| Year |
Citation |
Score |
| 2024 |
Zulfiqar H, Guo Z, Ahmad RM, Ahmed Z, Cai P, Chen X, Zhang Y, Lin H, Shi Z. Deep-STP: a deep learning-based approach to predict snake toxin proteins by using word embeddings. Frontiers in Medicine. 10: 1291352. PMID 38298505 DOI: 10.3389/fmed.2023.1291352 |
0.345 |
|
| 2024 |
Liu Z, Zhang C, Zhang Q, Zhang Y, Yu DJ. TM-search: An Efficient and Effective Tool for Protein Structure Database Search. Journal of Chemical Information and Modeling. PMID 38270339 DOI: 10.1021/acs.jcim.3c01455 |
0.337 |
|
| 2024 |
Zheng W, Wuyun Q, Li Y, Zhang C, Freddolino PL, Zhang Y. Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data. Nature Methods. PMID 38167654 DOI: 10.1038/s41592-023-02130-4 |
0.356 |
|
| 2023 |
Zheng W, Wuyun Q, Freddolino PL, Zhang Y. Integrating deep learning, threading alignments, and a multi-MSA strategy for high-quality protein monomer and complex structure prediction in CASP15. Proteins. PMID 37650367 DOI: 10.1002/prot.26585 |
0.328 |
|
| 2023 |
Zhang C, Zhang X, Freddolino PL, Zhang Y. BioLiP2: an updated structure database for biologically relevant ligand-protein interactions. Nucleic Acids Research. PMID 37522378 DOI: 10.1093/nar/gkad630 |
0.408 |
|
| 2023 |
Pearce R, Huang X, Omenn GS, Zhang Y. De novo protein fold design through sequence-independent fragment assembly simulations. Proceedings of the National Academy of Sciences of the United States of America. 120: e2208275120. PMID 36656852 DOI: 10.1073/pnas.2208275120 |
0.367 |
|
| 2022 |
Zhu YH, Zhang C, Yu DJ, Zhang Y. Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction. Plos Computational Biology. 18: e1010793. PMID 36548439 DOI: 10.1371/journal.pcbi.1010793 |
0.31 |
|
| 2022 |
LaLone CA, Blatz DJ, Jensen MA, Vliet SMF, Mayasich S, Mattingly KZ, Transue TR, Melendez W, Wilkinson A, Simmons CW, Ng C, Zhang C, Zhang Y. From Protein Sequence to Structure: The Next Frontier in Cross Species Extrapolation for Chemical Safety Evaluations. Environmental Toxicology and Chemistry. PMID 36524855 DOI: 10.1002/etc.5537 |
0.32 |
|
| 2022 |
Pearce R, Li Y, Omenn GS, Zhang Y. Fast and accurate Ab Initio Protein structure prediction using deep learning potentials. Plos Computational Biology. 18: e1010539. PMID 36112717 DOI: 10.1371/journal.pcbi.1010539 |
0.352 |
|
| 2022 |
Sun Y, Jiao Y, Shi C, Zhang Y. Deep learning-based molecular dynamics simulation for structure-based drug design against SARS-CoV-2. Computational and Structural Biotechnology Journal. PMID 36091720 DOI: 10.1016/j.csbj.2022.09.002 |
0.307 |
|
| 2022 |
Zhang C, Shine M, Pyle AM, Zhang Y. US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes. Nature Methods. PMID 36038728 DOI: 10.1038/s41592-022-01585-1 |
0.357 |
|
| 2022 |
Bell EW, Schwartz JH, Freddolino PL, Zhang Y. PEPPI: Whole-proteome Protein-protein Interaction Prediction through Structure and Sequence Similarity, Functional Association, and Machine Learning. Journal of Molecular Biology. 434: 167530. PMID 35662463 DOI: 10.1016/j.jmb.2022.167530 |
0.346 |
|
| 2022 |
Zheng W, Wuyun Q, Zhou X, Li Y, Freddolino PL, Zhang Y. LOMETS3: integrating deep learning and profile alignment for advanced protein template recognition and function annotation. Nucleic Acids Research. PMID 35420129 DOI: 10.1093/nar/gkac248 |
0.356 |
|
| 2022 |
MacCarthy EA, Zhang C, Zhang Y, Dukka KC. GPU-I-TASSER: a GPU accelerated I-TASSER protein structure prediction tool. Bioinformatics (Oxford, England). PMID 34978562 DOI: 10.1093/bioinformatics/btab871 |
0.366 |
|
| 2021 |
Yang P, Zheng W, Ning K, Zhang Y. Decoding the link of microbiome niches with homologous sequences enables accurately targeted protein structure prediction. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34873061 DOI: 10.1073/pnas.2110828118 |
0.341 |
|
| 2021 |
Mortuza SM, Zheng W, Zhang C, Li Y, Pearce R, Zhang Y. Improving fragment-based ab initio protein structure assembly using low-accuracy contact-map predictions. Nature Communications. 12: 5011. PMID 34408149 DOI: 10.1038/s41467-021-25316-w |
0.348 |
|
| 2021 |
Li Y, Zhang C, Zheng W, Zhou X, Bell EW, Yu DJ, Zhang Y. Protein inter-residue contact and distance prediction by coupling complementary coevolution features with deep residual networks in CASP14. Proteins. PMID 34382712 DOI: 10.1002/prot.26211 |
0.339 |
|
| 2021 |
Zheng W, Zhang C, Li Y, Pearce R, Bell EW, Zhang Y. Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. Cell Reports Methods. 1. PMID 34355210 DOI: 10.1016/j.crmeth.2021.100014 |
0.34 |
|
| 2021 |
Zheng W, Li Y, Zhang C, Zhou X, Pearce R, Bell EW, Huang X, Zhang Y. Protein structure prediction using deep learning distance and hydrogen-bonding restraints in CASP14. Proteins. PMID 34331351 DOI: 10.1002/prot.26193 |
0.309 |
|
| 2021 |
Zhao KL, Liu J, Zhou XG, Su JZ, Zhang Y, Zhang GJ. MMpred: a distance-assisted multimodal conformation sampling for de novo protein structure prediction. Bioinformatics (Oxford, England). PMID 34185079 DOI: 10.1093/bioinformatics/btab484 |
0.326 |
|
| 2021 |
Pearce R, Zhang Y. Toward the solution of the protein structure prediction problem. The Journal of Biological Chemistry. 100870. PMID 34119522 DOI: 10.1016/j.jbc.2021.100870 |
0.414 |
|
| 2021 |
Li Y, Zhang C, Bell EW, Zheng W, Zhou X, Yu DJ, Zhang Y. Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks. Plos Computational Biology. 17: e1008865. PMID 33770072 DOI: 10.1371/journal.pcbi.1008865 |
0.309 |
|
| 2021 |
Gong W, Guerler A, Zhang C, Warner E, Li C, Zhang Y. Integrating multimeric threading with high-throughput experiments for structural interactome of Escherichia coli. Journal of Molecular Biology. 166944. PMID 33741411 DOI: 10.1016/j.jmb.2021.166944 |
0.34 |
|
| 2021 |
Pearce R, Zhang Y. Deep learning techniques have significantly impacted protein structure prediction and protein design. Current Opinion in Structural Biology. 68: 194-207. PMID 33639355 DOI: 10.1016/j.sbi.2021.01.007 |
0.311 |
|
| 2020 |
Zhou XG, Peng CX, Liu J, Zhang Y, Zhang GJ. Underestimation-Assisted Global-Local Cooperative Differential Evolution and the Application to Protein Structure Prediction. Ieee Transactions On Evolutionary Computation : a Publication of the Ieee Neural Networks Council. 24: 536-550. PMID 33603321 DOI: 10.1109/Tevc.2019.2938531 |
0.333 |
|
| 2020 |
Zhang W, Bell EW, Yin M, Zhang Y. EDock: blind protein-ligand docking by replica-exchange monte carlo simulation. Journal of Cheminformatics. 12: 37. PMID 33430966 DOI: 10.1186/S13321-020-00440-9 |
0.437 |
|
| 2020 |
