Structural Bioinformatics Team Publications
Alfi, A., Popov, A., Kumar, A., Zhang, K. Y. J., Dubiley, S., Severinov, K., Tagami, S. (2022) Cell-Free Mutant Analysis Combined with Structure Prediction of a Lasso Peptide Biosynthetic Protease B2. ACS Synth. Biol., 11, 2022-2028. https://doi.org/10.1021/acssynbio.2c00176.
Dileep, K. V., Ihara, K., Mishima-Tsumagari, C., Kukimoto-Niino, M., Yonemochi, M., Hanada, K., Shirouzu, M., Zhang, K. Y. J. (2022) Crystal structure of human acetylcholinesterase in complex with tacrine: implications for drug discovery. Int. J. Biol. Macromol., 210, 172-181. https://doi.org/10.1016/j.ijbiomac.2022.05.009.
Kaushik, R., Kumar, N., Zhang, K. Y. J., Srivastava, P., Bhatia, S., Malik, Y. S. (2022) A novel structure-based approach for identification of vertebrate susceptibility to SARS-CoV-2: implications for future surveillance programmes. Environ. Res., 212, 113303. https://doi.org/10.1016/j.envres.2022.113303.
Rajpoot, S., Kumar, A., Zhang, K. Y. J., Hua, G. S., Baig, M. S. (2022) TIRAP-mediated activation of p38 MAPK in inflammatory signalling. Sci. Rep., 12, 5601. https://doi.org/10.1038/s41598-022-09528-8.
Gupta, P., Kadamberi, I. P., Mittal, S., Tsaih, S.-W., George, J., Kumar, S., Vijayan, D. K., Geethadevi, A., Parashar, D., Topchyan, P., McAlarnen, L., Volkman, B. F., Cui, W., Zhang, K. Y. J., Di Vizio, D., Chaluvally-Raghavan, P., Pradeep, S. (2022) Tumor Derived Extracellular Vesicles Drive T Cell Exhaustion in Tumor Microenvironment through Sphingosine Mediated Signaling and Impacting Immunotherapy Outcomes in Ovarian Cancer. Adv. Sci., 9, 2104452. https://doi.org/10.1002/advs.202104452.
Rajpoot, S., Solanki, K., Kumar, A., Zhang, K. Y. J., Pullamsetti, S. S., Savai, R., Faisal, S. M., Pan, Q., Baig, M. S. (2022) In-silico design of a novel tridecapeptide targeting spike protein of SARS-CoV-2 variants of concern. Int. J. Pept. Res. Ther., 28, 28. https://doi.org/10.1007/s10989-021-10339-0.
Tam, C., Zhang, K. Y. J. (2022) FPredX: interpretable models for the prediction of spectral maxima, brightness and oligomeric states of fluorescent proteins. Proteins: Struct., Funct., Bioinf., 90, 732-746. https://doi.org/10.1002/prot.26270.
Padhi, A. K., Janezic, M., Zhang, K. Y. J. (2022) Molecular Dynamics Simulations: Principles, Methods, and Applications in Protein Conformational Dynamics. In: Tripathi, T. and Dubey, V.K. (Eds.) Advances in Protein Molecular and Structural Biology Methods, Elsevier, USA. pp. 439-454. https://doi.org/10.1016/B978-0-323-90264-9.00026-X.
Kaushik, R., Zhang, K. Y. J. (2022) ProFitFun: A Protein Tertiary Structure Fitness Function for Quantifying the Accuracies of Model Structures. Bioinformatics, 38, 369–376. https://doi.org/10.1093/bioinformatics/btab666.
Yagi, S., Padhi, A. K., Vucinic, J., Barbe, S., Schiex, T., Nakagawa, R., Simoncini, D., Zhang, K. Y. J., Tagami, S. (2021) Seven amino acid types suffice to create the core fold of RNA polymerase. J. Am. Chem. Soc., 143, 15998–16006. https://doi.org/10.1021/jacs.1c05367.
News & Views:
• 生命誕生初期のタンパク質を再現する試み -7種類のアミノ酸で古代タンパク質は創れる- RIKEN Press ReleaseTam, C., Kumar, A., Zhang, K. Y. J. (2021) NbX: Machine Learning Guided Re-ranking of Nanobody-Antigen Binding Poses. Pharmaceuticals, 14, 968. https://doi.org/10.3390/ph14100968.
Kumar, N., Kaushik, R., Tennakoon, C., Uversky, V. N., Mishra, A., Sood, R., Srivastava, P., Tripathi, M., Zhang, K. Y. J., Bhatia, S. (2021) Evolutionary signatures governing the codon usage bias in coronaviruses and their implications for viruses infecting various bat species. Viruses, 13, 1847. https://doi.org/10.3390/v13091847.
Remya, C., Dileep, K. V., Reddy, E. K., Mantosh, K., Lakshmi, K., Jacob, R. S., Sajith, A. M., Variyar, E. J., Anwar, S., Zhang, K. Y. J., Sadasivan, C., Omkumar, R. V. (2021) Neuroprotective derivatives of tacrine that target NMDA receptor and acetyl cholinesterase - Design, synthesis and biological evaluation. Comput. Struct. Biotechnol. J., 19, 4517-4537. https://doi.org/10.1016/j.csbj.2021.07.041.
Padhi, A. K., Kumar, A., Haruna, K., Sato, H., Tamura, H., Nagatoishi, S., Tsumoto, K., Yamaguchi, A., Iraha, F., Takahashi, M., Sakamoto, K., Zhang, K. Y. J. (2021) An integrated computational pipeline for designing high-affinity nanobodies with expanded genetic codes. Brief. Bioinformatics, 22, 1-17. https://doi.org/10.1093/bib/bbab338.
Chitranshi, N., Kumar, A., Sheriff, S., Gupta, V., Godinez, A., Saks, D., Sarkar, S., Shen, T., Mirzaei, M., Basavarajappa, D., Abyadeh, M., Singh, S. K., Dua, K., Zhang, K. Y. J., Graham, S. L., Gupta, V. (2021) Identification of novel cathepsin B inhibitors with implications in Alzheimer’s disease: Computational refining and biochemical evaluation. Cells, 10, 1946. https://doi.org/10.3390/cells10081946.
Rajpoot, S., Ohishi, T., Kumar, A., Pan, Q., Banerjee, S., Zhang, K. Y. J., Baig, M. S. (2021) A novel therapeutic peptide blocks SARS-CoV-2 spike protein binding with host cell ACE2 receptor. Drugs in R&D, 21, 273-283. https://doi.org/10.1007/s40268-021-00357-0.
Kukimoto-Niino, M., Katsura, K., Kaushik, R., Ehara, H., Yokoyama, T., Uchikubo-Kamo, T., Nakagawa, R., Mishima-Tsumagari, C., Yonemochi, M., Ikeda, M., Hanada, K., Zhang, K. Y. J., Shirouzu, M. (2021) Cryo-EM structure of the human ELMO1-DOCK5-Rac1 complex ELMO1-DOCK5-Rac1 structure. Sci. Adv., 7, eabg3147. https://doi.org/10.1126/sciadv.abg3147.
