User:Wendy Zheng

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Contact Info

Wendy Zheng (an artistic interpretation)
Wendy Zheng (an artistic interpretation)
  • Wendy Zheng //Wenyun ZHENG
  • Associate Professor / Ph. D
  • School of Pharmacy, East China University of Science and Technology
  • Address 1: No. 130 Meilong Road,Shanghai, P. R. China, 200237
  • Tel & Fax: 86-21-64251287; 13641936878
  • Email: zwy@ecust.edu.cn; zwyhtc15@gmail.com

郑文云,女, 理学博士,华东理工大学 药学院 副教授,药学专业硕士研究生导师;药物科学系副主任。上海市新药设计重点实验室研究人员。获得上海市优秀青年骨干教师人才基金资助。中国生物技术药物协会、中国/上海生物工程学会会员。


研究领域: 细胞分子生物学与生物技术药学

研究方向: 1)抗癌蛋白多肽及其药理药效学研究; 2)生化药学与微生物合成生物学。

==受教育经历==:

2003/09 – 2005/06,沈阳药科大学,生物制药学院, 博士; (导师:杨胜利院士)

1996/09 – 1999/06,沈阳农业大学,生物科技学院, 硕士; (导师:高德三教授)

1992/09 – 1996/06,沈阳农业大学,生物科技学院, 学士;


==研究工作经历==:

2013/07 – 2014/07, University of Minnesota, USA 国家公派访问学者

2008/09 – 2013/06, 华东理工大学,药学院药物科学系, 副教授

2005/09 – 2008/08, 华东理工大学,药学院药物科学系, 讲师

2003/09 – 2005/08, 华东理工大学,生物工程学院生物学系, 讲师

1999/09 – 2003/08, 沈阳农业大学,生物科技学院, 讲师

==Education==:

  • Sep.2003- Jul.2006 Ph.D School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, P.R. China; Major: Microbiological and Biochemical Pharmacy
  • Sep.1996 – Jul.1999 M.S School of Biotechnology and Bioscience,Shenyang Agricultural University, P.R. China; Major: Biotechnology in Sericulture
  • Sep.1992 – Jul.1996 B.S School of Biotechnology and Bioscience, Shenyang Agricultural University, P.R. China; Major: Biotechnology

==Work Experiences==:

  • Jul. 2013-Jul. 2014: University of Minnesota, USA, CSC Visting Schoolar
  • Oct. 2006-present: Associate Professor and MD student adviser, School of Pharmacy, East China University of Science and Technology
  • Sep. 2003-Aug. 2005: Lecturer, School of Biotechnology and Bioscience, East China University of Science and Technology
  • Sep. 1999 - Aug. 2003: Lecturer, School of Biotechnology and Bioscience, Shenyang Agricultural University

Research interests

  1. .Drug deliver and stability systems of biological macromolecules
  2. .Protein engineering and recombinant proteins/enzymes
  3. .Discovery and designing of novel drugs or targets to important diseases

Research Skills:

  1. . Extensive knowledge of cell biology and microbiology: Mastered technologies on culture and operation of animal and cancerous cells and familiar with fermentation and multiple microbiological manipulations.
  2. . Extensive knowledge of molecular biology and biochemistry: mastered technologies on preparation and analyses of protein (enzyme), nucleic acid, and drugs and familiar with the microbial cell factories.

Publications

1.Nanjing Lin#, Wenyun Zheng#, Linfeng Li, Ping Wang, Xingyuan Ma*, A novel system enhancing the endosomal escapes of peptides promotes Bak BH3 peptide inducing apoptosis in lung cancer A549 cells.Targeted Oncology.2013.DOI:10.1007/s11523-013-0282-9, IF[2011]=3.614 (#Contributed equally to this work)

