Research Topics
Genomes and Genes | Yang ZhangSummaryAffiliation: University of Kansas Country: USA Publications
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Detail Information
Publications
Revisiting the Plasmodium falciparum RIFIN family: from comparative genomics to 3D-model predictionEmanuele Bultrini
Dipartimento di Malattie Infettive, Parassitarie ed Immunomediate, Istituto Superiore di Sanita, Viale Regina Elena, 299, 00161 Roma, Italy
BMC Genomics 10:445. 2009..Despite recent advances, our knowledge of the regulation of RIFIN gene expression is still poor and the biological role of the protein products remain obscure...
Template-based modeling and free modeling by I-TASSER in CASP7Yang Zhang
Center for Bioinformatics, Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, USA
Proteins 69:108-17. 2007..Especially, there is no high-resolution model below 2 A for the FM targets. These problems highlight the issues that need to be addressed in the next generation of atomic-level I-TASSER development especially for the FM target modeling...- Protein structure prediction: when is it useful?Yang Zhang
Center for Bioinformatics and Department of Molecular Biosciences, University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA
Curr Opin Struct Biol 19:145-55. 2009..Unfortunately, there has been no essential progress in the development of techniques for detecting remotely homologous templates and for predicting novel protein structures... - I-TASSER server for protein 3D structure predictionYang Zhang
Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, 2030 Becker Dr, Lawrence, KS 66047, USA
BMC Bioinformatics 9:40. 2008..Our laboratory has since then received numerous requests about the public availability of the I-TASSER algorithm and the usage of the I-TASSER predictions... - Monte Carlo refinement of rigid-body protein docking structures with backbone displacement and side-chain optimizationStephan Lorenzen
Center for Bioinformatics, University of Kansas, Kansas 66047, USA
Protein Sci 16:2716-25. 2007..In most cases, clear binding funnels around the native structure can be observed. The results show the potential of Monte Carlo refinement methods and emphasize their applicability for protein-protein docking... - Progress and challenges in protein structure predictionYang Zhang
Center for Bioinformatics and Department of Molecular Biosciences, University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, United States
Curr Opin Struct Biol 18:342-8. 2008..However, predicting structures for proteins larger than 150 residues still remains a challenge, with bottlenecks from both force field and conformational search... - I-TASSER: fully automated protein structure prediction in CASP8Yang Zhang
Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, Lawrence, Kansas 66047, USA
Proteins 77:100-13. 2009..There are also problems related with domain-splitting and mirror image recognition which mainly influences the performance of I-TASSER modeling in the FM-based structure predictions... - Recognizing protein substructure similarity using segmental threadingSitao Wu
Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA
Structure 18:858-67. 2010..This significant improvement should have important impact on protein structure modeling and functional inference... - A comprehensive assessment of sequence-based and template-based methods for protein contact predictionSitao Wu
Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, 2030 Becker Dr, Lawrence, KS 66047, USA
Bioinformatics 24:924-31. 2008..The maximum yield should be obtained by the combination of both sequence- and template-based predictions... - MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure informationSitao Wu
Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, 2030 Becker Dr, Lawrence, Kansas 66047, USA
Proteins 72:547-56. 2008..0 x 10(-13), which demonstrates the effect of additional structural information on the protein fold recognition. The MUSTER server is freely available to the academic community at http://zhang.bioinformatics.ku.edu/MUSTER... - PROTS: a fragment based protein thermo-stability potentialYunqi Li
Applied Bioinformatics Laboratory, The University of Kansas, Lawrence, Kansas 66047, USA
Proteins 80:81-92. 2012..In addition, this white-box predictor allows easy interpretation of the factors that influence mutation induced protein stability changes at the residue level... - Ab initio modeling of small proteins by iterative TASSER simulationsSitao Wu
Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, Lawrence, KS 66047, USA
BMC Biol 5:17. 2007..The aim of this study was to extend the TASSER (threading/assembly/refinement) method for the ab initio modeling and examine systemically its ability to fold small single-domain proteins... - LOMETS: a local meta-threading-server for protein structure predictionSitao Wu
Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, 2030 Becker Dr, Lawrence, KS 6604, USA
Nucleic Acids Res 35:3375-82. 2007..The LOMETS server is freely available to the academic community at http://zhang.bioinformatics.ku.edu/LOMETS... - Identification of near-native structures by clustering protein docking conformationsStephan Lorenzen
Center of Bioinformatics, Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66046, USA
Proteins 68:187-94. 2007..A collection of multiple decoy sets of comparable quality will be the key to improve the clustering result from meta-docking servers... - REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networksYunqi Li
Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, Lawrence, 66047, USA
Proteins 76:665-76. 2009..The REMO algorithm has been exploited in the recent CASP8 experiment which demonstrated significant improvements of the I-TASSER models in both atomic-level structural refinement and hydrogen-bonding network construction... - ANGLOR: a composite machine-learning algorithm for protein backbone torsion angle predictionSitao Wu
Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, Lawrence, KS, USA
PLoS ONE 3:e3400. 2008..Thus, although the average accuracy of the ANGLOR prediction is still low, the portion of the accurately predicted dihedral angles may be useful in assisting protein fold recognition and ab initio 3D structure modeling... - HAAD: A quick algorithm for accurate prediction of hydrogen atoms in protein structuresYunqi Li
Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, Lawrence, Kansas, USA
PLoS ONE 4:e6701. 2009..Both an executable and the source code of HAAD are freely available at http://zhang.bioinformatics.ku.edu/HAAD... - Improving protein structure prediction using multiple sequence-based contact predictionsSitao Wu
Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, Lawrence, KS 66047, USA
Structure 19:1182-91. 2011..These findings demonstrate a new avenue to improve the accuracy of protein structure prediction especially for free-modeling targets... - MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programmingSrayanta Mukherjee
Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, 2030 Becker Dr, Lawrence, KS 66047, USA
Nucleic Acids Res 37:e83. 2009..MM-align is about two times faster than TM-align because of omitting the cross-alignment zone of the DP matrix. It also shows that the enhanced alignment of the interfaces helps in identifying biologically relevant protein complex pairs... - Recognizing protein-ligand binding sites by global structural alignment and local geometry refinementAmbrish Roy
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109 2218, USA
Structure 20:987-97. 2012..These data demonstrate the power of structure-based approaches to protein-ligand interaction predictions applicable for genome-wide structural and functional annotations... - Intra-chain 3D segment swapping spawns the evolution of new multidomain protein architecturesAndras Szilagyi
Institute of Enzymology, Hungarian Academy of Sciences, Karolina ut 29, H 1113 Budapest, Hungary
J Mol Biol 415:221-35. 2012.... - Parkin, A Top Level Manager in the Cell's Sanitation DepartmentCarolyn A Rankin
Molecular Biosciences Department, University of Kansas, Lawrence KS 66045, USA
Open Biochem J 5:9-26. 2011..This set allows for binding of two rather than just one zinc ion, opening the possibility that the number of zinc ions bound acts as a molecular switch to modulate Parkin function... - Ab initio structural modeling of and experimental validation for Chlamydia trachomatis protein CT296 reveal structural similarity to Fe(II) 2-oxoglutarate-dependent enzymesKyle E Kemege
Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
J Bacteriol 193:6517-28. 2011..Additionally, functional analyses did not support prior reports that CT296 has properties shared with divalent cation repressors such as Fur... - TASSER: an automated method for the prediction of protein tertiary structures in CASP6Yang Zhang
Center of Excellence in Bioinformatics, University at Buffalo, Buffalo, New York 14203, USA