News & Views:
• 細胞の動きを制御するタンパク質の巧妙な仕組み RIKEN Press ReleaseBalan, S., Iwayama, Y., Ohnishi, T., Fukuda, M., Shirai, A., Yamada, A., Weirich, S., Schuhmacher, M. K., Vijayan, D. K., Endo, T., Hisano, Y., Kotoshiba, K., Toyota, T., Otowa, T., Kuwabara, H., Tochigi, M., Watanabe, A., Ohba, H., Maekawa, M., Toyoshima, M., Sasaki, T., Nakamura, K., Tsujii, M., Matsuzaki, H., Zhang, K. Y. J., Jeltsch, A., Shinkai, Y., Yoshikawa, T. (2021) A loss of function variant in SUV39H2 identified in autism spectrum disorder causes altered H3K9-trimethylation and dysregulation of protocadherin β cluster genes in the developing brain. Molecular Psychiatry, 26, 7550–7559. https://doi.org/10.1038/s41380-021-01199-7.
News & Views:
• ヒストンメチル化による自閉症の新しいメカニズムを発見 RIKEN Press ReleaseYamashita, M., Kuehn, H. S., Okuyama, K., Okada, S., Inoue, Y., Mitsuiki, N., Imai, K., Takagi, M., Kanegane, H., Takeuchi, M., Shimojo, N., Tsumura, M., Padhi, A. K., Zhang, K. Y. J., Boisson, B., Casanova, J.-L., Ohara, O., Rosenzweig, S. D., Taniuchi, I., Morio, T. (2021) A Variant in Human AIOLOS Impairs Adaptive Immunity by Interfering with IKAROS. Nat. Immunol., 22, 893–903. https://doi.org/10.1038/s41590-021-00951-z.
News & Views:
• 新たな疾患発症メカニズムによる免疫不全症(AIOLOS異常症)の発見 RIKEN Press ReleaseChen, W., Chen, Q., Kumar, A., Jiang, X., Zhang, K. Y. J., Yang, Q. (2021) Structure-based virtual screening of highly potent inhibitors of the nematode chitinase CeCht1. J. Enzyme Inhib. Med. Chem., 36, 1198-1204. https://doi.org/10.1080/14756366.2021.1931862.
Muhammad, E. F., Kumar, A., Wahab, H. A., Zhang, K. Y. J. (2021) Identification of 1,2,4-triazolylthioethanone scaffold for the design of new acetylcholinesterase inhibitors. Molecular Informatics, 40, 2100020. https://doi.org/10.1002/minf.202100020.
Bhattacharya, S., Nautiyal, A. K., Bhattacharya, R., Padhi, A. K., Junghare, V., Bhambri, M., Dasgupta, D., Zhang, K. Y. J., Ghosh, D., Hazra, S. (2021) A comprehensive characterization of novel CYP-BM3 homolog (CYP-BA) from Bacillus aryabhattai. Enzyme Microb. Technol., 148, 109806. https://doi.org/10.1016/j.enzmictec.2021.109806.
Viswanadhapalli, S., Dileep, K.V., Zhang, K. Y. J., Nair, H., Vadlamudi, R. K. (2021) Targeting LIF/LIFR signaling in cancer. Genes & Diseases, https://doi.org/10.1016/j.gendis.2021.04.003.
Berenger, F., Kumar, A., Zhang, K. Y. J., Yamanishi, Y. (2021) Lean-Docking: Exploiting Ligands’ Predicted Docking Scores to Accelerate Molecular Docking. J. Chem. Inf. Model., 61, 2341−2352. https://doi.org/10.1021/acs.jcim.0c01452.
Kumar, N., Kaushik, R., Tennakoon, C., Uversky, V. N., Longhi, S., Zhang, K. Y. J., Bhatia, S. (2021) Insights into the evolutionary forces that shape the codon usage in the viral genome segments encoding intrinsically disordered protein regions. Brief. Bioinformatics, 22, 1-12. https://doi.org/10.1093/bib/bbab145.
Vrancken, J. P. M., Noguchi, H., Zhang, K. Y. J., Tame, J. R. H., Voet, A. R. D. (2021) The symmetric designer protein Pizza as a scaffold for metal coordination. Proteins: Struct., Funct., Bioinf., 89, 945-951. https://doi.org/10.1002/prot.26072.
Chen, Q., Chen, W., Kumar, A., Jiang, X., Janezic, M., Zhang, K. Y. J., Yang, Q. (2021) Crystal structure and structure-based discovery of inhibitors of the nematode chitinase CeCht1. J. Agric. Food Chem., 69, 3519−3526. https://dx.doi.org/10.1021/acs.jafc.1c00162.
Kumar, N., Kaushik, R., Tennakoon, C., Uversky, V. N., Longhi, S., Zhang, K. Y. J., Bhatia, S. (2021) Comprehensive intrinsic disorder analysis of 6,108 viral proteomes: From the extent of intrinsic disorder penetrance to functional annotation of disordered viral proteins. J. Proteome Res., 20, 2704-2713. https://dx.doi.org/10.1021/acs.jproteome.1c00011.
Janezic, M., Dileep, K. V., Zhang, K. Y. J. (2021) A multi-dimensional computational exploration of congenital myasthenic syndrome causing mutations in human choline acetyltransferase. J. Cell. Biochem., 122, 787-800. https://doi.org/10.1002/jcb.29913.
Bhattacharya, S., Padhi, A. K., Junghare, V., Das, N., Ghosh, D., Roy, P., Zhang, K. Y. J., Hazra, S. (2021) Understanding the molecular interactions of inhibitors against Bla1 beta-lactamase towards unraveling the mechanism of antimicrobial resistance. Int. J. Biol. Macromol., 177, 337-350. https://doi.org/10.1016/j.ijbiomac.2021.02.069.
Remya, C., Dileep, K. V., Variyar, E. J., Zhang, K. Y. J., Omkumar, R. V., Sadasivan, C. (2021) Chemical similarity assisted search for acetylcholinesterase inhibitors: Molecular modeling and evaluation of their neuroprotective properties. Int. J. Biol. Macromol., 174, 466-476. https://doi.org/10.1016/j.ijbiomac.2021.01.148.
Dileep, K. V., Sakai, N., Ihara, K., Kato-Murayama, M., Nakata, A., Ito, A., Sivaraman, D. M., Shin, J. W., Yoshida, M., Shirouzu, M., Zhang, K. Y. J. (2021) Piperidine-4-carboxamide as a new scaffold for designing secretory glutaminyl cyclase inhibitors. Int. J. Biol. Macromol., 170, 415-423. https://doi.org/10.1016/j.ijbiomac.2020.12.118.
Malik, Y. S., Ansari, M. I., Kattoor, J. J., Kaushik, R., Sircar, S., Subbaiyan, A., Tiwari, R., Dhama, K., Ghosh, S., Tomar, S., and Zhang, K. Y. J. (2021) Evolutionary and codon usage preference insights on spike glycoprotein of SARS-CoV-2. Brief. Bioinformatics, 22, 1006-1022. https://doi.org/10.1093/bib/bbaa383.
Shiroma, Y., Fujita, G., Yamamoto, T., Takahashi, R., Kumar, A., Zhang, K. Y. J., Ito, A., Osada, H., Yoshida, M., and Tahara, H. (2020) Identification of a Selective RelA Inhibitor Based on DSE-FRET Screening Methods. Int. J. Mol. Sci., 21, 9150. https://doi.org/10.3390/ijms21239150.