2.Liqun Wang, Yanyan Kang, Wenyun Zheng*, Linfeng Li, Lei Shi, Xingyuan Ma.Effect on apoptosis and cell cycle of recombinant double negative 4 dominant mutation Survivin (T34/117A) in breast cancer cell B-Cap-37. Biomedicine & Pharmacotherapy, 2013, In Press, Available online 25 November. (http://dx.doi.org/10.1016/j.biopha.2013.11.001)

3.Wenyun Zheng, Wenyao Zhang, Wei Hu, and Yi Yang,Exploring the Smallest Active Fragment of HsQSOX1b and Discovery of a Highly Efficient Oxidative Engine, PLOS ONE. 2012,7 (7): e40935. doi:10.1371 IF[2012]=3.73

4.Yuxin Xu#, Wenyun Zheng#,Tianwen Wang, Ping Wang, Ling Zhu, Xingyuan Ma*., Genetic protein TmSm(T34A) enhances sensitivity of chemotherapy to breast cancer cell lines as a synergistic drug to doxorubicin. Biomedicine & Pharmacotherapy, 2012, 66(5): 368-372 (#Contributed equally to this work)

5.Hailong Chen, Xingyuan Ma*, Zhi Li, Qiaoyun Shi, Wenyun Zheng, Yang Liu, Ping Wang. Functionalization of single-walled carbon nanotubes enables efficient intracellular delivery of siRNA targeting MDM2 to inhibit breast cancer cells growth. Biomedicine & Pharmacotherapy, 2012, 66 (5) :334-338. IF[2011]=2.000

6.Wenyun Zheng, Yanyan Chu, Qin Yin, Charles Yang, Wenyao Zhang, Yun Tang, Yi Yang. Crucial effect of the First CXXC Motif of Human QSOX 1b on the Activity to different substrates. J ournal of Biochemistry. 2011, 149(3):293-300

7.Wenyun Zheng, Yanyan Kang, Linfeng Li, Yuxin Xu, Xingyuan Ma, Levels of effectiveness of gene therapies targeting survivin and its splice variants in human breast cancer cells. Drug Discoveries & Therapeutics. 2011, 5(6):293-298

8.Xingyuan Ma, Bi Yao, Wenyun Zheng, Linfeng Li*. Comparative study on characterization of recombinant B subunit of E. coli heat-labile enterotoxin (rLTB) prepared from E. coli and P. patoris. J. Microbiol. Biotechnol. 2010, 20(3):550-557. IF[2011]=1.381

9.Chu YY, Yang C, Chen XJ, Zheng WY, Yang Y*, Tang Y*. Structure–function analysis of human protein Ero1-Lα. Biochemical and Biophysical Research Communications, 2009, 389(4) : 645-650.

10.Yanyan Chu, Charles Yang, Xianjun Chen, Wenyun Zheng, Yi Yang, Yun Tang,Structure–function analysis of human protein Ero1-La,Biochemical and Biophysical Research Communications, 2009, 389:645–650.

11.Haiyi Zhang, Yu Zheng, QinghaiLiu, Xinyi Tao, Wenyun Zheng, Xingyuan Ma*, Dongzhi Wei*. Development of a fed-batch process for the production of anticancerdrug TATm-survivin(T34A) in Escherichia coli. Biochemical Engineering Journal. 2009, 43(2):163–168. IF[2011]=2.645

12.Xingyuan Ma*, Wenyun Zheng, Haiyi Zhang,Xinyi Tao,Qinghai Liu,Dongzhi Wei*. Large scale preparation and characterization of a genetically engineering protein and biological activity of suppressing proliferation and rapid pro-apoptosis to carcinoma cells. Journal of Biotechnology. 2008, S75-S98 (13-P-022). IF[2011]=3.045

13.Zheng Wenyun, Ma Xingyuan, Wei Dongzhi, Ma Yushu, Wang Tianwen, Wang Jinzhia, Liu Qinghai, Yang Shengli, High-level expression, purification and pro-apoptosis activity of HIV-TAT-Survivin (T34A) mutant to cancer cells in vitro, Journal of Biotechnology, 2006, 123:367-378. IF[2011]=3.045