Proteins 61:91-8. 2005..47 [fold recognition (FR), 37 targets/domains], and 0.30 [new fold (NF), 10 targets/domains]. This highlights the need to develop novel (or improved) approaches to identify very distant targets as well as better NF algorithms... - TOUCHSTONEX: protein structure prediction with sparse NMR dataWei Li
Center of Excellence in Bioinformatics, University at Buffalo, Buffalo, New York 14203, USA
Proteins 53:290-306. 2003.... - TASSER-Lite: an automated tool for protein comparative modelingShashi Bhushan Pandit
Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, GA 30318, USA
Biophys J 91:4180-90. 2006..TASSER-Lite is provided on the web at (http://cssb.biology.gatech.edu/skolnick/webservice/tasserlite/index.html)... - Nonlinear ultrasonic nature of organic liquid and organic liquid mixtureYi gang Lu
School of Physics, South China University of Technology, Guangzhou 510640, China
Ultrasonics 44:e1419-22. 2006.... - Structure modeling of all identified G protein-coupled receptors in the human genomeYang Zhang
Center of Excellence in Bioinformatics, University at Buffalo, Buffalo, New York, USA
PLoS Comput Biol 2:e13. 2006..All predicted GPCR models are freely available for noncommercial users on our Web site (http://www.bioinformatics.buffalo.edu/GPCR)... - Scoring function for automated assessment of protein structure template qualityYang Zhang
Center of Excellence in Bioinformatics, University at Buffalo, Buffalo, New York 14203, USA
Proteins 57:702-10. 2004..These data suggest that the TM-score is a useful complement to the fully automated assessment of protein structure predictions. The executable program of TM-score is freely downloadable at http://bioinformatics.buffalo.edu/TM-score... - Application of sparse NMR restraints to large-scale protein structure predictionWei Li
Center of Excellence in Bioinformatics, University at Buffalo, Buffalo, New York 14203, USA
Biophys J 87:1241-8. 2004..5 A with N/4 restraints. Thus, TOUCHSTONEX can be a tool for NMR-based rapid structure determination, as well as used in other experimental methods that can provide tertiary restraint information... - Tertiary structure predictions on a comprehensive benchmark of medium to large size proteinsYang Zhang
Center of Excellence in Bioinformatics, University at Buffalo, Buffalo, New York 14203, USA
Biophys J 87:2647-55. 2004.... - Automated structure prediction of weakly homologous proteins on a genomic scaleYang Zhang
Center of Excellence in Bioinformatics, University at Buffalo, 901 Washington Street, Buffalo, NY 14203, USA
Proc Natl Acad Sci U S A 101:7594-9. 2004.... - SPICKER: a clustering approach to identify near-native protein foldsYang Zhang
Center of Excellence in Bioinformatics, University at Buffalo, 901 Washington St, Buffalo, New York 14203, USA
J Comput Chem 25:865-71. 2004..Although native fold identification from divergent decoy structures remains a challenge, our overall results show significant improvement over our previous clustering algorithms... - Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignmentAdrian K Arakaki
Center of Excellence in Bioinformatics, University at Buffalo, 901 Washington Street, Buffalo, NY 14203-1199, USA
Bioinformatics 20:1087-96. 2004..AVAILABILITY: See http://www.bioinformatics.buffalo.edu/resources/aft/.. - TOUCHSTONE: a unified approach to protein structure predictionJeffrey Skolnick
Center of Excellence in Bioinformatics, University at Buffalo, Buffalo, New York 14203, USA
Proteins 53:469-79. 2003..Improvements in the approach are needed in the FR/NF and NF categories. Nevertheless, TOUCHSTONE was one of the best performing algorithms over all categories in CASP5... - The protein structure prediction problem could be solved using the current PDB libraryYang Zhang
Center of Excellence in Bioinformatics, University at Buffalo, 901 Washington Street, Buffalo, NY 14203, USA
Proc Natl Acad Sci U S A 102:1029-34. 2005..These results are highly suggestive that the protein-folding problem can in principle be solved based on the current PDB library by developing efficient fold recognition algorithms that can recover such initial alignments... - TOUCHSTONE II: a new approach to ab initio protein structure predictionYang Zhang
Center of Excellence in Bioinformatics, University at Buffalo, Buffalo, New York 14203, USA
Biophys J 85:1145-64. 2003..These procedures are readily automated and are being implemented on a genomic scale... - Hierarchical chain model of spider capture silk elasticityHaijun Zhou
Max-Planck-Institute of Colloids and Interfaces, 14424 Potsdam, Germany