Padhi, A. K., Zhang, K. Y. J. (2020) Mechanistic insights into the loss-of-function mechanisms of rare human D-amino acid oxidase variants implicated in amyotrophic lateral sclerosis. Sci. Rep., 10:17146. https://doi.org/10.1038/s41598-020-74048-2.
Mhaske, A., Dileep, K.V., Kumar, M., Poojary, M., Pandhare, K., Zhang, K. Y. J., Scaria, V., Binukumar, B. K. (2020) ATP7A Clinical Genetics Resource - a comprehensive clinically annotated database and resource for genetic variants in ATP7A gene. Comput. Struct. Biotechnol. J., 18, 2347-2356. https://doi.org/10.1016/j.csbj.2020.08.021.
Kumar, A., Zhong, Y., Albrecht, A., Sang, P. B., Maples, A., Liu, Z., Vinayachandran, V., Reja, R., Lee, C-F., Kumar, A., Chen, J., Xiao, J., Park, B., Shen, J., Liu, B., Person, M. D., Trybus, K. M., Zhang, K. Y. J., Pugh, B. F., Kamm, K. E., Milewicz, D. M., Shen, X., Kapoor, P. (2020) Actin R256 mono-methylation is a conserved post-translational modification involved in transcription. Cell Rep., 32, 108172. https://doi.org/10.1016/j.celrep.2020.108172.
Kaushik, R., Zhang, K. Y. J. (2020) A Protein Sequence Fitness Function for Identifying Natural and Non-Natural Proteins. Proteins: Struct., Funct., Bioinf., 88, 1271–1284. https://doi.org/10.1002/prot.25900.
Kalita, P., Padhi, A. K., Zhang, K. Y. J., Tripathi, T. (2020) Design of a Peptide-Based Subunit Vaccine against Novel Coronavirus SARS-CoV-2. Microb. Pathog., 145, 104236. https://doi.org/10.1016/j.micpath.2020.104236.
Yue, X., Wu, F., Wang, J., Kim, K., Santhamma, B., Dileep, K. V., Zhang, K. Y. J., Viswanadhapalli, S., Vadlamudi, R. K., Ahmed, G., Feng, Z., Nickisch, K., Hu, W. (2020) EC330, a small molecule compound, is a potential novel inhibitor of LIF signaling. J. Mol. Cell Biol., 12, 477-480. https://doi.org/10.1093/jmcb/mjaa008.
Jiang, X., Kumar, A., Motomura, Y., Liu, T., Zhou, Y., Moro, K., Zhang, K. Y. J., Yang, Q. (2020) A series of compounds bearing a dipyrido-pyrimidine scaffold acting as novel human and insect pest chitinases inhibitors. J. Med. Chem., 63, 987-1001. doi:10.1021/acs.jmedchem.9b01154.
Nair, H. B., Santhamma, B., Dileep, K.V., Binkley, P., Acosta, K., Zhang, K. Y. J., Schenken, R., Nickisch, K. (2019) EC313-a tissue selective SPRM reduces the growth and proliferation of uterine fibroids in a human uterine fibroid tissue xenograft model. Sci. Rep., 9, 17279. doi:10.1038/s41598-019-53467-w.
Kumar, A., Zhang, K. Y. J. (2019) Improving ligand 3D shape similarity-based pose prediction with a continuum solvent model. J. Comput-Aided Mol. Des., 33, 1045-1055. doi:10.1007/s10822-019-00220-0.
Vijayan, D. K. and Zhang, K. Y. J. (2019) Human glutaminyl cyclase: Structure, function, inhibitors and involvement in Alzheimer’s disease. Pharmacol. Res., 147, 104342. doi:10.1016/j.phrs.2019.104342.
Viswanadhapalli, S., Luo, Y., Sareddy, G. R., Santhamma, B., Zhou, M., Li, M., Ma, S., Sonavane, R., Pratap, U. P., Altwegg, K. A., Li, X., Chang, A., Chávez-Riveros, A., Dileep, K. V., Zhang, K. Y. J., Pan, X., Murali, R., Bajda, M., Raj, G. V., Brenner, A., Manthati, V., Rao, M., Tekmal, R. R., Nair, H. B., Nickisch, K. J., and Vadlamudi, R. K. (2019) EC359-A first-in-class small molecule inhibitor for targeting oncogenic LIFR signaling in triple negative breast cancer. Mol. Cancer Ther., 18, 1341-1354. DOI:10.1158/1535-7163.MCT-18-1258.
Kumar, A., Zhang, K. Y. J. (2019) Human Chitinases: Structure, Function, and Inhibitor Discovery. In: Yang, Q. and Fukamizo, T. (eds.), Targeting Chitin-containing Organisms, pp. 221–251. Singapore: Springer Nature. doi:10.1007/978-981-13-7318-3_11
Simoncini, D., Zhang, K. Y. J., Schiex, T., Barbe, S. (2019) A Structural Homology Approach for Computational Protein Design with Flexible Backbone. Bioinformatics, 35, 2418-2426. doi:10.1093/bioinformatics/bty975.
Berenger, F., Zhang, K. Y. J. and Yamanishi, Y. (2019) Chemoinformatics and structural bioinformatics in OCaml. J. Cheminform. 11:10. doi:10.1186/s13321-019-0332-0
Noguchi, H., Addy, C., Simoncini, D., Wouters, S., Mylemans, B., Van Meervelt, L., Schiex, T., Zhang, K. Y. J., Tame, J. R. H., Voet, A. R. D. (2019) Computational design of symmetrical 8-bladed ß-propeller proteins. IUCrJ, 6, 46-55. doi:10.1107/S205225251801480X
Kumar, A., Zhang, K. Y. J. (2019) Shape similarity guided pose prediction: Lessons from D3R Grand Challenge 3. J. Comput-Aided Mol. Des., 33, 47-59. doi:10.1007/s10822-018-0142-x
Kumar, A., Zhang, K. Y. J. (2018) Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery. Frontiers in Chemistry, 6:315. doi:10.3389/fchem.2018.00315.
Simoncini, D., Zhang, K. Y. J. (2018) Population-based sampling and fragment-based de novo protein structure prediction. In: Guenther, R. and Steel, D. (eds.), Encyclopedia of Bioinformatics and Computational Biology, vol. 1, pp. 774–784. Oxford: Elsevier. https://doi.org/10.1016/B978-0-12-811414-8.20507-5
Kumar, A., Zhang, K. Y. J. (2018) A cross docking pipeline for improving pose prediction and virtual screening performance. J. Comput-Aided Mol. Des., 32, 163-173. DOI:10.1007/s10822-017-0048-z.
Berenger, F., Simoncini, D., Voet, A., Shrestha, R., Zhang, K. Y. J. (2017) Fragger: a protein fragment picker for structural queries. F1000Research, 6, 1722. doi:10.12688/f1000research.12486.1.
Terada, D., Voet, A. R. D., Noguchi, H., Kamata, K., Ohki, M., Addy, C., Fujii, Y., Yamamoto, D., Ozeki, Y., Tame, J. R. H., Zhang, K. Y. J. (2017) Computational design of a symmetrical ß-trefoil lectin with cancer cell binding activity. Sci. Rep., 7, 5943. doi:10.1038/s41598-017-06332-7.