14.Xingyuan Ma, Wenyun Zheng, Dongzhi Wei, Yushu Ma, Tianwen Wang, Jinzhi Wang, Qinghai Liu and Shengli Yang. Construction, Expression, and Purification of HIV-TAT-survivin (T34A) mutant: a Pro-apoptosis protein in E.coli. Protein Expression and Purification, 2006, 47:36-44. IF[2011]=1.587

15.Xingyuan Ma, Wenyun Zheng, Tianwen Wang, Dongzhi Wei, Yushu Ma. Optimization and high-level expression of a functional GST-tagged rHLT-B in E. coli and GM1 binding ability of purified rHLT-B. Journal of Microbiology, 2006, 44(6): 293-300. IF[2011]=1.095

16.Xingyuan Ma, Zheng Wenyun*, Tianwen Wang. Leukocyte function-associated antigen-1 structure, function and application prospects. Protein and Peptide Letters, 2006, 13: 397-400. IF[2011]=1.942

17.Xingyuan Ma, Wenyun Zheng, Dongzhi Wei, Yushu Ma, Tianwen Wang, Jinzhi Wang, Qinghai Liu and Shengli Yang. Construction, Expression, and Purification of HIV–TAT-Survivin (T34A) Mutant: a Pro-Apoptosis Protein in Escherichia coli, Protein Expression and Purification, 2006, 47:36-44.

18.Zheng Wenyun, Ma Xingyuan, Wei Dongzhi, Ma Yushu, Wang Tianwen, Wang Jinzhia, Liu Qinghai, Yang Shengli. Preparation of recombinant HIV-TATm-survivin (T34A) protein and its pro-apoptosis activity to four cancer cell lines in Vitro, Chinese Journal of Biotechnology, 2006.22(2): 285-92

19.Wenyun Zheng, Xingyuan Ma, Dongzhi Wei, Tianwen Wang, Yushu Ma, Shengli Yang. Molecular Cloning and Bioinformatics Analysis of a Novel Spliced Variant of Survivin from Human Breast Cancer Cells, DNA Sequence, 2005, 16 (5): 321–328.

20.Zheng,W., Ma,X., Wang,T., Ma,Y., Wei,D. and Yang,S.. Homo sapiens breast cancer cell lines B-cap37, Survivin-Image gene mRNA, partical cds. Accession No. AY830084, Protein_ID= "AAW22624.1",Genebank. 2005.

21.郑文云; 马兴元; 魏东芝; 王锦之; 刘清海; 马昱澍; 杨胜利; 重组HIV-TATm-Survivin(T34A)蛋白制备及其促癌细胞凋亡活性研究. 生物工程学报 2006年22卷02期 285-292页

22.胡薇,张文耀,郑文云,杨弋。 FAD辅助的人源重组静息巯基氧化酶HsQSOX1b活性的测定和功能结构域研究,中国科技论文在线(2011):(http://www.paper.edu.cn/index.php/default/releasepaper/content/2011-05-234)


==会议论文==:

1.郑文云,张文耀,胡薇,杨弋。HsQSOX1b最小功能结构域及其功能,第十届全国酶学学术讨论会(2011杭州)论文集 B-18:P30。

2.Wenyun Zheng, Yanyan Kang, Linfeng Li, Xingyuan Ma*. Effects on Human Breast Cancer Cells in vitro by Designed Derivatives from Survivin and its Splice Variant Genes. 中国生物化学与分子生物学会第十届会员代表大会暨全国学术会议(2010南京) 论文集 D-16: P172。

3.Zheng Wenyun. Multiple Important Roles of Cysteine and its Derivants in Biochemistry. 中国生物化学与分子生物学会 工业生化与分子生物学学术研讨会 (2010昆明) 会议论文集P86。

4.Zhao Yuzheng, Yang Charles, Zheng Wenyun, Yang Yi. Subcellular localization of disulfide proteome。第六届中国蛋白质组学大会, (2010泰州)会议论文集B-18:P46。

