Yang Zhang - Publications

Affiliations: 
computational biology University of Michigan, Ann Arbor, Ann Arbor, MI 

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

Year Citation  Score
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  1
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  1
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  1
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  1
2017 Ai C, Zhang Y. Estimation of partially specified spatial panel data models with fixed-effects Econometric Reviews. 36: 6-22. DOI: 10.1080/07474938.2015.1113641  0.32
2017 Liang S, Zhang Y, Sun Z, Chang Y. Laboratory study on the evolution of waves parameters due to wave breaking in deep water Wave Motion. 68: 31-42. DOI: 10.1016/j.wavemoti.2016.08.010  0.36
2017 Yang Z, Yu T, Zhang Y, Sun Z. Influence of cage clearance on the heating characteristics of high-speed ball bearings Tribology International. 105: 125-134. DOI: 10.1016/j.triboint.2016.09.041  0.36
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  1
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  1
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  1
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  1
2015 Cao B, Du Y, Li J, Li H, Li L, Zhang Y, Zou J, Liu Q. Comparison of Five Slope Correction Methods for Leaf Area Index Estimation From Hemispherical Photography Ieee Geoscience and Remote Sensing Letters. DOI: 10.1109/LGRS.2015.2440438  1
2014 Yokoyama KD, Zhang Y, Ma J. Tracing the evolution of lineage-specific transcription factor binding sites in a birth-death framework. Plos Computational Biology. 10: e1003771. PMID 25144359 DOI: 10.1371/journal.pcbi.1003771  0.68
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  1
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  1
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  1
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  1
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  1
2006 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  1
2006 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  1
2006 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  1
2006 Grimm V, Zhang Y, Skolnick J. Benchmarking of dimeric threading and structure refinement. Proteins. 63: 457-65. PMID 16463265 DOI: 10.1002/prot.20878  1
2006 Lee SY, Zhang Y, Skolnick J. TASSER-based refinement of NMR structures. Proteins. 63: 451-6. PMID 16456861 DOI: 10.1002/prot.20902  1
2005 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  1
2005 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  1
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  1
2004 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  1
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  1
2004 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  1
2004 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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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