BMC Structural Biology

Curriculum Vitae Date: 1/12/2012Samad Jahandideh, Ph.D.Postdoc fellowThe Section on Statistical GeneticsDepartment of BiostatisticsThe University of Alabama at BirminghamBirmingham, AL 35294-0022Phone: (205) 975-9208FAX: (205) 975-2540Email: sjahandideh@PERSONAL DETAILSGender: MaleBirth date: 09/14/1981Birthplace: Darab, Fars Province, IRANMarital status: MarriedPresent citizenship: IranianEmail: sjahandideh@EDUCATIONPostdoctoral fellow: Department of Biostatistics, School of Public Health, University of Alabama at Birmingham 2010 to present.2005-2010 Ph.D. in Biophysics2003-2005 M.Sc. in Biophysics1999-2003 B.Sc. in Molecular Biology and GeneticsRESEARCH INTERESTSBioinformatics, Modeling and Molecular Dynamics, Systems Biology, Molecular De novo protein design, Structure-Activity relationship (SAR and QSAR), Network biology, Artificial intelligence, Bioelectromagnetics, Medical Informatics.ACADEMIC POSITION AND RESPONSIBILITIESAssistant Professor, Department of Medical Physics, Shiraz University of Medical Sciences, Shiraz, Iran2009 to 2010Vice-chancellor for research in Medical Physics Department, Shiraz University of Medical Sciences, Shiraz, Iran 2009 to 2010Membership in the supreme scientific evaluation committee of 1st research scientific congress for the national students of radiation biology science congress in Shiraz University of Medical Sciences, Shiraz, Iran 2010CONTINUING EDUCATION∙BST 695: Special Notes on Statistical Genetics, SSG, UAB, Spring 2011 Dr. Degui Zhi.∙GRD 717: Principles of Scientific Integrity, Fall 2011 Dr. Kincard.∙I have passed some educational courses during my PhD at Tarbiat Modares University including: Educational psychology, logic and methodology of science, Teaching methods, and Educational technology.TALKS AND PRESENTATIONS2011 SOPH research day poster presentation. Title: Application of density similarities to predict membrane protein types based on pseudo-amino acid composition.2009 On “Seminar on Systems Biology” Department of Biochemistry, SUMS, Shiraz, Iran2009 Monthly talks, Medical school, Shiraz University of Medical Sciences, Shiraz University, Shiraz, IranTitle: Systems biology and biological networks.2007 9th Congress of Biochemistry and Second International Congress of Biochemistry and Molecular Biology, Shiraz, Iran2006 First Iranian Congress of Biotechnology, Tehran University, Tehran, Iran2006 14th International Congress of Biology, Tarbiat Modares University, Tehran, IranDISTINCTIONS2009 Nation wide 1st rank in research by Iranian National Institute of Elite (Bonyad Melli Nokhbegan)2007 Fellow of National Institute of Elite (5000$ award)2005 First Rank Student among Biophysics Graduated Students at Tarbiat Modares University2005 Member of Science council of Tarbiat Modares University2009 Certification of teaching from Tarbiat Modares University, Tehran, IranTEACHING EXPERIENCE1- Biophysics and Radiational Biology, Azad University of Arak, Iran, 20072-Medical physics (Radiobiology) (MD students), SUMS, Iran, 20093-Non-ionizing radiations, SUMS, Iran, 20094-Health Physics (BS students), SUMS, Iran, 2009 and 20105-Cell and Molecular Biology (Medical Physics Master Students), SUMS, Iran, 20096-Bioinformatics (Biochemistry PhD Students), SUMS, Iran, 20107-Structural Bioinformatics (PhD student of Shahid Beheshti University of Medical Science), Iran, 2009 8-Health Physics (Radiobiology MS students), SUMS, Iran, 20109-Radiobiology (Medical Physics MS students), SUMS, Iran, 2009 and 201010-Thermodynamics and heat transport (BS students), SUMS, Iran, 201011-Biophysics (BS students), SUMS, Iran, 201012-Modeling of Physiological Systems, SUMS, Iran, 201013-Biophysics (Physiology MS students), SUMS, Iran, 201014-Non-ionizing radiations (Medical Physics MS students), SUMS, Iran, 201015-Electricity, Magnetics and applications in medicine (Medical Physics MS students), SUMS, Iran, 2010 16-Seminar (Medical Physics and Bio-medical Engineering MS students), SUMS, Iran, 2010LANGUAGESPersian (Native), English, ArabicPERSONAL INTERESTSChess, Mountaineering, Classical Music, Musical Instruments Designing and MakingCOMPUTER SKILLSProgramming Languages and packages: MATLAB, R, SPSS, and C++.Molecular modeling tools: SPDBV, Sirius, and macPyMolMolecular Dynamics package: GromacsGenome analysis tools: FASTQ format, SAM tools, and VCF toolsSoftware development tools: SVN, and wikiMicrosoft Office: Word, Excel, and Power PointEXPERIMENTAL EXPERIENCESFrom my BSc and part of my PhD I am familiar with some experimental techniques including: General techniques of genetics and molecular biology laboratories including Cell culture, PCR, RFLP, SSCP, Western blotting, Southern blotting, Gene cloning in prokaryotic systems, and flow cytometry.MANUSCRIPT REVIEWER TO1. Iranian Journal of Medical Hypotheses and Ideas 20072. BMC Genomics 20083. Cancer Letter 20084. The Open Bioinformatics Journal 20085. Neurocomputing 20096. Computers in Biology and Medicine 2009 and 20117. Computer Methods and Programs in Biomedicine 20098. Bioinformatics 20109. BMC Bioinformatics 201010. Iranian Journal of Chemistry & Chemical Engineering (3 Manuscripts) 201011. Amino acids 201112. Fresenius Environmental Bulletin 201113. Scientia Iranica 201114. Theoretical Computer Science 2011PUBLICATIONS (*Corresponding author, and #Equal contribution)1. Samad Jahandideh, Parviz Abdolmaleki*, Mina Jahandideh, and Sayyed Hamed Sadat Hayatshahi. Novel hybrid method for the evaluation of parameters contributing in determination of protein structural classes. Journal of Theoretical Biology, 244( 2) (2007) 275-81.2. Samad Jahandideh, Parviz Abdolmaleki*, Mina Jahandideh, and Ebrahim Barzegari Asadabadi. Sequence and structural parameters enhancing adaptation of proteins to low temperatures. Journal of Theoretical Biology, 246(1) 2007 159-66.3. Samad Jahandideh*, Parviz Abdolmaleki, and Ebrahim Barzegari Asadabadi. Prediction of future citations of a research paper from number of its internet downloads. Medical Hypotheses doi: 10. 1016/j.mehy.(2007).01.007.4. Samad Jahandideh, Parviz Abdolmaleki*, Mina Jahandideh, and Ebrahim Barzegari Asadabadi. Novel two-stage hybrid neural discriminant model for predicting proteins structural classes. Biophysical Chemistry, 128 (2007) 87-93. SELECTED AS TOP TEN HIGHLY CITED PAPER5. Mehdi Pour Sheikh Ali Asgary, Samad Jahandideh, Parviz Abdolmaleki*, and Anoshirvan Kazemnejad. Analysis and prediction of {beta}-turn types using multinomial logistic regression and artificial neural network. Bioinformatics, 23 (2007) 3125-30.6. Samad Jahandideh, Ebrahim Barzegari Asadabadi, Parviz Abdolmaleki, and Mina Jahandideh. Protein psychrophilicity: Role of residual structural properties in adaptation of proteins to low temperatures. Journal of Theoretical Biology, 248(4) (2007) 721-6.7. Samad Jahandideh, Amir Sabet Sabzevari, Parviz Abdolmaleki*, and Mina Jahandideh. γ-turn types prediction in proteins using the Support Vector Machine. Journal of Theoretical Biology, 249(4) (2007) 785-90.8. Mina Jahandideh, Seyyed Mohsen Hosseini Barkooie, Samad Jahandideh, Parviz Abdolmaleki*, Mohammad Mehdi Movahedi, Somayyeh Hoseini, Ebrahim Barzegari Asadabadi, Fatemeh Javani Jouni, Zahra Karami, and Nader Hodjati Firoozabadi. Elucidating the protein cold adaptation: Investigation of the parameters enhancing protein psychrophilicity. Journal of Theoretical Biology, 255 (2008) 113-18.9. Samad Jahandideh,Parviz Abdolmaleki*, and Mohammad Mehdi Movahedi. Prediction of proteins structural class in two states using the hybrid neural-logistic model. Journal of Science (University of Tehran), 33(4) (2007) 27-33.10. Samad Jahandideh*, Somayyeh Hoseini, and Mina Jahandideh. Toward more accuracy in protein structural bioinformatics: Have novel hybrid modeling procedures been born? Journal of Theoretical Biology, 256 (2009) 147.11. Samad Jahandideh*, Mina Jahandideh, Parviz Abdolmaleki, and Somayyeh Hoseini. A hybrid genetic-neural model for predicting protein structural classes. Biologia, 64/4: 