5.Xingyuan Ma, Yuxing Xv, Yanyan Kan, Zhu Lin, Linfeng Li, Wenyun Zheng*. A Multi-function Recombinant Protein drug to Carcinoma and Elucidating to its Molecular Mechanisms. 2011年亚洲生物技术论坛(ACB-2011)(上海)论文集P376。

6.Xingyuan Ma,* Yuxing Xv, Yanyan Kan, Wenyun Zheng, Jian Mo, Linfeng Li and Huizhan Zhang.Development & Researches of a Muti-function Recombinant Protein to breast Carcinoma and Elucidating to Primary Molecular Mechanism. 第三届中国北京蛋白质和多肽大会(PepCon-2010)(2010北京) 论文集P655。

7.Xingyuan Ma, Yuxing Xv, Yanyan Kan, Wenyun Zheng, Lin Zhu, Linfeng Li and Huizhan Zhang. Study on inducing apoptosis and suppressing proliferation effects of a recombinant protein targeted to survivin on human breast cancer cells and their molecular mechanism. 中国生物化学与分子生物学会第十届会员代表大会暨全国学术会议(2010南京) (论文集) D-16: P170。

8.林南静,李林凤,郑文云,安学勤,马兴元*。用于多肽药物转载的多元组合体系构建。中国生物化学与分子生物学会 工业生化与分子生物学学术研讨会(2012石家庄)文集P57。

9.赵玉政,杨毅,郑文云,杨弋。亚细胞结构的氧化还原梯度。第十一次中国生物物理大会,(2009桂林),论文集B-34: P55。

10.林南静,郑文云,任福正,安学勤,刘惠,马兴元*,王平*. 基于TAT与INF-7的多肽药物细胞内转载与促内吞逃逸体系的研究. 2013年中国生物化学与分子生物学工业分会学术年会(论文集)

11.李林凤,郑文云*,张翼1,康燕燕1,马兴元1*,王平.重组蛋白TATm-Survivin(T34A)抑制肺癌干细胞增殖和促凋亡的研究2013年中国生物化学与分子生物学工业分会学术年会(论文集)

12.Yi Zhang#, Wenyun Zheng#, Linfeng Li, 3, Ping Wang, Xingyuan Ma*.A Recombinant Protein TmSm(T34A) Induces Breast Cancer Stem Cells(BCSCs) Proliferation Inhibition, and Apoptosis in Vitro and Vivo. The 6th International Symposium on Biocatalysis and Biosynthetic Engineering (ISBBE 2013).

Projects

近年承担的主要科研项目

主持项目

1.国家自然科学基金 生命科学部青年基金项目: 胞外分泌型人巯基氧化酶1(Es-hQSOX1b)剪接体功能及其生物药学意义探索,(批准号:31300660)(起止年月:2014 年01月至2016 年 12 月)。课题负责人。

2.教育部博士点新教师科研基金项目:”分泌型hQSOX1b在细胞基质形成中的机制研究 “(课题编号:20120074120027)(起止年月:2012.11-2015.10) 课题负责人

3.上海市优秀青年骨干教师科研基金课题:“人源巯基氧化酶QSOX的结构与功能研究”(项目编号:YC1057107)(起止年月:2006.1-2007.12) 课题负责人

4.华东理工大学生物反应器工程国家重点实验室2008年度重点项目配套项目:“基于核酸适配子的细胞内成像技术”(起止年月:2008.12-2010.12) 课题负责人

参与项目

1.上市自然科学基金课题:“基于毕赤酵母PFLD1启动子的“绿色”基因表达体系创建”(项目编号:05ZR14033)。(起止年月:2006.1-2007.12) 第3

2.上海市生物医药科技攻关重点项目:基因工程抗癌新药TAT-Survivin突变体的中试研究和高危HPV检测试剂盒研究(课题编号:054319928)”(起止年月:2006.1-2007.12).第2