Zhang B, Zhang X, Pearce R, Shen HB, Zhang Y. A New Protocol for Atomic-Level Protein Structure Modeling and Refinement Using Low-to-Medium Resolution Cryo-EM Density Maps. Journal of Molecular Biology. PMID 32771523 DOI: 10.1016/J.Jmb.2020.07.027 |
0.416 |
|
| 2020 |
Chan WKB, Zhang Y. Ligand-Profile Based Virtual Screening of Human GPCRs. Journal of Molecular Biology. PMID 32652079 DOI: 10.1016/J.Jmb.2020.07.003 |
0.694 |
|
| 2020 |
Wei X, Zhang C, Freddolino PL, Zhang Y. Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons. Bioinformatics (Oxford, England). PMID 32470107 DOI: 10.1093/bioinformatics/btaa548 |
0.317 |
|
| 2020 |
Zhu YH, Hu J, Ge F, Li F, Song J, Zhang Y, Yu DJ. Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features. Briefings in Bioinformatics. PMID 32436937 DOI: 10.1093/Bib/Bbaa076 |
0.374 |
|
| 2020 |
Huang X, Pearce R, Zhang Y. FASPR: an open-source tool for fast and accurate protein side-chain packing. Bioinformatics (Oxford, England). PMID 32259206 DOI: 10.1093/Bioinformatics/Btaa234 |
0.455 |
|
| 2020 |
Zheng W, Zhou X, Wuyun Q, Pearce R, Li Y, Zhang Y. FUpred: Detecting protein domains through deep-learning based contact map prediction. Bioinformatics (Oxford, England). PMID 32227201 DOI: 10.1093/Bioinformatics/Btaa217 |
0.382 |
|
| 2020 |
Zhang C, Zheng W, Huang X, Bell EW, Zhou X, Zhang Y. Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1. Journal of Proteome Research. PMID 32200634 DOI: 10.1021/Acs.Jproteome.0C00129 |
0.364 |
|
| 2019 |
Liu J, Zhou XG, Zhang Y, Zhang GJ. CGLFold: a contact-assisted de novo protein structure prediction using global exploration and loop perturbation sampling algorithm. Bioinformatics (Oxford, England). PMID 31860059 DOI: 10.1093/Bioinformatics/Btz943 |
0.456 |
|
| 2019 |
Huang X, Pearce R, Zhang Y. Toward the Accuracy and Speed of Protein Side-Chain Packing: A Systematic Study on Rotamer Libraries. Journal of Chemical Information and Modeling. PMID 31851497 DOI: 10.1021/Acs.Jcim.9B00812 |
0.462 |
|
| 2019 |
Huang X, Zheng W, Pearce R, Zhang Y. SSIPe: accurately estimating protein-protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function. Bioinformatics (Oxford, England). PMID 31830252 DOI: 10.1093/Bioinformatics/Btz926 |
0.399 |
|
| 2019 |
Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, ... ... Zhang Y, et al. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biology. 20: 244. PMID 31744546 DOI: 10.1186/S13059-019-1835-8 |
0.548 |
|
| 2019 |
Zhang C, Zheng W, Mortuza SM, Li Y, Zhang Y. DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins. Bioinformatics (Oxford, England). PMID 31738385 DOI: 10.1093/Bioinformatics/Btz863 |
0.4 |
|
| 2019 |
Wang Y, Shi Q, Yang P, Zhang C, Mortuza SM, Xue Z, Ning K, Zhang Y. Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families. Genome Biology. 20: 229. PMID 31676016 DOI: 10.1186/S13059-019-1823-Z |
0.423 |
|
| 2019 |
Soules KR, Dmitriev A, LaBrie SD, Dimond ZE, May BH, Johnson DK, Zhang Y, Battaile KP, Lovell S, Hefty PS. Structural and ligand binding analyses of the periplasmic sensor domain of RsbU in Chlamydia trachomatis supports role in TCA cycle regulation. Molecular Microbiology. PMID 31637787 DOI: 10.1111/Mmi.14401 |
0.342 |
|
| 2019 |
Zheng W, Wuyun Q, Li Y, Mortuza SM, Zhang C, Pearce R, Ruan J, Zhang Y. Detecting distant-homology protein structures by aligning deep neural-network based contact maps. Plos Computational Biology. 15: e1007411. PMID 31622328 DOI: 10.1371/Journal.Pcbi.1007411 |
0.493 |
|
| 2019 |
Huang X, Pearce R, Zhang Y. EvoEF2: Accurate and fast energy function for computational protein design. Bioinformatics (Oxford, England). PMID 31588495 DOI: 10.1093/Bioinformatics/Btz740 |
0.331 |
|
| 2019 |
Zhang C, Lane L, Omenn GS, Zhang Y. A Blinded Testing of Function Annotation for uPE1 Proteins by the I-TASSER/COFACTOR Pipeline Using the 2018-2019 Additions to neXtProt and the CAFA3 Challenge. Journal of Proteome Research. PMID 31581775 DOI: 10.1021/Acs.Jproteome.9B00537 |
0.457 |
|
| 2019 |
Wu J, Liu B, Chan WKB, Wu W, Pang T, Hu H, Yan S, Ke X, Zhang Y. Precise modelling and interpretation of bioactivities of ligands targeting G protein-coupled receptors. Bioinformatics (Oxford, England). 35: i324-i332. PMID 31510691 DOI: 10.1093/Bioinformatics/Btz336 |
0.682 |
|
| 2019 |
Hong J, Luo Y, Zhang Y, Ying J, Xue W, Xie T, Tao L, Zhu F. Protein functional annotation of simultaneously improved stability, accuracy and false discovery rate achieved by a sequence-based deep learning. Briefings in Bioinformatics. PMID 31504150 DOI: 10.1093/bib/bbz081 |
0.308 |
|
| 2019 |
Wu J, Yin Q, Zhang C, Geng J, Wu H, Hu H, Ke X, Zhang Y. Function Prediction for G Protein-Coupled Receptors through Text Mining and Induction Matrix Completion. Acs Omega. 4: 3045-3054. PMID 31459527 DOI: 10.1021/acsomega.8b02454 |
0.309 |
|
| 2019 |
Zheng W, Zhang C, Bell EW, Zhang Y. I-TASSER gateway: A protein structure and function prediction server powered by XSEDE. Future Generations Computer Systems : Fgcs. 99: 73-85. PMID 31427836 DOI: 10.1016/J.Future.2019.04.011 |
0.487 |
|
| 2019 |
Li Y, Zhang C, Bell EW, Yu DJ, Zhang Y. Ensembling multiple raw coevolutionary features with deep residual neural networks for contact-map prediction in CASP13. Proteins. PMID 31407406 DOI: 10.1002/Prot.25798 |
0.349 |
|
| 2019 |
Vangaveti S, Vreven T, Zhang Y, Weng Z. Integrating ab initio and template-based algorithms for protein-protein complex structure prediction. Bioinformatics (Oxford, England). PMID 31393558 DOI: 10.1093/Bioinformatics/Btz623 |
0.478 |
|
| 2019 |
Zheng W, Li Y, Zhang C, Pearce R, Mortuza SM, Zhang Y. Deep-learning contact-map guided protein structure prediction in CASP13. Proteins. PMID 31365149 DOI: 10.1002/Prot.25792 |
0.375 |
|
| 2019 |
Zhou X, Hu J, Zhang C, Zhang G, Zhang Y. Assembling multidomain protein structures through analogous global structural alignments. Proceedings of the National Academy of Sciences of the United States of America. PMID 31341084 DOI: 10.1073/Pnas.1905068116 |
0.448 |
|
| 2019 |
Wang D, Geng L, Zhao YJ, Yang Y, Huang Y, Zhang Y, Shen HB. Artificial intelligence-based multi-objective optimization protocol for protein structure refinement. Bioinformatics (Oxford, England). PMID 31274151 DOI: 10.1093/Bioinformatics/Btz544 |
0.457 |
|
| 2019 |
Bell EW, Zhang Y. DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism. Journal of Cheminformatics. 11: 40. PMID 31175455 DOI: 10.1186/S13321-019-0362-7 |
0.333 |
|
| 2019 |
Zheng W, Zhang C, Wuyun Q, Pearce R, Li Y, Zhang Y. LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins. Nucleic Acids Research. PMID 31081035 DOI: 10.1093/Nar/Gkz384 |