News & Views:
• 腫瘍細胞の糖鎖と結合する人工レクチンを計算機科学で設計. Yokohama City University Press Release, July 27, 2017.
Matsuoka, M., Kumar, A., Muddassar, M., Matsuyama, A., Yoshida, M., Zhang, K. Y. J. (2017) Discovery of Fungal Denitrification Inhibitors by Targeting Copper Nitrite Reductase from Fusarium Oxysporum. J. Chem. Inf. Model., 57, 203-213. doi:10.1021/acs.jcim.6b00649.
Simoncini, D., Schiex, T., Zhang, K. Y. J. (2017) Balancing exploration and exploitation in population-based sampling improves fragment-based de novo protein structure prediction. Proteins: Struct., Funct., Bioinf., 85, 852-858. doi:10.1002/prot.25244.
Voet, A. R. D., Simoncini, D., Tame, J. R. H., Zhang, K. Y. J. (2017) Evolution-inspired computational design of symmetric proteins. Methods in Molecular Biology, 1529, 309-322. doi:10.1007/978-1-4939-6637-0_16.
Kumar, A., Kawamura, T., Kawatani, M., Osada, H., Zhang, K. Y. J. (2017) Identification and structure activity relationship of purine derivatives as novel MTH1 inhibitors. Chem. Biol. Drug Des., 89, 862-869. doi:10.1111/cbdd.12909.
Jiang, X., Kumar, A., Liu, T., Zhang, K. Y. J., Yang, Q. (2016) A Novel Scaffold for Developing Specific or Broad-spectrum Chitinase Inhibitors. J. Chem. Inf. Model., 56, 2413-2420. doi:10.1021/acs.jcim.6b00615.
Nagano, S., Banwell, E. F., Iwasaki, K., Michalak, M., Palka, R., Zhang, K. Y. J., Voet, A. R. D., Heddle, J. G. (2016) Understanding the Assembly of an Artificial Protein Nanotube. Advanced Materials Interfaces, 3, 1600846. doi:10.1002/admi.201600846.
Kumar, A., Zhang, K. Y. J. (2016) Prospective Evaluation of Shape Similarity Based Pose Prediction Method in D3R Grand Challenge 2015. J. Comput-Aided Mol. Des., 30, 685-693. doi:10.1007/s10822-016-9931-2.
Kumar, A., Zhang, K. Y. J. (2016) A pose prediction approach based on ligand 3D shape similarity. J. Comput-Aided Mol. Des., 30, 457-469. doi:10.1007/s10822-016-9923-2.
Prekovic, S., van Royen, M.E., Voet, A.R.D., Geverts, B., Houtman, R., Melchers, D., Zhang, K. Y. J., Van den Broeck, T., Smeets, E., Spans, L., Houtsmuller, A.B., Joniau, S., Claessens, F., Helsen, C. (2016) The effect of F877L and T878A mutations on androgen receptor response to Enzalutamide. Mol. Cancer Ther., 15, 1702-1712. doi:10.1158/1535-7163.MCT-15-0892.
Kumar, A., Ito, A., Hirohama, M., Yoshida, M., Zhang, K. Y. J. (2016) Identification of new SUMO activating enzyme 1 inhibitors using virtual screening and scaffold hopping. Bioorg. Med. Chem. Lett., 26, 1218-1223, DOI:10.1016/j.bmcl.2016.01.030.
Kumar, A., Zhang, K. Y. J. (2016) Application of Shape Similarity in Pose Selection and Virtual Screening in CSARdock2014 Exercise. J. Chem. Inf. Model., 56, 965-973, DOI:10.1021/acs.jcim.5b00279.
Saeed, A., Zaib, S., Ashraf, S., Iftikhar, J., Muddassar, M., Zhang, K. Y. J., Iqbal, J. (2015) Synthesis, cholinesterase inhibition and molecular modelling studies of coumarin linked thiourea derivatives. Bioorg. Chem., 63, 58-63. DOI:10.1016/j.bioorg.2015.09.009.
Voet, A. R. D., Noguchi, H., Addy, C., Zhang, K. Y. J., Tame, J. R. H. (2015) Biomineralization of a Cadmium Chloride Nanocrystal by a Designed Symmetrical Protein. Angew. Chem. Int. Ed., 54, 9857-9860. DOI:10.1002/anie.201503575.
News & Views:
• Engineering the world’s smallest nanocrystal. RIKEN Press Release, July 2, 2015.
• 人工的に設計したタンパク質による金属ナノ結晶の生成. RIKEN Press Release in Japanese, Aug. 26, 2015.
• バイオミネラリゼーションを利用したタンパク質の新素材. NanoTech Japan, Sept. 4, 2015.
• 「ピザ型」人工タンパク質で世界最小の結晶. The Sankei Shimbun, Sept. 10, 2015.
• Biomineralization: Nanocrystals by design. Li Shang & Gerd Ulrich Nienhaus, Nature Chem., Sept. 22, 2015, doi:10.1038/nchem.2357.
Nishimura, K., Addy, C., Shrestha, R., Voet, A. R. D., Zhang, K. Y. J., Ito, Y., Tame, J. R. H. (2015) The crystal and solution structure of YdiE from Escherichia coli. Acta Cryst., F71, 919-924. doi:10.1107/S2053230X15009140.
Mishra, V., Kumar, A., Ali, V., Zhang, K. Y. J., Nozaki, T. (2015) Characterization of pH-induced transitions of Entamoeba histolytica D-phosphoglycerate dehydrogenase. Int. J. Biol. Macromolec., 79, 284-289. doi:10.1016/j.ijbiomac.2015.04.058.
Kumar, A., Zhang, K. Y. J. (2015) Advances in the development of SUMO specific protease (SENP) inhibitors. Comput. Struct. Biotechnol. J., 13, 204-211. doi:10.1016/j.csbj.2015.03.001.
Simoncini, D., Nakata, H., Ogata, K., Nakamura, S., Zhang, K. Y. J. (2015) Quality assessment of predicted protein models using energies calculated by the fragment molecular orbital method. Molecular Informatics, 34, 97-104. DOI: 10.1002/minf.201400108.
Shrestha, R., Zhang, K. Y. J. (2015) A fragmentation and reassembly method for ab initio phasing. Acta Cryst., D71, 304-312. doi:10.1107/S1399004714025449.
Kumar, A., Zhang, K. Y. J. (2015) Hierarchical Virtual Screening Approaches in Small Molecule Drug Discovery. Methods, 71, 26-37. doi:10.1016/j.ymeth.2014.07.007.
Voet, A. R. D., Noguchi, H., Addy, C., Simoncini, D., Terada, D., Unzai, S., Park, S-Y., Zhang, K. Y. J., Tame, J. R. H. (2014) Computational design of a self-assembling symmetrical β-propeller protein. Proc. Natl. Acad. Sci. U.S.A., 111, 15102-15107, doi: 10.1073/pnas.1412768111.
News & Views:
• Perfect propeller proteins designed by computer. RIKEN Research Highlight, Dec. 12, 2014.