Phys Rev Lett 94:028104. 2005..Each module in this hierarchy has its own characteristic force. The repetitive patterns in the amino-acid sequence of the major flagelliform protein of spider capture silk is in support of this model... - TM-align: a protein structure alignment algorithm based on the TM-scoreYang Zhang
Center of Excellence in Bioinformatics, University at Buffalo 901 Washington Street, Buffalo, NY 14203, USA
Nucleic Acids Res 33:2302-9. 2005..This correlation could be used to assist in model selection in blind protein structure predictions. The TM-align program is freely downloadable at http://bioinformatics.buffalo.edu/TM-align... - On the origin and highly likely completeness of single-domain protein structuresYang Zhang
Center of Excellence in Bioinformatics, University at Buffalo, State University of New York, 901 Washington Street, Buffalo, NY 14203, USA
Proc Natl Acad Sci U S A 103:2605-10. 2006..Thus, the presence of active-site-like geometries also seems to be a consequence of the packing of compact, secondary structural elements. These results have significant implications for the evolution of protein structure and function... - Benchmarking of dimeric threading and structure refinementVera Grimm
Center of Excellence in Bioinformatics, University at Buffalo, Buffalo, New York, USA
Proteins 63:457-65. 2006..Preliminary results for three full-length dimeric models generated with the TASSER method show on average a significant improvement of the final model over the initial template... - Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genomeDaisuke Kihara
Laboratory of Computational Genomics, Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA
Proc Natl Acad Sci U S A 99:5993-8. 2002..8% of the 29 proteins) may have correct folds. Thus, the topology of a total of 58 proteins probably has been correctly predicted. Based on these results, ab initio protein structure prediction is becoming a practical approach... - Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein foldingYang Zhang
Laboratory of Computational Genomics, Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
Proteins 48:192-201. 2002..This mrRMSD correlation may be useful in blind prediction as an indicator of the likelihood of successful folds... - Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithmJeffrey Skolnick
Center of Excellence in Bioinformatics, University at Buffalo, 901 Washington St, Suite 300, Buffalo, NY 14203, USA
Proteins 56:502-18. 2004..genitalium, E. coli and S. cerevisiae genomes. Thus, progress has been made in identification of weakly homologous/analogous proteins, with very high alignment coverage, both in a comprehensive PDB benchmark as well as in genomes... - Mechanism of human S-adenosylmethionine decarboxylase proenzyme processing as revealed by the structure of the S68A mutantWilliam D Tolbert
Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853 1301, USA
Biochemistry 42:2386-95. 2003..Comparison to histidine decarboxylase and aspartate decarboxylase shows that these pyruvoyl-dependent enzymes evolved different catalytic strategies for forming the same cofactor... - Hydroxyl-substituted sulfonylureas as potent inhibitors of specific [3H]glyburide binding to rat brain synaptosomesRonald A Hill
Division of Basic Pharmaceutical Sciences, College of Pharmacy, The University of Louisiana at Monroe, Monroe, LA 71209, USA
Bioorg Med Chem 11:2099-113. 2003..Somewhat unexpectedly, several of the compounds were found to be comparably potent to glyburide as inhibitors of specific [(3)H]glyburide binding in rat brain preparations... - Chibby, a nuclear beta-catenin-associated antagonist of the Wnt/Wingless pathwayKen Ichi Takemaru
Howard Hughes Medical Institute, Room K536C Health Sciences Building, Campus Box 357750, Department of Pharmacology, and Center for Developmental Biology, University of Washington School of Medicine, Seattle, Washington 98195, USA
Nature 422:905-9. 2003..In addition, epistasis experiments indicate that chibby acts downstream of wingless and upstream of armadillo... - BlmIII and BlmIV nonribosomal peptide synthetase-catalyzed biosynthesis of the bleomycin bithiazole moiety involving both in cis and in trans aminoacylationLiangcheng Du
Division of Pharmaceutical Sciences and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53705, USA
Biochemistry 42:9731-40. 2003.... - Preliminary investigation of the three-dimensional structure of Salmonella typhimurium uridine phosphorylase in the crystalline stateMaria V Dontsova
Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