0.438 |
|
| 2019 |
Li Y, Hu J, Zhang C, Yu DJ, Zhang Y. ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks. Bioinformatics (Oxford, England). PMID 31070716 DOI: 10.1093/Bioinformatics/Btz291 |
0.448 |
|
| 2019 |
Han Z, Shao Q, Gong W, Wang S, Su J, Li C, Zhang Y. Interpreting the Dynamics of Binding Interactions of snRNA and U1A Using a Coarse-Grained Model. Biophysical Journal. PMID 30975455 DOI: 10.1016/J.Bpj.2019.03.008 |
0.323 |
|
| 2019 |
Pearce R, Huang X, Setiawan D, Zhang Y. EvoDesign: Designing Protein-Protein Binding Interactions Using Evolutionary Interface Profiles in Conjunction with an Optimized Physical Energy Function. Journal of Molecular Biology. PMID 30851277 DOI: 10.1016/J.Jmb.2019.02.028 |
0.459 |
|
| 2019 |
Li F, Zhang Y, Purcell AW, Webb GI, Chou KC, Lithgow T, Li C, Song J. Positive-unlabelled learning of glycosylation sites in the human proteome. Bmc Bioinformatics. 20: 112. PMID 30841845 DOI: 10.1186/S12859-019-2700-1 |
0.357 |
|
| 2019 |
Quan L, Wu H, Lyu Q, Zhang Y. DAMpred: Recognizing Disease-Associated nsSNPs through Bayes-Guided Neural-Network Model Built on Low-Resolution Structure Prediction of Proteins and Protein-Protein Interactions. Journal of Molecular Biology. PMID 30796987 DOI: 10.1016/J.Jmb.2019.02.017 |
0.418 |
|
| 2019 |
Shultis D, Mitra P, Huang X, Johnson J, Khattak NA, Gray F, Piper C, Czajka J, Hansen L, Wan B, Chinnaswamy K, Liu L, Wang M, Pan J, Stuckey J, ... ... Zhang Y, et al. Changing the Apoptosis Pathway through Evolutionary Protein Design. Journal of Molecular Biology. PMID 30625288 DOI: 10.1016/J.Jmb.2018.12.016 |
0.413 |
|
| 2019 |
Fan YX, Pan X, Zhang Y, Shen HB. LabCaS for Ranking Potential Calpain Substrate Cleavage Sites from Amino Acid Sequence. Methods in Molecular Biology (Clifton, N.J.). 1915: 111-120. PMID 30617800 DOI: 10.1007/978-1-4939-8988-1_10 |
0.37 |
|
| 2019 |
Xu D, Li H, Zhang Y. Fast and Accurate Calculation of Protein Depth by Euclidean Distance Transform. Research in Computational Molecular Biology : ... Annual International Conference, Recomb ... : Proceedings. Recomb (Conference : 2005-). 7821: 304-316. PMID 25035865 DOI: 10.1007/978-3-642-37195-0_30 |
0.313 |
|
| 2018 |
Deng H, Jia Y, Zhang Y. Protein structure prediction. International Journal of Modern Physics. B. 32. PMID 30853739 DOI: 10.1007/978-0-387-92738-1_11 |
0.455 |
|
| 2018 |
Hu R, Xiao J, Gu T, Yu X, Zhang Y, Chang J, Yang G, He G. Genome-wide identification and analysis of WD40 proteins in wheat (Triticum aestivum L.). Bmc Genomics. 19: 803. PMID 30400808 DOI: 10.1186/S12864-018-5157-0 |
0.38 |
|
| 2018 |
Zhang C, Wei X, Omenn GS, Zhang Y. Structure and Protein Interaction-based Gene Ontology Annotations Reveal Likely Functions of Uncharacterized Proteins on Human Chromosome 17. Journal of Proteome Research. PMID 30265558 DOI: 10.1021/Acs.Jproteome.8B00453 |
0.485 |
|
| 2018 |
Diamond JS, Zhang Y. THE-DB: a threading model database for comparative protein structure analysis of the E. coli K12 and human proteomes. Database : the Journal of Biological Databases and Curation. 2018. PMID 30239678 DOI: 10.1093/Database/Bay090 |
0.479 |
|
| 2018 |
Virtanen JJ, Zhang Y. MR-REX: molecular replacement by cooperative conformational search and occupancy optimization on low-accuracy protein models. Acta Crystallographica. Section D, Structural Biology. 74: 606-620. PMID 29968671 DOI: 10.1107/S2059798318005612 |
0.406 |
|
| 2018 |
Wu Q, Peng Z, Zhang Y, Yang J. COACH-D: improved protein-ligand binding sites prediction with refined ligand-binding poses through molecular docking. Nucleic Acids Research. PMID 29846643 DOI: 10.1093/Nar/Gky439 |
0.398 |
|
| 2018 |
Dong R, Pan S, Peng Z, Zhang Y, Yang J. mTM-align: a server for fast protein structure database search and multiple protein structure alignment. Nucleic Acids Research. PMID 29788129 DOI: 10.1093/Nar/Gky430 |
0.421 |
|
| 2018 |
Setiawan D, Brender J, Zhang Y. Recent advances in automated protein design and its future challenges. Expert Opinion On Drug Discovery. 1-18. PMID 29695210 DOI: 10.1080/17460441.2018.1465922 |
0.676 |
|
| 2018 |
Zhang C, Zheng W, Freddolino PL, Zhang Y. MetaGO: Predicting Gene Ontology of non-homologous proteins through low-resolution protein structure prediction and protein-protein network mapping. Journal of Molecular Biology. PMID 29534977 DOI: 10.1016/J.Jmb.2018.03.004 |
0.467 |
|
| 2018 |
Hu J, Liu Z, Yu DJ, Zhang Y. LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening. Bioinformatics (Oxford, England). PMID 29462237 DOI: 10.1093/Bioinformatics/Bty081 |
0.373 |
|
| 2018 |
Wu J, Zhang Q, Wu W, Pang T, Hu H, Chan WKB, Ke X, Zhang Y, Wren J. WDL-RF: Predicting Bioactivities of Ligand Molecules Acting with G Protein-coupled Receptors by Combining Weighted Deep Learning and Random Forest. Bioinformatics (Oxford, England). PMID 29432522 DOI: 10.1093/Bioinformatics/Bty070 |
0.691 |
|
| 2018 |
Hu J, Li Y, Zhang Y, Yu DJ. ATPbind: accurate protein-ATP binding site prediction by combining sequence-profiling and structure-based comparisons. Journal of Chemical Information and Modeling. PMID 29361215 DOI: 10.1021/Acs.Jcim.7B00397 |
0.371 |
|
| 2017 |
Dong R, Peng Z, Zhang Y, Yang J. mTM-align: an algorithm for fast and accurate multiple protein structure alignment. Bioinformatics (Oxford, England). PMID 29281009 DOI: 10.1093/Bioinformatics/Btx828 |
0.457 |
|
| 2017 |
Glusman G, Rose PW, Prlić A, Dougherty J, Duarte JM, Hoffman AS, Barton GJ, Bendixen E, Bergquist T, Bock C, Brunk E, Buljan M, Burley SK, Cai B, Carter H, ... ... Zhang Y, et al. Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework. Genome Medicine. 9: 113. PMID 29254494 DOI: 10.1186/S13073-017-0509-Y |
0.389 |
|
| 2017 |
Thomas JMH, Simkovic F, Keegan R, Mayans O, Zhang C, Zhang Y, Rigden DJ. Approaches to ab initio molecular replacement of α-helical transmembrane proteins. Acta Crystallographica. Section D, Structural Biology. 73: 985-996. PMID 29199978 DOI: 10.1107/S2059798317016436 |
0.416 |
|
| 2017 |
Wang J, Yang B, An Y, Marquez-Lago T, Leier A, Wilksch J, Hong Q, Zhang Y, Hayashida M, Akutsu T, Webb GI, Strugnell RA, Song J, Lithgow T. Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches. Briefings in Bioinformatics. PMID 29186295 DOI: 10.1093/Bib/Bbx164 |
0.326 |
|
| 2017 |
Zhang C, Mortuza SM, He B, Wang Y, Zhang Y. Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12. Proteins. PMID 29082551 DOI: 10.1002/Prot.25414 |
0.389 |
|
| 2017 |