Qing, X., Lee, X. Y., De Raeymaeker, J., Tame, J. R. H., Zhang, K. Y. J., De Maeyer, M., Voet, A. (2014) Pharmacophore modeling: advances, limitations and current utility in drug discovery. J Receptor Ligand Channel Res., 7, 81-92, doi:10.2147/JRLCR.S46843.
Kumar, A., Ito, A., Hirohama, M., Yoshida, M., Zhang, K. Y. J. (2014) Identification of Sumoylation Inhibitors Targeting a Predicted Pocket in Ubc9. J. Chem. Inf. Model., 54, 2784-2793, doi:10.1021/ci5004015.
• Selected as the cover for the October issue of JCIM.
Berenger, F., Voet, A., Lee, X.Y., Zhang, K. Y. J. (2014) A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening. J. Cheminformatics, 6:23, doi:10.1186/1758-2946-6-23.
Shrestha, R., Zhang, K. Y. J. (2014) Improving fragment quality for de novo structure prediction. Proteins: Struct., Funct., Bioinf., 82, 2240-2252, doi:10.1002/prot.24587.
Kumar, A., Ito, A., Hirohama, M., Yoshida, M., *Zhang, K. Y. J. (2014) Identification of sumoylation activating enzyme 1 inhibitors utilizing virtual screening approach. J. Cheminformatics, 6, 37. doi:10.1186/1758-2946-6-S1-P37.
Voet, A.R.D., Ito, A., Hirohama, M., Matsuoka, S., Tochio, N., Kigawa, T., Yoshida, M., Zhang, K. Y. J. (2014) Discovery of small molecule inhibitors targeting the SUMO-SIM interaction using a protein interface consensus approach. Med. Chem. Commun., 5, 783-786, doi:10.1039/c3md00391d.
Kumar, A., Ito, A., Takemoto, M., Yoshida, M., Zhang, K. Y. J. (2014) Identification of 1, 2, 5-Oxadiazoles as a New Class of SENP2 Inhibitors Using Structure Based Virtual Screening. J. Chem. Inf. Model., 54, 870–880, doi:10.1021/ci4007134.
Voet, A., Kumar, A., Berenger, F., Zhang, K. Y. J. (2014) Combining in silico and in cerebro approaches for virtual screening and pose prediction in SAMPL4. J. Comput-Aided Mol. Des., 28, 363-373, doi:10.1007/s10822-013-9702-2.
Hirohama, M., Voet, A.R.D., Ozawa, T., Saitoh, H., Nakao, Y., Zhang, K. Y. J., Ito, A., Yoshida, M. (2014) Assay methods for SUMO–SIM interactions in vivo and in vitro using a split-luciferase complementation system. Anal. Biochem., 448, 92-94. doi:10.1016/j.ab.2013.12.009.
Hirohama, M., Kumar, A., Fukuda, I., Matsuoka, S., Igarashi, Y., Saitoh, H., Takagi, M., Shin-ya, K., Honda, K., Kondoh, Y., Saito, T., Nakao, Y., Osada, H., Zhang, K. Y. J., Yoshida, M., Ito, A. (2013) Spectomycin B1 as a novel SUMOylation inhibitor that directly binds to SUMO E2. ACS Chemical Biology, 8, 2635-2642. doi:10.1021/cb400630z.
Voet, A., Berenger, F., Zhang, K. Y. J. (2013) The use of electrostatic similarities for the discovery of small molecule protein-protein interaction inhibitors. PLoS ONE, 8(10): e75762, 1-9. doi:10.1371/journal.pone.0075762.
Cavalluzzo, C., Christ, F., Voet, A., Sharma, A., Singh, B. K., Zhang, K. Y. J., Lescrinier, E., De Maeyer, M., Debyser, Z., Van der Eycken, E. (2013) Identification of small peptides inhibiting the integrase-LEDGF/p75 interaction through targeting the cellular co-factor. Journal of Peptide Science, 19, 651-658. doi:10.1002/psc.2543.
Kumar, A., Ito, A., Hirohama, M., Yoshida, M., Zhang, K. Y. J. (2013) Identification of quinazolinyloxy biaryl urea as a new class of SUMO activating enzyme 1 inhibitors. Bioorg. Med. Chem. Lett., 23, 5145-5149. doi:10.1016/j.bmcl.2013.07.022.
Simoncini, D., Zhang, K. Y. J. (2013) Efficient sampling in fragment-based protein structure prediction using an estimation of distribution algorithm. PLoS ONE, 8(7): e68954, 1-10. doi:10.1371/journal.pone.0068954
Kumar, A., Zhang, K. Y. J. (2013) An Investigation on the Effect of Key Water Molecules on Docking Performance in CSARdock Exercise. J. Chem. Inf. Model., 53, 1880-1892, doi:10.1021/ci400052w.
Voet, A., Banwell, E. F., Sahu, K. K., Heddle, J. G., Zhang, K. Y. J. (2013) Protein interface pharmacophore mapping tools for small molecule protein:protein interaction inhibitor discovery. Curr. Top. Med. Chem., 13, 989-1001.
Zhang, C., Ibrahim, P. N., Zhang. J., Burton, E. A., Habets, G., Zhang, Y., Powell, B., West, B. L., Matusow, B., Tsang, G., Shellooe, R., Carias, H., Nguyen, H., Marimuthu, A., Zhang, K. Y. J., Oh, A., Bremer, R., Hurt, C. R., Artis, D. R., Wu, G., Nespi, M., Spevak, W., Lin, P., Nolop, K., Hirth, P., Tesch, G. H., Bollag, G. (2013) Design and pharmacology of a highly specific dual FMS and KIT kinase inhibitor. Proc. Natl. Acad. Sci. U.S.A., 110, 5689–5694.
Kumar, A., Ito, A., Hirohama, M., Yoshida, M., Zhang, K. Y. J. (2013) Identification of sumoylation activating enzyme 1 inhibitors by structure based virtual screening. J. Chem. Inf. Model., 53, 809-820.
Tsuchiya, A., Asanuma, M., Hirai, G., Oonuma, K., Muddassar, M., Nishizawa, E., Koyama, Y., Otani, Y., Zhang, K. Y. J., Sodeoka, M. (2013) CDC25A-inhibitory RE Derivatives Bind to Pocket Adjacent to the Catalytic Site. Mol. BioSyst., 9, 1026-1034.
Kumar, A., Zhang, K. Y. J. (2013) Computational investigation of SENP:SUMO protein- protein interaction for structure based drug design. Molecular Informatics, 32, 267-280.
Voet, A., Helsen, C., Zhang, K. Y. J., Claessens, F. (2013) The discovery of novel hAR receptor antagonist chemotypes using a combined pharmacophore screening procedure. ChemMedChem., 8, 644-651.
Jose, R.A., Voet, A., Broos, K., Jakobi, A.J., Bruylants, G., Egle, B., Zhang, K. Y. J., De Maeyer, M., Deckmyn, H., De Borggraeve, W. M. (2012) An integrated fragment based screening approach for the discovery of small molecule modulators of the VWF-GPIbα interaction. Chem. Commun., 48, 11349-11351.
Shrestha, R., Simoncini, D., Zhang, K. Y. J. (2012) Error estimation guided rebuilding of de novo models increases the success rate for ab initio phasing. Acta Cryst., D68, 1522-1534.
Kumar, A., Voet, A., Zhang, K. Y. J. (2012) Fragment based drug design: from experimental to computational approaches. Curr. Med. Chem., 19, 5128-5147.