3.教育部高等学校科技创新工程重大项目培育资金项目“针对生物过程中二硫键形成机制的创新药物和技术研究”(课题编号:706023) (起止年月:2007.1-2008.12)。 第5

4.国家高技术研究发展计划(863计划)项目:“蛋白质表达系统中二硫键形成的关键技术” (课题编号:2006A02160)(起止年月:2007.1-2009.12)。 第3

5.国家自然基金重大研究计划面上项目:“细胞内蛋白质巯基氧化性修饰荧光探针及信号转导” (课题编号:90713026) (起止年月:2008.1-2010.10) 第3

6.国家教育部博士点新教师科研基金项目:“TATm-Survivin突变体促乳腺癌快速凋亡的研究”(课题编号:20070251011)(起止年月:2007.11-2009.10)。第3

7.国家“十一五”计划“重大新药创制”项目:“重组蛋白TATm-Survivin(T34A)质量体系和临床前药效学与安全性研究”(2009.1-2010.12) (项目编号:2009ZX09103-693) 第4。

8.国家教育部交叉学科与重大项目培育基金项目:“抗肿瘤靶向纳米载药系统研究” (2009.9-2012.12)(项目编号:WK0913002) 第3。

9.上海“浦江学者”计划资助项目:“存活素纳米抗体(Survivin-Nb)工程化酵母制备与抗肺癌及其干细胞活性研究” (项目编号:13PJD012)(2013.09.01-2015.8.31)第3。

10.国家“十一五””重大新药创制”上海市配套项目 (项目编号:2009ZX09103-693). 第3。


Patents

发明专利:

1.发明专利名称: 含有HIV转导结构域的生存素突变体及制备方法和应用, 发明人: 魏东芝; 马兴元; 郑文云; 马昱澍; 刘清海; 杨胜利。 中国专利授权号:ZL2005 1 0026847.8

2.发明专利名称:大肠杆菌热敏毒素B亚单位的真核表达方法 中国专利授权号:ZL 2005 1 0027957.6 发明人:魏东芝; 马兴元; 郑文云; 王天文; 罗 晨; 马昱澍

3.发明专利名称:一种用于原核分泌、融合表达大肠杆菌热敏毒素B亚单位的载体 中国专利授权号:ZL 2005 1 0028084.0发明人:魏东芝; 马兴元; 王天文; 郑文云

4.发明专利名称:一种肿瘤化疗药物的蛋白增敏剂, 中国专利授权号:ZL201010608978.8 (授权日:2013.11.20) 发明人:马兴元; 许玉馨; 郑文云; 朱玲

5.发明专利名称:非甲醇诱导型毕赤酵母蛋白表达系统及其用途, 公开号: CN101104859, 发明人:马兴元; 郑 宇; 郑文云; 刘美云; 魏东芝

6.发明专利名称:生产抗癌药物TAT(m)-Survivin(T34A)的工程菌的发酵放大工艺, 公开号: CN101157949, 发明人: 魏东芝; 马兴元; 张海毅; 姚雪凌; 王恒伟; 李明华; 郑文云; 赵 莉; 刘清海

7.发明专利名称:抗肿瘤药物TAT(m)-Survivin(T34A)的纯化复性方法, 公开号: CN101139388发明人: 魏东芝; 马兴元; 张海毅; 李明华; 郑文云; 赵 莉; 刘清海

8.发明专利名称:一种抗肿瘤蛋白质药物的质量稳定工艺, 公开号: CN102366628A发明人:马兴元; 朱玲;石磊; 唐莉莉; 郑文云; 莫剑

9.发明专利名称:单壁碳纳米管转载抗肿瘤药物技术及其应用, 公开号: CN102370988A, 发明人: 马兴元; 陈海龙; 林南静; 郑文云; 张翼; 安学勤