Acta Crystallogr Sect F Struct Biol Cryst Commun 61:337-40. 2005..The hexameric StUPh model reveals a close structural relationship to Escherichia coli uridine phosphorylase (EcUPh)... - The Bayesian operating point of the Canny edge detectorYang Zhang
Department of Electronic and Electrical Engineering, University of Sheffield, Sheffield S1 3JD, UK
IEEE Trans Image Process 15:3409-16. 2006..We demonstrate that the edge detection performance of the Canny detector is due almost entirely to the postprocessing stages of nonmaximal suppression and hysteresis thresholding... - TASSER-based refinement of NMR structuresSeung Yup Lee
Center of Excellence in Bioinformatics, University at Buffalo, Buffalo, New York, USA
Proteins 63:451-6. 2006..These results suggest that TASSER can be a useful tool to improve the quality of NMR structures... - [Development of an analysis system for X-ray cephalometry by Windows platform]Hai-bin Wang
The Fourth Military Medical University
Zhongguo Yi Liao Qi Xie Za Zhi 26:259-60, 264. 2002..It has been applied in orthodontic department of Stomatological Hospital of the Fourth Military Medical University, and it is quite convenient for doctors' cephalometry diagnosis... - Structural studies on 3-hydroxyanthranilate-3,4-dioxygenase: the catalytic mechanism of a complex oxidation involved in NAD biosynthesisYang Zhang
Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
Biochemistry 44:7632-43. 2005..On the basis of the crystal structures of HAD, mutagenesis studies were carried out in order to elucidate the enzyme mechanism. In addition, a new mechanism for the enzyme inactivation by 4-chloro-3-hydroxyanthranilate is proposed... - A protein chip approach for high-throughput antigen identification and characterizationShaohui Hu
Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
Proteomics 7:2151-61. 2007..Among them, we discovered that eIF1A expressed only in normal liver tissues, not in hepatocellular carcinoma in humans... - Crystal structure and function of 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase from Methanocaldococcus jannaschiiYang Zhang
Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853 1301, USA
Biochemistry 47:205-17. 2008..With approximately 50% sequence identity, P. furiosus PurP is structurally homologous to M. jannaschii PurP. A phylogenetic analysis was performed to explore the possible role of this functionally unclassified PurP... - Function of HAb18G/CD147 in invasion of host cells by severe acute respiratory syndrome coronavirusZhinan Chen
Department of Cell Biology, The Fourth Military Medical University, Xi an, China
J Infect Dis 191:755-60. 2005..Our findings provide some evidence for the cytologic mechanism of invasion by SARS-CoV and provide a molecular basis for screening anti-SARS drugs... - Application and evaluation of two air quality models for particulate matter for a southeastern U.S. episodeYang Zhang
Department of Marine, Earth and Atmospheric Sciences, North Carolina State University, Raleigh, NC, USA
J Air Waste Manag Assoc 54:1478-93. 2004..In addition to these uncertainties, the significant PM overpredictions by PMCAMx may be attributed to the lack of wet removal for PM and a likely underprediction in the vertical mixing during the daytime... - [A proteomic study of the serum proteins in BPH and HGPIN patients]Xiao jian Gu
Department of Urology, Affiliated Hospital of Nanjing University of Traditional Chinese Medicine, Nanjing, Jiangsu 210029, China
Zhonghua Nan Ke Xue 14:62-6. 2008..To evaluate two-dimensional gel electrophoresis (2DGE) and mass spectrometry in the studies of the serum proteins expressed in patients with BPH and those with high-grade prostatic intraepithelial neoplasm (HGPIN)... 
Large scale depletion of the high-abundance proteins and analysis of middle- and low-abundance proteins in human liver proteome by multidimensional liquid chromatographyMingxia Gao
Department of Chemistry and Research Center of Proteome, Fudan University, Shanghai, China
Proteomics 8:939-47. 2008..The strategy increases greatly the number of identified proteins and around 1213 proteins were identified, which was about 2.7 times as that of the nondepletion method...- Studies of phononlike low-energy excitations of protein molecules by inelastic x-ray scatteringDazhi Liu
Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Phys Rev Lett 101:135501. 2008..This suggests that the large amplitude motions of wavelengths corresponding to this specific Q range are intimately correlated with the increase of biological activities of the proteins...