Simoncini, D., Berenger, F., Shrestha, R., Zhang, K. Y. J. (2012) A probabilistic fragment-based protein structure prediction algorithm. PLoS ONE 7(7): e38799, 1-11, doi: 10.1371/journal.pone.0038799.
Voet, A., Zhang, K. Y. J. (2012) Pharmacophore modeling as a virtual screening tool for the discovery of small molecule protein-protein interaction inhibitors. Current Pharmaceutical Design., 18, 4586-4598.
Mishra, V., Kumar, A., Ali, V., Nozaki, T., Zhang, K. Y. J., Bhakuni, V. (2012) Novel protein-protein interactions between Entamoeba histolyticad-phosphoglycerate dehydrogenase and phosphoserine aminotransferase. Biochime, 94, 1676-1686.
Kumar, A., Zhang, K. Y. J. (2012) Computational Fragment-based Screening Using RosettaLigand: the SAMPL3 Challenge. J. Comput-Aided Mol. Des., 26, 603-616.
Mishra, V., Kumar, A., Ali, V., Nozaki, T., Zhang, K. Y. J., Bhakuni, V. (2012) Glu-108 is essential for subunit assembly and dimer stability of d-phosphoglycerate dehydrogenase from Entamoeba histolytica. Molecular and Biochemical Parasitology., 181, 117-124.
Mishra, V., Kumar, A., Ali, V., Nozaki, T., Zhang, K. Y. J., Bhakuni, V. . (2012) Role of conserved active site tryptophan-101 in functional activity and stability of phosphoserine aminotransferase from an enteric human parasite. Amino Acids, 43, 483-491.
Cowtan, K.D., Zhang, K.Y.J., Main, P. (2012). DM/DMMULTI software for phase improvement by density modification. International Tables for Crystallography, Vol. F - Crystallography of Biological Macromolecules, Chapter 15.3, pp 407-412. Eds. E. Arnold, D. M. Himmel and M. G. Rossmann, published for The International Union of Crystallography by Kluwer Academic Publishers, Dordrecht/Boston/London. doi:10.1107/97809553602060000849.
Zhang, K.Y.J., Cowtan, K.D., Main, P. (2012). Phase improvement by iterated density modification. International Tables for Crystallography, Vol. F – Crystallography of Biological Macromolecules, Chapter 15.1, pp 385-400. Eds. E. Arnold, D. M. Himmel and M. G. Rossmann, published for The International Union of Crystallography by Kluwer Academic Publishers, Dordrecht/Boston/London. doi:10.1107/97809553602060000847.
Berenger, F., Shrestha, R., Zhou, Y., Simoncini, D., Zhang, K. Y. J. (2011) Durandal: fast exact clustering of protein decoys. J. Comp. Chem., 33, 471-474.
Shrestha, R., Berenger F., Zhang, K. Y. J. (2011) Accelerating ab initio phasing with de novo models. Acta Cryst. D67, 804-812.
Berenger, F., Zhou, Y., Shrestha, R. and Zhang, K. Y. J. (2011). Entropy-accelerated exact clustering of protein decoys. Bioinformatics, 27(7), 939-945. doi: 10.1093/bioinformatics/btr072.
Bollag G., Hirth P., Tsai J., Zhang J., Ibrahim P. N., Cho H., Spevak W., Zhang C., Zhang Y., Habets G., Burton E. A., Wong B., Tsang G., West B. L., Powell B., Shellooe R., Marimuthu A., Nguyen H., Zhang K. Y. J., Artis D. R., Schlessinger J., Su F., Higgins B., Iyer R., D'Andrea K., Koehler A., Stumm M., Lin P. S., Lee R. J., Grippo J., Puzanov I., Kim K. B., Ribas A., McArthur G. A., Sosman J. A., Chapman P. B., Flaherty K. T., Xu X., Nathanson K. L. and Nolop K. (2010). Clinical efficacy of a RAF inhibitor needs broad target blockade in BRAF-mutant melanoma. Nature, 467, 596-599.
News & Views:
• Dual fronts poised to transform melanoma therapy. Asher Mullard, Nature Reviews Drug Discovery 10, 325-326 (2011).
• Industry makes strides in melanoma. Ken Garber, Nature Biotechnology, 28, 763-764 (2010).
• Targeting mutant BRAF in metastatic melanoma. Alexandra Flemming, Nature Reviews Drug Discovery 9, 841 (2010).
• Rare victory in fight against melanoma. Heidi Ledford, Nature 467, 140-141 (2010).
• Science “News of the week” reporting the approval of Zelboraf (Aug. 26, 2011).
• Nature “The week in science” reporting the approval of Zelboraf (Aug. 25, 2011).
• ABC News coverage on the approval of Zelboraf (Aug. 17, 2011).
• FDA news release announcing the approval of Zelboraf (Aug. 17, 2011).
• Zelboraf wins Prix Galien USA 2013 Award for best pharmaceutical agent.
Berenger, F., Coti, C., and Zhang, K. Y. J. (2010). PAR: a PARallel and distributed job crusher. Bioinformatics, 26(22), 2918-2919. doi:10.1093/bioinformatics/btq542.
Artis, D. R., Lin, J. J., Zhang, C., Wang, W., Mehra, U., Perreault, M., Erbe, D., Krupka, H. I., England, B. P., Arnold, J., Plotnikov, A. N., Marimuthu, A., Nguyen, H., Will, S., Signaevsky, M., Kral, J., Cantwell, J., Settachatgull, C., Yan, D. S., Fong, D., Oh, A., Shi, S., Womack, P., Powell, B., Habets, G., West, B. L., Zhang, K. Y. J., Milburn, M. V., Vlasuk, G. P., Hirth, K. P., Nolop, K., Bollag, G., Ibrahim, P. N., Tobin, J. F. (2009). Scaffold-based discovery of indeglitazar, a PPAR pan-active anti-diabetic agent. Proc. Natl. Acad. Sci. U.S.A., 106, 262-267.
News & Views:
• Tailoring nuclear receptor activation. Peter Kirkpatrick, Nature Reviews Drug Discovery 8, 107 (2009).
Tsai, J., Lee, J. T., Wang, W., Zhang, J. Z., Cho, H., Mamo, S., Bremer, R., Gillette, S., Kong, J., Haass, N. K., Sproesser, K., Li, L., Smalley, K. S.M., Fong, D., Zhu, Y. L., Marimuthu, A., Nguyen, H., Lam, B., Liu, J., Cheung, I., Rice, J., Suzuki, Y., Luu, C., Settachatgul, C., Shellooe, R., Cantwell, J., Kim, S. H., Schlessinger, J., Zhang, K. Y. J., West, B., Powell, B., Habets, G., Zhang, C., Ibrahim, P. N., Hirth, P., Artis, D. R., Herlyn, M., Bollag, G. (2008). Discovery of a Novel Selective Inhibitor of Oncogenic B-Raf Kinase with Potent Anti-Melanoma Activity. Proc. Natl. Acad. Sci. U.S.A., 105, 3041-3046.
News & Views:
• Scaffold to selectivity. Charlotte Harrison, Nature Reviews Drug Discovery 7, 390 (2008).