10.发明专利名称: 一种survivin及其突变体转基因酵母系统及其应用, 公开号: CN102367422A, 发明人: 马兴元; 刘琨; 李林凤; 姚碧; 郑文云

11.发明专利名称:一种疫苗黏膜免疫佐剂分子的制备方法, 公开号: CN102382853A, 发明人: 马兴元; 姚碧; 郑文云; 刘琨

12.发明专利名称: QSOX及其突变体蛋白的制备方法和应用, 公开号: CN101503679, 发明人:杨弋; 郑文云; 尹琴; 徐磊。

13.发明专利名称:多基因共表达体系及含二硫键功能性蛋白的生产方法.公开号:201110039867.4 公开号: CN102643847A. 发明人:杨弋;郑文云;张文耀。

14.发明专利名称:一种增强多肽药物从细胞内体逃离的蛋白载药系统及其应用. 公开(公告)号: CN103230599A (公开日: 2013.08.07) 发明人:马兴元; 林南静; 郑文云; 李林凤; 刘蕙.


Teaching & Education

1.《生物化学》(48学时,3学分)

2.《分子生物学》 (32学时,2学分)

Useful links

Protein engineering

  1. David Baker's lab: http://depts.washington.edu/bakerpg/drupal/

Metabolic engineering and synthetic biology

  1. http://keaslinglab.lbl.gov/
  • Online tools
  1. Multiple alignment: http://www.ebi.ac.uk/Tools/msa/clustalw2/
  1. 在线基因表达密码子优化: http://www.jcat.de/
  • Information resources

"References texts and information resources."

Videos

  • ScienceHack: Search engine for science videos with a review system for videos.

Please add new resources useful to the community here. Keep this page organized by following the format and organization already here.

  • See also Vectors for information and links related to cloning vectors.
  • See also Searching the literature for information and links on searching the biological literature.
  • See also Synthetic Biology for information and links on Synthetic Biology.

Videos

  • ScienceHack: Search engine for science videos with a review system for videos.

Information resources

References texts and information resources.

Bacterial physiology

  • Escherichia coli statistics by Institute for Biomolecular Design
    • Several tables describing statistical data on E. coli compiled from several sources.
  • EcoSal by ASM Press
    • An incomplete web version of the publication Escherichia coli and Salmonella: Cellular and Molecular Biology. [Subscription required]
  • EcoGene
    • Database of all E. coli genes and sequences
  • Ecocyc
    • Comprehensive biochemical pathway and gene function site for E. coli

Lab techniques

  • Polony Protocols by Church and Mitra Lab
    • Polonies are colonies of PCR amplicons derived from a single molecule of nucleic acid.
  • Protocol-online by Dr. Long-Cheng Li
    • A database of research protocols in a variety of life science fields. It has a popular discussion forum.

Protein

RNA

  • Appendix by Ambion, Inc.
    • Website with many useful nucleic acid parameters.

Research

Online tools

Tools available to use online.

General

  • Colibri by Institut Pasteur
    • E. coli genome site; get sequences, see the position of your gene in the chromosome, see the function of your gene, and other fun stuff. You can also search for protein sequences/motifs within the E. coli genome.
  • NCBI
    • Various tools and databases for molecular biology.
  • The public instance of the JBEI Registry
    • A DNA part, plasmid, microbial strain, and Arabidopsis Seed online repository with physical sample tracking capabilities
    • A site where you can explore the various features of the JBEI Registry software, and even get some work done!
    • Try out the integrated online tools, including DNA sequence editing and annotation (Vector Editor) and auto-aligning sequencing trace files against a template.
    • Follow a link to the underlying open-source software source code.
  • PaR-PaR Laboratory Automation Platform
    • PaR-PaR allows researchers to use liquid-handling robots effectively, enabling experiments that would not have been considered previously. After minimal training, a biologist can independently write complicated protocols for a robot within an hour.
  • Biopolymer calculator by Schepartz lab
    • Calculate extinction coefficients, Tm's, and base composition for your DNA or RNA; calculate amino acid composition and extinction coefficient for your protein
    • Currently under construction, with promises that it will be back online soon.
  • Science Gateway
    • Collection of science-related links, including links to journals, catalogs, and tools. See their about page.
  • BioNumbers
    • The database of useful biological numbers.