Wang Y, Wang J, Li R, Shi Q, Xue Z, Zhang Y. ThreaDomEx: a unified platform for predicting continuous and discontinuous protein domains by multiple-threading and segment assembly. Nucleic Acids Research. PMID 28498994 DOI: 10.1093/Nar/Gkx410 |
0.34 |
|
| 2017 |
Wang Y, Virtanen J, Xue Z, Zhang Y. I-TASSER-MR: automated molecular replacement for distant-homology proteins using iterative fragment assembly and progressive sequence truncation. Nucleic Acids Research. PMID 28472524 DOI: 10.1093/Nar/Gkx349 |
0.355 |
|
| 2017 |
Zhang C, Freddolino PL, Zhang Y. COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information. Nucleic Acids Research. PMID 28472402 DOI: 10.1093/Nar/Gkx366 |
0.489 |
|
| 2017 |
He B, Mortuza SM, Wang Y, Shen HB, Zhang Y. NeBcon: Protein contact map prediction using neural network training coupled with naïve Bayes classifiers. Bioinformatics (Oxford, England). PMID 28369334 DOI: 10.1093/Bioinformatics/Btx164 |
0.434 |
|
| 2017 |
Li H, Zhang Y, Guan Y, Menon R, Omenn GS. Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks. Methods in Molecular Biology (Clifton, N.J.). 1558: 415-436. PMID 28150250 DOI: 10.1007/978-1-4939-6783-4_20 |
0.432 |
|
| 2017 |
Brender JR, Shultis D, Khattak NA, Zhang Y. An Evolution-Based Approach to De Novo Protein Design. Methods in Molecular Biology (Clifton, N.J.). 1529: 243-264. PMID 27914055 DOI: 10.1007/978-1-4939-6637-0_12 |
0.692 |
|
| 2017 |
Zhang Y, Yang R, Zhang W, Hu Z, Zhao W. Structural characterization and physicochemical properties of protein extracted from soybean meal assisted by steam flash-explosion with dilute acid soaking Food Chemistry. 219: 48-53. DOI: 10.1016/j.foodchem.2016.09.079 |
0.312 |
|
| 2016 |
Xiong P, Zhang C, Zheng W, Zhang Y. BindProfX: Assessing mutation-induced binding affinity change by protein interface profiles with pseudo counts. Journal of Molecular Biology. PMID 27899282 DOI: 10.1016/J.Jmb.2016.11.022 |
0.36 |
|
| 2016 |
An Y, Wang J, Li C, Leier A, Marquez-Lago T, Wilksch J, Zhang Y, Webb GI, Song J, Lithgow T. Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI. Briefings in Bioinformatics. PMID 27777222 DOI: 10.1093/bib/bbw100 |
0.306 |
|
| 2016 |
Li C, Lv D, Zhang L, Yang F, Wang C, Su J, Zhang Y. Approach to the unfolding and folding dynamics of add A-riboswitch upon adenine dissociation using a coarse-grained elastic network model. The Journal of Chemical Physics. 145: 014104. PMID 27394096 DOI: 10.1063/1.4954992 |
0.314 |
|
| 2016 |
Quan L, Lv Q, Zhang Y. STRUM: Structure-based prediction of protein stability changes upon single-point mutation. Bioinformatics (Oxford, England). PMID 27318206 DOI: 10.1093/Bioinformatics/Btw361 |
0.397 |
|
| 2016 |
Wang Y, Virtanen J, Xue Z, Tesmer JJ, Zhang Y. Using iterative fragment assembly and progressive sequence truncation to facilitate phasing and crystal structure determination of distantly related proteins. Acta Crystallographica. Section D, Structural Biology. 72: 616-628. PMID 27139625 DOI: 10.1107/S2059798316003016 |
0.48 |
|
| 2016 |
Li HD, Menon R, Eksi R, Guerler A, Zhang Y, Omenn GS, Guan Y. A Network of Splice Isoforms for the Mouse. Scientific Reports. 6: 24507. PMID 27079421 DOI: 10.1038/Srep24507 |
0.305 |
|
| 2015 |
Yang J, Zhang Y. Protein Structure and Function Prediction Using I-TASSER. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. 52: 5.8.1-5.8.15. PMID 26678386 DOI: 10.1002/0471250953.Bi0508S52 |
0.484 |
|
| 2015 |
Brender JR, Zhang Y. Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles. Plos Computational Biology. 11: e1004494. PMID 26506533 DOI: 10.1371/Journal.Pcbi.1004494 |
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Deng H, Jia Y, Zhang Y. 3DRobot: Automated Generation of Diverse and Well-packed Protein Structure Decoys. Bioinformatics (Oxford, England). PMID 26471454 DOI: 10.1093/Bioinformatics/Btv601 |
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Yang J, Wang Y, Zhang Y. ResQ: An approach to unified estimation of B-factor and residue-specific error in protein structure prediction. Journal of Molecular Biology. PMID 26437129 DOI: 10.1016/J.Jmb.2015.09.024 |
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| 2015 |
Bai C, Zhang Y, Zhao X, Hu Y, Xiang S, Miao J, Lou C, Zhang L. Exploiting a precise design of universal synthetic modular regulatory elements to unlock the microbial natural products in Streptomyces. Proceedings of the National Academy of Sciences of the United States of America. PMID 26374838 DOI: 10.1073/Pnas.1511027112 |
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| 2015 |
Zhang W, Yang J, He B, Walker SE, Zhang H, Govindarajoo B, Virtanen J, Xue Z, Shen HB, Zhang Y. Integration of QUARK and I-TASSER for Ab Initio Protein Structure Prediction in CASP11. Proteins. PMID 26370505 DOI: 10.1002/Prot.24930 |
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| 2015 |
Yang J, Zhang W, He B, Walker SE, Zhang H, Govindarajoo B, Virtanen J, Xue Z, Shen HB, Zhang Y. Template-based protein structure prediction in CASP11 and retrospect of I-TASSER in the last decade. Proteins. PMID 26343917 DOI: 10.1002/Prot.24918 |
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| 2015 |
Yang J, He BJ, Jang R, Zhang Y, Shen HB. Accurate disulfide-bonding network predictions improve ab initio structure prediction of cysteine-rich proteins. Bioinformatics (Oxford, England). PMID 26254435 DOI: 10.1093/Bioinformatics/Btv459 |
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| 2015 |
Dong Q, Menon R, Omenn GS, Zhang Y. Structural Bioinformatics Inspection of neXtProt PE5 Proteins in the Human Proteome. Journal of Proteome Research. 14: 3750-61. PMID 26193931 DOI: 10.1021/Acs.Jproteome.5B00516 |
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| 2015 |
Zhang J, Yang J, Jang R, Zhang Y. GPCR-I-TASSER: A Hybrid Approach to G Protein-Coupled Receptor Structure Modeling and the Application to the Human Genome. Structure (London, England : 1993). 23: 1538-1549. PMID 26190572 DOI: 10.1016/j.str.2015.06.007 |
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| 2015 |
Shultis D, Dodge G, Zhang Y. Crystal structure of designed PX domain from cytokine-independent survival kinase and implications on evolution-based protein engineering. Journal of Structural Biology. PMID 26073968 DOI: 10.1016/J.Jsb.2015.06.009 |
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| 2015 |
Chan WK, Zhang H, Yang J, Brender JR, Hur J, Özgür A, Zhang Y. GLASS: a comprehensive database for experimentally validated GPCR-ligand associations. Bioinformatics (Oxford, England). PMID 25971743 DOI: 10.1093/Bioinformatics/Btv302 |