Zhang, K. Y. J., Milburn, M. V., Artis, D. R. (2007). Scaffold-based drug discovery. Chapter 6 in Structure-based Drug Discovery, pp129-153, Eds. Harren Jhoti and Andrew Leach, Springer, Dordrecht/Boston/London.
Zhang, K. Y. J. (2006). Crystal structure of PDE families and the potential for rational drug design . Chapter 29 in Cyclic Nucleotide Phosphodiesterases in Health and Disease, pp 583-605, Eds. Joseph A. Beavo, Sharron H. Francis and Miles D. Houslay, CRC Press, Boca Raton/London/New York.
Cronk, J. D., Rowlett, R. S., Zhang, K. Y. J., Tu, C., Endrizzi, J. A., Lee, J., Gareiss, P. C. & Preiss, J. R. (2006). Identification of a Novel Noncatalytic Bicarbonate Binding Site in Eubacterial beta-Carbonic Anhydrase. Biochemistry 45, 4351-4361.
Schubbert, S., Zenker, M., Rowe, S. L., Boll, S., Klein, C., Bollag, G., van der Burgt, I., Musante, L., Kalscheuer, V., Wehner, L. E., Nguyen, H., West, B., Zhang, K. Y. J., Sistermans, E., Rauch, A., Niemeyer, C. M., Shannon, K. & Kratz, C. P. (2006). Germline KRAS mutations cause Noonan syndrome. Nature Genetics 38, 331-336.
Zhang, K. Y. J., Ibrahim, P. N., Gillette, S. & Bollag, G. (2005). Phosphodiesterase-4 as a potential drug target. Expert Opinion on Therapeutic Targets 9, 1283-1305.
Houslay, M. D., Schafer, P. & Zhang, K. Y. J. (2005). Keynote review: Phosphodiesterase-4 as a therapeutic target. Drug Discovery Today 10, 1503-1519.
Lin, J. J., Wang, W. R., Krupka, H. I., Mehra, U., Zhang, C., Marimuthu, A., Powell, B., Hurt, C. R., Ibrahim, P. N., Artis, D. R., Bollag, G., Zhang, K. Y. J., Milburn, M. V. (2005) Discovery of novel and efficacious pan PPAR agonists through Scaffold-Based Drug Discovery approach. Steroids, 70, 476-476.
Card, G. L., Blasdel, L., England, B. P., Zhang, C., Suzuki, Y., Gillette, S., Fong, D., Ibrahim, P. N., Artis, D. R., Bollag, G., Milburn, M. V., Kim, S. H., Schlessinger, J. & Zhang, K. Y. J. (2005). A family of phosphodiesterase inhibitors discovered by cocrystallography and scaffold-based drug design. Nature Biotechnology 23, 201-207.
News & Views:
• Small is beautiful. Peter Kirkpatrick, Nature Reviews Drug Discovery 4, 190 (2005).
• A new school for screening. Harren Jhoti, Nature Biotechnology 23, 184 - 186 (2005).
Card, G. L., England, B. P., Suzuki, Y., Fong, D., Powell, B., Lee, B., Luu, C., Tabrizizad, M., Gillette, S., Ibrahim, P. N., Artis, D. R., Bollag, G., Milburn, M. V., Kim, S. H., Schlessinger, J. & Zhang, K. Y. J. (2004). Structural Basis for the Activity of Drugs that Inhibit Phosphodiesterases. Structure 12, 2233-2247.
News & Views:
• Structure-Based Drug Design: Seeking selectivity. Joanna Owens, Nature Reviews Drug Discovery 4, 1061 (2005).
Zhang, K. Y. J., Card, G. L., Suzuki, Y., Artis, D. R., Fong, D., Gillette, S., Hsieh, D., Neiman, J., West, B. L., Zhang, C., Milburn, M. V., Kim, S. H., Schlessinger, J. & Bollag, G. (2004). A Glutamine Switch Mechanism for Nucleotide Selectivity by Phosphodiesterases. Molecular Cell 15, 279-286.
News & Views:
• A view into the catalytic pocket of cyclic nucleotide phosphodiesterases. Marco Conti, Nature Structural & Molecular Biology, 11, 809 - 810 (2004).
• Flipping the switch. Helen Pilcher, Nature 430, 627 (2004).
Michels, J., O'Neill, J. W., Dallman, C. L., Mouzakiti, A., Habens, F., Brimmell, M., Zhang, K. Y. J., Craig, R. W., Marcusson, E. G., Johnson, P. W. & Packham, G. (2004). Mcl-1 is required for Akata6 B-lymphoma cell survival and is converted to a cell death molecule by efficient caspase-mediated cleavage. Oncogene 23, 4818-4827.
Manion, M. K., O'Neill, J. W., Giedt, C. D., Kim, K. M., Zhang, K. Y. J. & Hockenbery, D. M. (2004). Bcl-XL mutations suppress cellular sensitivity to antimycin A. Journal of Biological Chemistry 279, 2159-2165.
Michels, J., O'Neill, J.W., Zhang, K.Y.J., Craig, R.W., Marcusson, E.G., Johnson, P.W.M., Packham, G. (2003) The anti-apoptotic Bcl-2 family protein Mcl-1 is a pivotal regulator of cell survival in B-cell lymphoma. Blood, 102, 227A-227A.
Zhang, K. Y. J. (2003). Multidimensional histograms for density modification. Methods in Enzymology, 374, 188-203.
Michels, J., O'Neill, J. W., Dallman, C. L., Marcusson, E. G., Zhang, K. Y. J., Johnson, P. W., Craig, R. W., Packham, G. (2003) Mcl-1, an anti-apoptotic Bcl-2 family protein, is required for B-lymphoma cell survival and is converted to a cell death molecule by efficient caspase-mediated cleavage. Clinical Cancer Research, 9, 6158S-6158S.
Kuhlman, B., O'Neill, J. W., Kim, D. E., Zhang, K.Y.J., Baker, D. (2002). Accurate Computer Based Design of a New Backbone Conformation in the Second Turn of Protein L. Journal Molecular Biology, 315, 471-477.
O'Neill, J. W., Johnsen, K, Kim, D. E., Baker, D., Zhang, K.Y.J. (2001). Single site mutations induce 3D domain-swapping in the B1 domain of Protein L from Peptostreptococcus magnus. Structure, 9, 1017-1027.
Kuhlman, B., O'Neill, J. W., Kim, D. E., Zhang, K.Y.J., Baker, D. (2001). Conversion of Monomeric Protein L to an Obligate Dimer by Computational Protein Design. Proc. Natl. Acad. Sci. U.S.A., 98, 10687-10691.
Kim, K.M., Baker, D., Zhang, K.Y.J. (2001). Posttranslational modification of the N-terminal His-tag interferes with the crystallization of the wild type and mutant SH3 domains from chicken src tyrosine kinase. Acta Cryst. D57, 759-762.
Kim, K.M., Giedt, C.D., Basañez, G., O’Neil, J.W., Hill, J.J., Han, Y.H., Tzung, S.P., Zimmerberg, J., Hockenbery, D.M., Zhang, K.Y.J. (2001). Biophysical characterization of recombinant human Bcl-2 and its interactions with an inhibitory ligand, antimycin A. Biochemistry, 40, 4911-4922.