DNA

  • Clipboard by Austin Che
    • Web tool for getting complement, reverse complement, translation and restriction enzyme analysis of a DNA sequence
  • Gene Design by Boeke lab
    • Collection of online tools for codon optimization and shuffling, restriction site editing, and so on.
  • NEB Cutter by New England Biolabs, Inc.
    • Tool for finding restriction sites, et cetera.
  • Primer3
    • Tool that lets you pick & evaluate primers from a DNA sequence
  • UNAFold
    • Replacement for mFold for predicting nucleic acid folding. Downloadable and some applications are available online also.
  • SIDD
    • Stress induced DNA duplex destabilization. Finds destabilized sites in superhelical DNA.
  • j5, DeviceEditor, and VectorEditor online tools
    • j5: DNA assembly design automation for (combinatorial) flanking homology (e.g., SLIC/Gibson/CPEC/SLiCE/yeast) and type IIs-mediated (e.g., Golden Gate/FX cloning) assembly methods
    • DeviceEditor: a visual DNA design canvas that serves as front-end for j5
    • VectorEditor: a visual DNA editing and annotation tool
    • The j5 and DeviceEditor software has been exclusively licensed to TeselaGen Biotechnologies for commercial use and distribution.

RNA

  • mFold by Michael Zuker.
    • This is the main page with links to sites for predicting RNA and DNA folds, calculating Tm's and free energies.
    • (This has been replaced with the DINAMelt server running UNAfold)
  • Vienna RNA software package: RNA secondary structure prediction and design
  • Sfold: Statistical Folding and Rational Design of Nucleic Acids. Predicts accessible RNA sites

Protein

  • AGADIR by Serrano lab
    • An algorithm to predict the helical content of peptides.
  • AVID by Keating lab
    • An integrative framework for discovering functional relationships among proteins.
  • Cn3D by NCBI
    • A helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service. It doesn't read PDB files but can be more straightforward to use than DeepView.
  • ExPASy Proteomics server by the Swiss Institute of Bioinformatics
    • Collection of links to many pages to calculate parameters of your favorite proteins
    1. Compute pI/Mw
      • A tool which allows the computation of the theoretical pI (isoelectric point) and Mw (molecular weight) for a list of Swiss-Prot and/or TrEMBL entries or for user entered sequences.
    2. ProtParam
      • A tool which allows the computation of various physical and chemical parameters for a given protein stored in Swiss-Prot or TrEMBL or for a user entered sequence.
    3. Translate
      • Translate is a tool which allows the translation of a nucleotide (DNA/RNA) sequence to a protein sequence.
  • GETAREA 1.1 by Sealy Center for Structural Biology
    • Solvent accessible surface areas, atomic solvation energies, and their gradients for macromolecules
  • PAIRCOIL2 by Keating and Berger labs
    • Tool to predict the parallel coiled coil fold from sequence using pairwise residue probabilities.
  • ProteinProspector by UCSF Mass Spectrometry Facility
    • Proteomics tools for mining sequence databases in conjunction with Mass Spectrometry experiments.

Statistical tests

Calculators

Office applications

  • gOffice by Silveroffice, Inc.
    • Suite of office applications offered over the web

Writing

  • Writely by Upstartle, LLC.
    • A beta word processor run over the web
  • WriteBoard by 37signals
    • Permits writing of shareable, web-based text documents

Spreadsheets

  • NumSum by TrimPath
    • Permits sharable, web-based spreadsheets
  • iRows by Itai Raz and Yoah Bar-David
    • Permits web-based spreadsheets

Software resources

Software available to download.

General

  • Vector NTI by Informax, Inc.
    • Free-to-academics tool for sequence analysis and data management.