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| 2015 |
Yang J, Zhang Y. I-TASSER server: new development for protein structure and function predictions. Nucleic Acids Research. 43: W174-81. PMID 25883148 DOI: 10.1093/Nar/Gkv342 |
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| 2015 |
Jang R, Wang Y, Xue Z, Zhang Y. NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment. Journal of Biomolecular Nmr. PMID 25737244 DOI: 10.1007/S10858-015-9914-Y |
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| 2015 |
Keegan RM, Bibby J, Thomas J, Xu D, Zhang Y, Mayans O, Winn MD, Rigden DJ. Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models. Acta Crystallographica. Section D, Biological Crystallography. 71: 338-43. PMID 25664744 DOI: 10.1107/S1399004714025784 |
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| 2015 |
Cheng S, Zhang Y, Brooks CL. PCalign: a method to quantify physicochemical similarity of protein-protein interfaces. Bmc Bioinformatics. 16: 33. PMID 25638036 DOI: 10.1186/S12859-015-0471-X |
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| 2015 |
Li F, Li C, Wang M, Webb GI, Zhang Y, Whisstock JC, Song J. GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome. Bioinformatics (Oxford, England). 31: 1411-9. PMID 25568279 DOI: 10.1093/Bioinformatics/Btu852 |
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| 2015 |
Yang J, Yan R, Roy A, Xu D, Poisson J, Zhang Y. The I-TASSER Suite: protein structure and function prediction. Nature Methods. 12: 7-8. PMID 25549265 DOI: 10.1038/Nmeth.3213 |
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| 2015 |
Sun HP, Huang Y, Wang XF, Zhang Y, Shen HB. Improving accuracy of protein contact prediction using balanced network deconvolution. Proteins. 83: 485-96. PMID 25524593 DOI: 10.1002/Prot.24744 |
0.411 |
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| 2015 |
Xu YY, Yang F, Zhang Y, Shen HB. Bioimaging-based detection of mislocalized proteins in human cancers by semi-supervised learning. Bioinformatics (Oxford, England). 31: 1111-9. PMID 25414362 DOI: 10.1093/Bioinformatics/Btu772 |
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| 2015 |
Du H, Brender JR, Zhang J, Zhang Y. Protein structure prediction provides comparable performance to crystallographic structures in docking-based virtual screening. Methods (San Diego, Calif.). 71: 77-84. PMID 25220914 DOI: 10.1016/J.Ymeth.2014.08.017 |
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| 2015 |
Zhang J, Yang J, Jang R, Zhang Y. GPCR-I-TASSER: A Hybrid Approach to G Protein-Coupled Receptor Structure Modeling and the Application to the Human Genome Structure. 23: 1538-1549. DOI: 10.1016/J.Str.2015.06.007 |
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| 2014 |
Szilagyi A, Zhang Y. Template-based structure modeling of protein-protein interactions. Current Opinion in Structural Biology. 24: 10-23. PMID 24721449 DOI: 10.1016/J.Sbi.2013.11.005 |
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| 2014 |
Quan S, Wang L, Petrotchenko EV, Makepeace KA, Horowitz S, Yang J, Zhang Y, Borchers CH, Bardwell JC. Super Spy variants implicate flexibility in chaperone action. Elife. 3: e01584. PMID 24497545 DOI: 10.7554/Elife.01584 |
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| 2014 |
Zhang Y. Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10 Proteins. 82: 175-187. PMID 23760925 DOI: 10.1002/Prot.24341 |
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| 2013 |
Mitra P, Shultis D, Brender JR, Czajka J, Marsh D, Gray F, Cierpicki T, Zhang Y. An evolution-based approach to De Novo protein design and case study on Mycobacterium tuberculosis. Plos Computational Biology. 9: e1003298. PMID 24204234 DOI: 10.1371/Journal.Pcbi.1003298 |
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| 2013 |
Yan R, Xu D, Yang J, Walker S, Zhang Y. A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction. Scientific Reports. 3: 2619. PMID 24018415 DOI: 10.1038/Srep02619 |
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| 2013 |
Xu D, Li H, Zhang Y. Protein depth calculation and the use for improving accuracy of protein fold recognition. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 805-16. PMID 23992298 DOI: 10.1089/cmb.2013.0071 |
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| 2013 |
Yang J, Roy A, Zhang Y. Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. Bioinformatics (Oxford, England). 29: 2588-95. PMID 23975762 DOI: 10.1093/Bioinformatics/Btt447 |
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| 2013 |
Yang J, Jang R, Zhang Y, Shen HB. High-accuracy prediction of transmembrane inter-helix contacts and application to GPCR 3D structure modeling Bioinformatics. 29: 2579-2587. PMID 23946502 DOI: 10.1093/Bioinformatics/Btt440 |
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| 2013 |
Xue Z, Xu D, Wang Y, Zhang Y. ThreaDom: extracting protein domain boundary information from multiple threading alignments. Bioinformatics (Oxford, England). 29: i247-56. PMID 23812990 DOI: 10.1093/Bioinformatics/Btt209 |
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| 2013 |
Xu YY, Yang F, Zhang Y, Shen HB. An image-based multi-label human protein subcellular localization predictor (iLocator) reveals protein mislocalizations in cancer tissues. Bioinformatics (Oxford, England). 29: 2032-40. PMID 23740749 DOI: 10.1093/Bioinformatics/Btt320 |
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| 2013 |
Xu D, Zhang Y. Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment. Scientific Reports. 3: 1895-1895. PMID 23719418 DOI: 10.1038/Srep01895 |
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| 2013 |
Mitra P, Shultis D, Zhang Y. EvoDesign: De novo protein design based on structural and evolutionary profiles. Nucleic Acids Research. 41: W273-280. PMID 23671331 DOI: 10.1093/Nar/Gkt384 |
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| 2013 |
Omenn GS, Menon R, Zhang Y. Innovations in proteomic profiling of cancers: alternative splice variants as a new class of cancer biomarker candidates and bridging of proteomics with structural biology. Journal of Proteomics. 90: 28-37. PMID 23603631 DOI: 10.1016/J.Jprot.2013.04.007 |
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| 2013 |
Zhang Y, Skolnick J. Segment assembly, structure alignment and iterative simulation in protein structure prediction. Bmc Biology. 11: 44. PMID 23587325 DOI: 10.1186/1741-7007-11-44 |
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| 2013 |