Cronk, J.D., Endrizzi, J.A., Cronk, M.R., O'Neill, J.W., Zhang, K.Y.J. (2001). Crystal structure of E. coli β-carbonic anhydrase, an enzyme with an unusual pH-dependent activity. Protein Science, 10, 911-922.
O'Neill, J. W., Kim, D. E., Baker, D., Zhang, K.Y.J. (2001). Structures of the B1 domain of Protein L from Peptostreptococcus magnus with a tyrosine to tryptophan substitution. Acta Cryst. D57, 480-487.
Tzung, S.P., Kim, K.M., Basanez, G., Zimmerberg, J., Simon, J., Zhang, K.Y.J., Hockenbery, D.M. (2001). Antimycin A mimics a cell-death-inducing Bcl-2 homolgy domain 3. Nature Cell Biology, 3, 183-191.
Cowtan, K.D., Zhang, K.Y.J., Main, P. (2001). DM/DMMULTI software for phase improvement by density modification. International Tables for Crystallography, Vol. F - Crystallography of Biological Macromolecules, Chapter 25.2.2, pp 705-710. Eds. M. G. Rossmann and E. Arnold, published for The International Union of Crystallography by Kluwer Academic Publishers, Dordrecht/Boston/London. doi:10.1107/97809553602060000724.
Zhang, K.Y.J., Cowtan, K.D., Main, P. (2001). Phase improvement by iterated density modification. International Tables for Crystallography, Vol. F – Crystallography of Biological Macromolecules, Chapter 15.1, pp 311-324. Eds. M. G. Rossmann and E. Arnold, published for The International Union of Crystallography by Kluwer Academic Publishers, Dordrecht/Boston/London. doi:10.1107/97809553602060000687.
Cronk, J.D., O'Neill, J.W., Cronk, M.R., Endrizzi, J.A., Zhang, K.Y.J. (2000). Cloning, crystallization and preliminary characterization of a beta carbonic anhydrase from Escherichia coli. Acta Cryst. D56, 1176-1179.
Johnsen, K, O'Neill, J. W., Kim, D. E., Baker, D., Zhang, K.Y.J. (2000). Crystallization and preliminary X-ray diffraction studies of mutants of B1 IgG-binding domain of Protein L from Peptostreptococcus magnus. Acta Cryst. D56, 506-508.
Tzung, S.P., Kim, K.M., Basanez, G., Zimmerberg, J., Zhang, K.Y.J., Hockenbery, D.M. (1999) Antimycin a mimics a BH3 domain-containing peptide and selectively induces apoptosis in cell lines overexpressing Bcl-xL. Clinical Cancer Research, 5, 3815S-3816S.
Nieh, Y. P., Zhang, K.Y.J. (1999). A two-dimensional histogram-matching method for protein phase refinement and extension. Acta Cryst. D55, 1893-1900.
Cowtan, K. D., Zhang, K.Y.J. (1999). Density modification for macromolecular phase improvement. Progress in Biophysics and Molecular Biology, Ed. Sir Thomas Blundell, Pergamon Press, Elsevier Science, 72, 245-270.
Ewaskow, S., Sidorova, J., Lycan, D., Hendle, J., Zhang, K.Y.J., Breeden, L. (1998). Mutation and modeling analysis of the Saccharomyces cerevisiae SWI6 ankyrin repeats. Biochemistry, 37, 4437-4450.
Goldstein, A., Zhang, K.Y.J. (1998). The 2D histogram as a constraint for protein phase improvement. Acta Cryst. D54, 1230 - 1244.
Fearnhead, H. O., McCurrach, M. E., O'Neill, J., Zhang, K.Y.J., Lowe, S. W., Lazebnik, Y. A. (1997). Oncogene-dependent apoptosis in extracts from drug-resistant cells. Genes and Development, 11, 1266-1276.
Zhang, K.Y.J., Cowtan, K.D., Main, P. (1997). Combining constraints for electron density modification. Methods in Enzymology, 277(B), 53-64.
Bowie, J.U., Zhang, K.Y.J., Wilmanns, M. & Eisenberg, D. (1996). Three-dimensional Profiles for Measuring Compatibility of an Amino Acid Sequence with Three-Dimensional Structure. Methods in Enzymology, 266, 598-616.
Zhang, K.Y.J., Eisenberg, D. (1994). Solid State Phase Transition in the Crystal Structure of Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase. Acta Cryst., D50, 258-262.
Zhang, K.Y.J., Eisenberg, D. (1994. The Three-dimensional Profile Method Using Residue Preference as a Continuous Function of its Environments. Protein Science, 3, 687-695.
Zhang, K.Y.J., Cascio, D., Eisenberg, D. (1994). Crystal Structure of Ribulose 1,5-bisphosphate Carboxylase/Oxygenase Complexed with a Transition State Analog, 2-Carboxy-D-arabinitol 1,5-Bisphosphate. Protein Science, 3, 64-69.
Eisenberg, D., Bowie, J. U., Luthy, R., Wilmanns, M., Wesson, L., Zhang, K.Y.J. (1993). 3-D profiles: principles and applications. Protein Engineering, 6(8), 1003-1029.
Zhang, K.Y.J. (1993). Crystallographic Phase Retrieval Through Image Processing Under Constraints. in Digital Image Recovery and Synthesis II, Paul S. Idell, Editor, Proc. SPIE 2029, 128-136.
Zhang, K.Y.J. (1993). Progress in Macromolecular Phasing. Journal of Bio Science and Technology, 1, 17-20.
Yeates,T.O., Zhang, K.Y.J. (1993). Ambiguities in Ab Initio Phasing. Science, 259, 1771-1772.
Zhang, K.Y.J. (1993). SQUASH - Combining Constraints for Macromolecular Phase Refinement and Extension. Acta Cryst., D49, 213-222.
Zhang, K.Y.J., Main P. (1990). The Use of Sayre's Equation with Solvent Flattening and Histogram Matching for Phase Refinement and Extension of Protein Structures. Acta Cryst., A46, 377-381.
Zhang, K.Y.J., Main, P. (1990). Histogram Matching as a Density Modification Technique for Phase Refinement and Extension of Protein Molecules, Acta Cryst., A46, 41-46.
Zhang, K.Y.J., Main P. (1988). Histogram Matching as a New Density Modification Method for Phase Refinement and Extension of Protein Molecules. Proceedings of Daresbury Study Weekend: Improving Protein Phases, pp57-64, DL/SCI/R26, Feb. 5-6, 1988, SERC, Daresbury, Warrington, UK.
Shao, M.C., Zhang, K.Y.J., Zhang, Z. Y., Tang, Y.Q. (1988). Crystal structure investigation of vanadyl complexes of tridentate ligand. I. Crystal structures of bis[(1-(2,4-pentanedionato(nitrobenzoyl)hydrazone)-2-ethoxy)oxovanadium] and bis[(1-(2,4-pentanedionato(3-nitrobenzoyl)hydrazone)-2-methoxy)oxovanadium]. Scientia Sinica, Ser. B (Engl. Ed.), 31(7), 781-788.
Zhang, K.Y.J., Shao, M.C., Tang, Y.Q. (1985). Crystal Structure of Sodium Octadecavanadate Na12V18O42.24H2O. Molecular Science and Chemical Research, 5(1), 1-7(Ch.).