLncRNAs Database.

Zhou B, Zhao H, Yu J, Guo C, Dou X, Song F, Hu G, Cao Z, Qu Y, Yang Y, Zhou Y, Wang J.

Methods Mol Biol. 2019;1933:431-437. doi: 10.1007/978-1-4939-9045-0_27.

PMID:
30945202
3.

SPRINT-Gly: Predicting N- and O-linked glycosylation sites of human and mouse proteins by using sequence and predicted structural properties.

Taherzadeh G, Dehzangi A, Golchin M, Zhou Y, Campbell MP.

Bioinformatics. 2019 Mar 23. pii: btz215. doi: 10.1093/bioinformatics/btz215. [Epub ahead of print]

PMID:
30903686
4.

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

Cao Z, Zhang X, Wang C, Liu L, Zhao L, Wang J, Zhou Y.

J Chem Phys. 2019 Feb 28;150(8):084106. doi: 10.1063/1.5082351.

PMID:
30823753
5.

SPOT-Peptide: Template-Based Prediction of Peptide-Binding Proteins and Peptide-Binding Sites.

Litfin T, Yang Y, Zhou Y.

J Chem Inf Model. 2019 Feb 25;59(2):924-930. doi: 10.1021/acs.jcim.8b00777. Epub 2019 Feb 14.

PMID:
30698427
6.
7.

Reactivation of Dihydroorotate Dehydrogenase-Driven Pyrimidine Biosynthesis Restores Tumor Growth of Respiration-Deficient Cancer Cells.

Bajzikova M, Kovarova J, Coelho AR, Boukalova S, Oh S, Rohlenova K, Svec D, Hubackova S, Endaya B, Judasova K, Bezawork-Geleta A, Kluckova K, Chatre L, Zobalova R, Novakova A, Vanova K, Ezrova Z, Maghzal GJ, Magalhaes Novais S, Olsinova M, Krobova L, An YJ, Davidova E, Nahacka Z, Sobol M, Cunha-Oliveira T, Sandoval-Acuña C, Strnad H, Zhang T, Huynh T, Serafim TL, Hozak P, Sardao VA, Koopman WJH, Ricchetti M, Oliveira PJ, Kolar F, Kubista M, Truksa J, Dvorakova-Hortova K, Pacak K, Gurlich R, Stocker R, Zhou Y, Berridge MV, Park S, Dong L, Rohlena J, Neuzil J.

Cell Metab. 2019 Feb 5;29(2):399-416.e10. doi: 10.1016/j.cmet.2018.10.014. Epub 2018 Nov 15.

PMID:
30449682
8.

Accurate Single-Sequence Prediction of Protein Intrinsic Disorder by an Ensemble of Deep Recurrent and Convolutional Architectures.

Hanson J, Paliwal K, Zhou Y.

J Chem Inf Model. 2018 Nov 26;58(11):2369-2376. doi: 10.1021/acs.jcim.8b00636. Epub 2018 Nov 13.

PMID:
30395465
9.

Single-sequence-based prediction of protein secondary structures and solvent accessibility by deep whole-sequence learning.

Heffernan R, Paliwal K, Lyons J, Singh J, Yang Y, Zhou Y.

J Comput Chem. 2018 Oct 5;39(26):2210-2216. doi: 10.1002/jcc.25534. Epub 2018 Oct 14.

PMID:
30368831
10.

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

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, Seib KL, Zhou Y.

FASEB J. 2019 Feb;33(2):2095-2104. doi: 10.1096/fj.201700613RR. Epub 2018 Sep 27.

PMID:
30260702
11.

YesU from Bacillus subtilis preferentially binds fucosylated glycans.

Tiralongo J, Cooper O, Litfin T, Yang Y, King R, Zhan J, Zhao H, Bovin N, Day CJ, Zhou Y.

Sci Rep. 2018 Sep 3;8(1):13139. doi: 10.1038/s41598-018-31241-8.

12.

Detecting Proline and Non-Proline Cis Isomers in Protein Structures from Sequences Using Deep Residual Ensemble Learning.

Singh J, Hanson J, Heffernan R, Paliwal K, Yang Y, Zhou Y.

J Chem Inf Model. 2018 Sep 24;58(9):2033-2042. doi: 10.1021/acs.jcim.8b00442. Epub 2018 Aug 29.

PMID:
30118602
13.

Computational Prediction of Carbohydrate-Binding Proteins and Binding Sites.

Zhao H, Taherzadeh G, Zhou Y, Yang Y.

Curr Protoc Protein Sci. 2018 Nov;94(1):e75. doi: 10.1002/cpps.75. Epub 2018 Aug 14. Review.

PMID:
30106511
14.

Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networks.

Hanson J, Paliwal K, Litfin T, Yang Y, Zhou Y.

Bioinformatics. 2018 Dec 1;34(23):4039-4045. doi: 10.1093/bioinformatics/bty481.

PMID:
29931279
15.

Predicting lysine-malonylation sites of proteins using sequence and predicted structural features.

Taherzadeh G, Yang Y, Xu H, Xue Y, Liew AW, Zhou Y.

J Comput Chem. 2018 Aug 15;39(22):1757-1763. doi: 10.1002/jcc.25353. Epub 2018 May 14.

PMID:
29761520
16.

Molecular Dynamics Simulations of Human Antimicrobial Peptide LL-37 in Model POPC and POPG Lipid Bilayers.

Zhao L, Cao Z, Bian Y, Hu G, Wang J, Zhou Y.

Int J Mol Sci. 2018 Apr 13;19(4). pii: E1186. doi: 10.3390/ijms19041186.

17.

A survey of Type III restriction-modification systems reveals numerous, novel epigenetic regulators controlling phase-variable regulons; phasevarions.

Atack JM, Yang Y, Seib KL, Zhou Y, Jennings MP.

Nucleic Acids Res. 2018 Apr 20;46(7):3532-3542. doi: 10.1093/nar/gky192.

18.

Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids.

Cao Z, Bian Y, Hu G, Zhao L, Kong Z, Yang Y, Wang J, Zhou Y.

Int J Mol Sci. 2018 Mar 16;19(3). pii: E885. doi: 10.3390/ijms19030885.

19.

SPIN2: Predicting sequence profiles from protein structures using deep neural networks.

O'Connell J, Li Z, Hanson J, Heffernan R, Lyons J, Paliwal K, Dehzangi A, Yang Y, Zhou Y.

Proteins. 2018 Jun;86(6):629-633. doi: 10.1002/prot.25489. Epub 2018 Mar 25.

PMID:
29508448

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