Abrusán G, Zhang Y, Szilágyi A. Structure prediction and analysis of DNA transposon and LINE retrotransposon proteins. The Journal of Biological Chemistry. 288: 16127-38. PMID 23530042 DOI: 10.1074/Jbc.M113.451500 |
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| 2013 |
Guerler A, Govindarajoo B, Zhang Y. Mapping monomeric threading to protein-protein structure prediction. Journal of Chemical Information and Modeling. 53: 717-25. PMID 23413988 DOI: 10.1021/Ci300579R |
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| 2013 |
Abrusán G, Szilágyi A, Zhang Y, Papp B. Turning gold into ‘junk’: transposable elements utilize central proteins of cellular networks Nucleic Acids Research. 41: 3190-3200. PMID 23341038 DOI: 10.1093/Nar/Gkt011 |
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| 2013 |
Wu S, Li N, Ma J, Shen H, Jiang D, Chang C, Zhang C, Li L, Zhang H, Jiang J, Xu Z, Ping L, Chen T, Zhang W, Zhang T, ... ... Zhang Y, et al. First proteomic exploration of protein-encoding genes on chromosome 1 in human liver, stomach, and colon. Journal of Proteome Research. 12: 67-80. PMID 23256928 DOI: 10.1021/Pr3008286 |
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| 2013 |
Fan YX, Zhang Y, Shen HB. LabCaS: labeling calpain substrate cleavage sites from amino acid sequence using conditional random fields. Proteins. 81: 622-634. PMID 23180633 DOI: 10.1002/Prot.24217 |
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| 2013 |
Yang J, Roy A, Zhang Y. BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions. Nucleic Acids Research. 41: D1096-103. PMID 23087378 DOI: 10.1093/Nar/Gks966 |
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| 2013 |
Xu D, Zhang Y. Toward optimal fragment generations for ab initio protein structure assembly Proteins: Structure, Function and Bioinformatics. 81: 229-239. PMID 22972754 DOI: 10.1002/Prot.24179 |
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| 2013 |
Mitra P, Shultis D, Brender JR, Czajka J, Marsh D, Gray F, Cierpicki T, Zhang Y. Illustrative examples of the EBM design on M. tuberculosis proteins. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1003298.G006 |
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| 2013 |
Mukherjee S, Lee KI, Zhang Y, Fisher M, Im W. Modeling, Ion Conductance, and Electrostatic Properties of the Protective Antigen Pore Structure of Anthrax Toxin Biophysical Journal. 104: 63a. DOI: 10.1016/J.Bpj.2012.11.386 |
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| 2012 |
Garma L, Mukherjee S, Mitra P, Zhang Y. How many protein-protein interactions types exist in nature? Plos One. 7: e38913. PMID 22719985 DOI: 10.1371/Journal.Pone.0038913 |
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| 2012 |
Deng H, Jia Y, Wei Y, Zhang Y. What is the best reference state for designing statistical atomic potentials in protein structure prediction? Proteins. 80: 2311-22. PMID 22623012 DOI: 10.1002/Prot.24121 |
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| 2012 |
Roy A, Yang J, Zhang Y. COFACTOR: an accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Research. 40: W471-7. PMID 22570420 DOI: 10.1093/Nar/Gks372 |
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| 2012 |
Roy A, Zhang Y. Recognizing protein-ligand binding sites by global structural alignment and local geometry refinement. Structure (London, England : 1993). 20: 987-97. PMID 22560732 DOI: 10.1016/J.Str.2012.03.009 |
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| 2012 |
Xu D, Zhang Y. Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field Proteins: Structure, Function and Bioinformatics. 80: 1715-1735. PMID 22411565 DOI: 10.1002/Prot.24065 |
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| 2012 |
Qi X, Hong L, Zhang Y. A variational model for oligomer-formation process of GNNQQNY peptide from yeast prion protein Sup35. Biophysical Journal. 102: 597-605. PMID 22325283 DOI: 10.1016/J.Bpj.2011.12.036 |
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| 2012 |
Dror I, Shazman S, Mukherjee S, Zhang Y, Glaser F, Mandel-Gutfreund Y. Predicting nucleic acid binding interfaces from structural models of proteins. Proteins. 80: 482-9. PMID 22086767 DOI: 10.1002/Prot.23214 |
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| 2012 |
Szilágyi A, Zhang Y, Závodszky P. Intra-chain 3D segment swapping spawns the evolution of new multidomain protein architectures. Journal of Molecular Biology. 415: 221-35. PMID 22079367 DOI: 10.1016/J.Jmb.2011.10.045 |
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Li Y, Zhang J, Tai D, Middaugh CR, Zhang Y, Fang J. PROTS: a fragment based protein thermo-stability potential. Proteins. 80: 81-92. PMID 21976375 DOI: 10.1002/Prot.23163 |
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Lee HS, Zhang Y. BSP-SLIM: a blind low-resolution ligand-protein docking approach using predicted protein structures. Proteins. 80: 93-110. PMID 21971880 DOI: 10.1002/Prot.23165 |
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| 2011 |
dos Reis MA, Aparicio R, Zhang Y. Improving protein template recognition by using small-angle x-ray scattering profiles. Biophysical Journal. 101: 2770-81. PMID 22261066 DOI: 10.1016/J.Bpj.2011.10.046 |
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| 2011 |
Zhang J, Liang Y, Zhang Y. Atomic-Level Protein Structure Refinement Using Fragment-Guided Molecular Dynamics Conformation Sampling Structure. 19: 1784-1795. PMID 22153501 DOI: 10.1016/J.Str.2011.09.022 |
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| 2011 |
Xu D, Zhang Y. Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophysical Journal. 101: 2525-34. PMID 22098752 DOI: 10.1016/J.Bpj.2011.10.024 |
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| 2011 |
Roy A, Xu D, Poisson J, Zhang Y. A protocol for computer-based protein structure and function prediction. Journal of Visualized Experiments : Jove. e3259. PMID 22082966 DOI: 10.3791/3259 |
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| 2011 |
Xu D, Zhang J, Roy A, Zhang Y. Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement. Proteins. 79: 147-60. PMID 22069036 DOI: 10.1002/Prot.23111 |
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| 2011 |
Menon R, Roy A, Mukherjee S, Belkin S, Zhang Y, Omenn GS. Functional implications of structural predictions for alternative splice proteins expressed in Her2/neu-induced breast cancers. Journal of Proteome Research. 10: 5503-11. PMID 22003824 DOI: 10.1021/Pr200772W |
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| 2011 |