DNA

  • PerlPrimer: Open source PCR primer design. Written in Perl/Tk.
  • Artemis by the Sanger Center
    • A free DNA sequence viewer and annotation tool (Java based).
  • GeneDesigner by DNA2.0
    • Combine genetic building blocks by drag-and-drop, codon optimize, restriction site editing, sequence oligo design etc. See BMC Bioinformatics 2006 Jun 6;7(1):285 for more detail.
    • Free to download and works on Mac or PC. User agreement is somewhat restrictive, i.e. you cannot sell genes designed using the tool without permission.

RNA

  • XRNA: Java tools for creating RNA secondary structure diagrams

Protein

  • Dang by Richardsons' lab
    • A command-line tool that generates a table of several useful geometric measurements for each residue or base from a PDB file.
  • DeepView by GlaxoSmithKline & Swiss Institute of Bioinformatics
    • Awesome program for viewing and studying protein structure.
  • Modeller by Sali lab
    • Program for homology or comparative modeling of protein three-dimensional structures by satisfaction of spatial restraints.
  • PyMOL
    • Molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. The latest version does not run on OSX 10.3. (from Kathleen).
  • VMD by Theoretical and Computational Biophysics Group at UIUC
    • Molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. Generates pretty high resolution pictures of protein structures.

Geospatial modelling

Links to some labs

Protein engineering

1.David Baker's lab: http://depts.washington.edu/bakerpg/drupal/ 2.Michael Levitt: http://csb.stanford.edu/levitt/ 3.Protein science: http://fold.doe-mbi.ucla.edu/overview 4.Protein design lab: http://www.cmps.lu.se/biostruct/people/ingemar_andre/ Metabolic engineering and synthetic biology

1.http://keaslinglab.lbl.gov/ SMT

1.Xie,XS. http://bernstein.harvard.edu/pages/AboutProfXie.html DNA chemistry

1.http://dna.caltech.edu/DNAresearch_perspective.html 2.https://www2.physics.ox.ac.uk/research/self-assembled-structures-and-devices 3.http://cadnano.org/windows-installation Enzymes

1.http://en.wikipedia.org/wiki/Malic_enzyme 2.http://en.wikipedia.org/wiki/Malate_dehydrogenase 3.http://seemanlab4.chem.nyu.edu/ Online tools 1.Multiple alignment: http://www.ebi.ac.uk/Tools/msa/clustalw2/ 2.Tools:http://www.nature.com/nmeth/journal/v9/n4/abs/nmeth.1923.html 3.Signal: http://www.cbs.dtu.dk/services/SignalP/ 4.Solubility: http://mips.helmholtz-muenchen.de/prosoII/prosoII.seam#

hottopics : De novo protein design

http://www.jbc.org/content/272/4/2031.full this article discussed some key points that should be taken into account in de novo protein design. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1459523/

Gene Network Modeling

  • Ingeneue by George von Dassow, Eli Meir, Edwin Munro, and Garret Odell at the Center for Cell Dynamics
    • An open-source java program for modeling gene regulatory networks. Users can rapidly build networks by specifying their topology, initial conditions, connectivity, and known parameters. Ingeneue can then search/explore paramter space for desired behavior, simulate the effects of noise and mutation, and generate statistics/time graphs of the system.

Toolbars

[2]

  1. 1.表达蛋白溶解性预测:http://mips.helmholtz-muenchen.de/prosoII/prosoII.seam#
  • Important Journals
  1. Cell: http://www.cell.com
  2. NPG: http://www.nature.com
  3. Science: http://www.sciencemag.org
  4. PNAS: http://www.pnas.org
  5. JBC: http://www.jbc.org
  6. ASM Journals: http://journlas.asm.org
  7. Biology-direct: http://www.biology-direct.com

http://openwetware.org/wiki/User:Ford_Xingyuan_Ma

Other Researcher ID: http://www.researcherid.com/rid/H-3477-2011

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