Kemege KE, Hickey JM, Lovell S, Battaile KP, Zhang Y, Hefty PS. Ab initio structural modeling of and experimental validation for Chlamydia trachomatis protein CT296 reveal structural similarity to Fe(II) 2-oxoglutarate-dependent enzymes. Journal of Bacteriology. 193: 6517-28. PMID 21965559 DOI: 10.1128/Jb.05488-11 |
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| 2011 |
Wu S, Szilagyi A, Zhang Y. Improving Protein Structure Prediction Using Multiple Sequence-Based Contact Predictions Structure. 19: 1182-1191. PMID 21827953 DOI: 10.1016/J.Str.2011.05.004 |
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| 2011 |
Du H, Hu Z, Bazzoli A, Zhang Y. Prediction of inhibitory activity of epidermal growth factor receptor inhibitors using grid search-projection pursuit regression method. Plos One. 6: e22367. PMID 21811593 DOI: 10.1371/Journal.Pone.0022367 |
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| 2011 |
Mukherjee S, Zhang Y. Protein-protein complex structure predictions by multimeric threading and template recombination. Structure (London, England : 1993). 19: 955-66. PMID 21742262 DOI: 10.1016/J.Str.2011.04.006 |
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| 2011 |
Rankin CA, Roy A, Zhang Y, Richter M. Parkin, A Top Level Manager in the Cell's Sanitation Department. The Open Biochemistry Journal. 5: 9-26. PMID 21633666 DOI: 10.2174/1874091X01105010009 |
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Bazzoli A, Tettamanzi AGB, Zhang Y. Computational Protein Design and Large-Scale Assessment by I-TASSER Structure Assembly Simulations Journal of Molecular Biology. 407: 764-776. PMID 21329699 DOI: 10.1016/J.Jmb.2011.02.017 |
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| 2010 |
Zhang J, Zhang Y. A Novel Side-Chain Orientation Dependent Potential Derived from Random-Walk Reference State for Protein Fold Selection and Structure Prediction Plos One. 5. PMID 21060880 DOI: 10.1371/Journal.Pone.0015386 |
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Zhang J, Zhang Y. GPCRRD: G protein-coupled receptor spatial restraint database for 3D structure modeling and function annotation. Bioinformatics (Oxford, England). 26: 3004-5. PMID 20926423 DOI: 10.1093/Bioinformatics/Btq563 |
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Wu S, Zhang Y. Recognizing Protein Substructure Similarity Using Segmental Threading Structure. 18: 858-867. PMID 20637422 DOI: 10.1016/J.Str.2010.04.007 |
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| 2010 |
Roy A, Kucukural A, Zhang Y. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols. 5: 725-38. PMID 20360767 DOI: 10.1038/Nprot.2010.5 |
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Xu J, Zhang Y. How significant is a protein structure similarity with TM-score = 0.5? Bioinformatics (Oxford, England). 26: 889-95. PMID 20164152 DOI: 10.1093/Bioinformatics/Btq066 |
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SOMARELLI JA, MESA A, ROY A, ZHANG Y, HERRERA RJ. A three-dimensional model of the U1 small nuclear ribonucleoprotein particle Entomological Research. 40: 104-112. DOI: 10.1111/J.1748-5967.2010.00266.X |
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Xu D, Zhang Y. Generating triangulated macromolecular surfaces by Euclidean Distance Transform. Plos One. 4: e8140. PMID 19956577 DOI: 10.1371/Journal.Pone.0008140 |
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| 2009 |
Bultrini E, Brick K, Mukherjee S, Zhang Y, Silvestrini F, Alano P, Pizzi E. Revisiting the Plasmodium falciparum RIFIN family: from comparative genomics to 3D-model prediction. Bmc Genomics. 10: 445. PMID 19769795 DOI: 10.1186/1471-2164-10-445 |
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| 2009 |
Zhang Y. I-TASSER: fully automated protein structure prediction in CASP8. Proteins. 77: 100-113. PMID 19768687 DOI: 10.1002/Prot.22588 |
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Li Y, Roy A, Zhang Y. HAAD: A quick algorithm for accurate prediction of hydrogen atoms in protein structures. Plos One. 4: e6701. PMID 19693270 DOI: 10.1371/Journal.Pone.0006701 |
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| 2009 |
Mukherjee S, Zhang Y. MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming. Nucleic Acids Research. 37: e83. PMID 19443443 DOI: 10.1093/Nar/Gkp318 |
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| 2009 |
Zhang Y. Protein structure prediction: when is it useful? Current Opinion in Structural Biology. 19: 145-155. PMID 19327982 DOI: 10.1016/J.Sbi.2009.02.005 |
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| 2009 |
Li Y, Zhang Y. REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks. Proteins. 76: 665-676. PMID 19274737 DOI: 10.1002/Prot.22380 |
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Wu S, Zhang Y. ANGLOR: a composite machine-learning algorithm for protein backbone torsion angle prediction. Plos One. 3. PMID 18923703 DOI: 10.1371/Journal.Pone.0003400 |
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| 2008 |
Zhang Y. Progress and challenges in protein structure prediction. Current Opinion in Structural Biology. 18: 342-348. PMID 18436442 DOI: 10.1016/J.Sbi.2008.02.004 |
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| 2008 |
Wu S, Zhang Y. A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinformatics (Oxford, England). 24: 924-31. PMID 18296462 DOI: 10.1093/Bioinformatics/Btn069 |
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Wu S, Zhang Y. MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins. 72: 547-556. PMID 18247410 DOI: 10.1002/Prot.21945 |
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| 2008 |
Zhang Y. I-TASSER server for protein 3D structure prediction. Bmc Bioinformatics. 9: 40. PMID 18215316 DOI: 10.1186/1471-2105-9-40 |
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| 2007 |
Lorenzen S, Zhang Y. Monte Carlo refinement of rigid‐body protein docking structures with backbone displacement and side‐chain optimization Protein Science. 16: 2716-2725. PMID 17965193 DOI: 10.1110/Ps.072847207 |
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| 2007 |
Zhang Y. Template‐based modeling and free modeling by I‐TASSER in CASP7 Proteins. 69: 108-117. PMID 17894355 DOI: 10.1002/Prot.21702 |
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| 2007 |
Wu S, Skolnick J, Zhang Y. Ab initio modeling of small proteins by iterative TASSER simulations. Bmc Biology. 5: 17. PMID 17488521 DOI: 10.1186/1741-7007-5-17 |
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Wu S, Zhang Y. LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Research. 35: 3375-3382. PMID 17478507 DOI: 10.1093/Nar/Gkm251 |
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| 2007 |
Lorenzen S, Zhang Y. Identification of near-native structures by clustering protein docking conformations. Proteins. 68: 187-194. PMID 17397057 DOI: 10.1002/Prot.21442 |
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| 2007 |
Zhang Y, Skolnick J. Scoring function for automated assessment of protein structure template quality Proteins: Structure, Function, and Bioinformatics. 68: 1020-1020. DOI: 10.1002/Prot.21643 |
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Pandit SB, Zhang Y, Skolnick J. TASSER-Lite: an automated tool for protein comparative modeling. Biophysical Journal. 91: 4180-90. PMID 16963505 DOI: 10.1529/Biophysj.106.084293 |
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Zhang Y, Devries ME, Skolnick J. Structure modeling of all identified G protein-coupled receptors in the human genome. Plos Computational Biology. 2: e13. PMID 16485037 DOI: 10.1371/Journal.Pcbi.0020013 |
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Zhang Y, Hubner IA, Arakaki AK, Shakhnovich E, Skolnick J. On the origin and highly likely completeness of single-domain protein structures. Proceedings of the National Academy of Sciences of the United States of America. 103: 2605-10. PMID 16478803 DOI: 10.1073/Pnas.0509379103 |
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Grimm V, Zhang Y, Skolnick J. Benchmarking of dimeric threading and structure refinement. Proteins. 63: 457-65. PMID 16463265 DOI: 10.1002/Prot.20878 |
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Lee SY, Zhang Y, Skolnick J. TASSER-based refinement of NMR structures. Proteins. 63: 451-6. PMID 16456861 DOI: 10.1002/Prot.20902 |
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Zhang Y, DeVries ME, Skolnick J. Correction: Structure Modeling of All Identified G Protein–Coupled Receptors in the Human Genome Plos Computational Biology. 2. DOI: 10.1371/Journal.Pcbi.0020029 |
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Zhang Y, Arakaki AK, Skolnick J. TASSER: an automated method for the prediction of protein tertiary structures in CASP6. Proteins. 61: 91-8. PMID 16187349 DOI: 10.1002/Prot.20724 |
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Zhang Y, Skolnick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Research. 33: 2302-9. PMID 15849316 DOI: 10.1093/Nar/Gki524 |
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| 2005 |
Zhou H, Zhang Y. Hierarchical chain model of spider capture silk elasticity. Physical Review Letters. 94: 28104-28104. PMID 15698235 DOI: 10.1103/Physrevlett.94.028104 |
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| 2005 |
Zhang Y, Skolnick J. The protein structure prediction problem could be solved using the current PDB library. Proceedings of the National Academy of Sciences of the United States of America. 102: 1029-34. PMID 15653774 DOI: 10.1073/Pnas.0407152101 |
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Zhang Y, Skolnick J. Scoring function for automated assessment of protein structure template quality Proteins: Structure, Function and Genetics. 57: 702-710. PMID 15476259 DOI: 10.1002/Prot.20264 |
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| 2004 |
Zhang Y, Skolnick J. Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins Biophysical Journal. 87: 2647-2655. PMID 15454459 DOI: 10.1529/Biophysj.104.045385 |
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Li W, Zhang Y, Skolnick J. Application of sparse NMR restraints to large-scale protein structure prediction Biophysical Journal. 87: 1241-1248. PMID 15298926 DOI: 10.1529/Biophysj.104.044750 |
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Skolnick J, Kihara D, Zhang Y. Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm Proteins: Structure, Function and Genetics. 56: 502-518. PMID 15229883 DOI: 10.1002/Prot.20106 |
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| 2004 |
Zhang Y, Skolnick J. Automated structure prediction of weakly homologous proteins on a genomic scale Proceedings of the National Academy of Sciences of the United States of America. 101: 7594-7599. PMID 15126668 DOI: 10.1073/Pnas.0305695101 |
0.647 |
|
| 2004 |
Zhang Y, Skolnick J. SPICKER: A clustering approach to identify near-native protein folds Journal of Computational Chemistry. 25: 865-871. PMID 15011258 DOI: 10.1002/Jcc.20011 |
0.598 |
|
| 2004 |
Arakaki AK, Zhang Y, Skolnick J. Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment. Bioinformatics (Oxford, England). 20: 1087-96. PMID 14764543 DOI: 10.1093/Bioinformatics/Bth044 |
0.592 |
|
| 2003 |
Skolnick J, Zhang Y, Arakaki AK, Kolinski A, Boniecki M, Szilágyi A, Kihara D. TOUCHSTONE: a unified approach to protein structure prediction. Proteins. 53: 469-79. PMID 14579335 DOI: 10.1002/Prot.10551 |
0.57 |
|
| 2003 |
Li W, Zhang Y, Kihara D, Huang YJ, Zheng D, Montelione GT, Kolinski A, Skolnick J. TOUCHSTONEX: Protein structure prediction with sparse NMR data Proteins: Structure, Function and Genetics. 53: 290-306. PMID 14517980 DOI: 10.1002/Prot.10499 |
0.603 |
|
| 2003 |
Zhang Y, Kolinski A, Skolnick J. TOUCHSTONE II: A new approach to ab initio protein structure prediction Biophysical Journal. 85: 1145-1164. PMID 12885659 DOI: 10.1016/S0006-3495(03)74551-2 |
0.61 |
|
| 2002 |
Zhang Y, Kihara D, Skolnick J. Local energy landscape flattening: Parallel hyperbolic Monte Carlo sampling of protein folding Proteins: Structure, Function and Genetics. 48: 192-201. PMID 12112688 DOI: 10.1002/Prot.10141 |
0.569 |
|
| 2002 |
Kihara D, Zhang Y, Lu H, Kolinski A, Skolnick J. Ab initio protein structure prediction on a genomic scale: Application to the Mycoplasma genitalium genome Proceedings of the National Academy of Sciences of the United States of America. 99: 5993-5998. PMID 11959918 DOI: 10.1073/Pnas.092135699 |
0.64 |
|
| 2001 |
Zhang Y, Zhou H, Ou-Yang ZC. Stretching Single-Stranded DNA: Interplay of Electrostatic, Base-Pairing, and Base-Pair Stacking Interactions Biophysical Journal. 81: 1133-1143. PMID 11463654 DOI: 10.1016/S0006-3495(01)75770-0 |
0.316 |
|
| 2001 |
Zhou H, Zhang Y, Ou-Yang ZC. Stretch-Induced Hairpin-Coil Transitions in Designed Polynucleotide Chains Physical Review Letters. 86: 356-359. PMID 11177830 DOI: 10.1103/Physrevlett.86.356 |
0.347 |
|
| 2001 |
Zhang Y, Skolnick J. Parallel-hat tempering: A Monte Carlo search scheme for the identification of low-energy structures Journal of Chemical Physics. 115: 5027-5032. DOI: 10.1063/1.1396672 |
0.508 |
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