649-654, 2009.12. Samad Jahandideh*, Somayyeh Hoseini, Mina Jahandideh, Afsaneh Hoseini, and Ali Salehzadeh Yazdi, Analysis of factors that induce cysteine bonding state, Computers in Biology and Medicine, 39 (2009) 332-33913. Sepideh Jahandideh, Samad Jahandideh*, Ebrahim Barzegari Asadabadi, Mehrdad Askarian, Mohammad Mehdi Movahedi, Somayyeh Hosseini, and Mina Jahandideh, The use of artificial neural networks and multiple linear regression to predict rate of medical waste generation. Waste Management, 2009 29(11):2874-9.14. Lukasz Kurgan*, Ali A Razib, Sara Aghakhani, Scott Dick, Marcin Mizianty, and Samad Jahandideh, CRYSTALP2: sequence-based protein crystallization propensity prediction. BMC structural biology, 31 (2009) 9:50.15. Samad Jahandideh, Parviz Abdolmaleki*, and Mohammad Mehdi Movahedi, Comparing Performances of Logistic Regression and Neural Networks for predicting Melatonin Excretion Patterns in the Rat Exposed to ELF Magnetic Fields. Bioelectromagnetics, 31(2) (2010) 164-71.16. Samad Jahandideh*, Somayyeh Hoseini, Mina Jahandideh, Afsaneh Hoseini, and Fatemeh Miri Disfani, γ-turn types prediction in proteins using the two-stage hybrid neural discriminant model, Journal of Theoretical Biology, 259(3) (2009) 517-22.17. Samad Jahandideh, Parviz Abdolmaleki*, and Mohammad Mehdi Movahedi, Prediction of melatonin excretion patterns in the rat exposed to ELF magnetic fields based on support vector machine and linear discriminant analysis. Micron, 41(7) (2010) 882-5.18. Ebrahim Barzegari Asadabadi, Parviz Abdolmaleki*, Seyyed Mohsen Hosseini Barkooie, Samad Jahandideh, Mohammad Ali Rezaei, Marziyeh Fadaie, and Shahrokh Safarian. A combinatorial feature selection approach to describe the QSAR of dual site inhibitors of acetylcholinesterase, Computers in Biology and Medicine, 39 (2009) 1089–95.19. Abase Mahdavi#, and Samad Jahandideh#,*. Application of Kullback–Leibler information to predict membrane protein types based on pseudo-amino acid composition. Journal of Theoretical Biology, 276 (2011) 132–37.20. Ebrahim Barzegari Asadabadi, Parviz Abdolmaleki, Seyyed Mohsen Hosseini Barkooie, and Samad Jahandideh.A QSAR study of dual site inhibitors of acetylcholinesterase, Journal of Science (University of Tehran), Accepted.21. Esmaeil Behmard, Parviz Abdolmaleki*, Ebrahim Barzegari Asadabadi, and Samad Jahandideh. Prevalent Mutations of Human Prion Protein: A Molecular Modeling and Molecular Dynamics Study. JMSD, 29(2) (2011) 379-89.22. Fatemeh Saberian, and Samad Jahandideh*. Introduction of novel research area in the field of bioelectromagnetics. Bioelectromagnetics newsletter, Published, Sep 2010.23. Sedigheh Mahdavi, Ali Mohades Khorasani, Samad Jahandideh, and Ali Masoudi-Nejad. Recognition Protein-RNA Interaction interfaces via the Voronoi Diagram. JICS., (2010) 7:S1-A6124. Sedigheh Mahdavi, Ali Mohades, Ali Salehzadeh Yazdi, Samad Jahandideh, and Ali Masoudi-Nejad*. Computational Analysis of RNA-Protein Interaction interfaces via the Voronoi Diagram. Journal of Theoretical Biology, (2011) 10;293C:55-6425. Esmaeil Behmard, Parviz Abdolmaleki*, Ebrahim Barzegari Asadabadi, and Samad Jahandideh. Mutation in a valine residue induces drastic changes in 3D structure of human prion protein. Central European Journal of Biology (Accepted).MANUSCRIPTS UNDER REVIEW AND IN PREPARATION1. Samad Jahandideh*, Vinodh Srinivasasainagendra, and Degui Zhi*, Comprehensive comparative analysis and identification of RNA-binding protein domains: multi-class classification and feature selection (Submitted).2- Samad Jahandideh*, and Degui Zhi, Comprehensive computational approaches for studying the effects of nsSNPs in HuPrP gene (In preparation).3- Degui Zhi*, Guillaume Obozinski, Vinodh Srinivasasainagendra, Samad Jahandideh, John-Marc Chandonia, and Steven Brenner. Optimized superfamily signatures for functional classification of proteins (In preparation). CITATION-OVERVIEWREFEREESDr. Degui Zhi, Ph.D., Assistant professor at University of Alabama at Birmingham, Birminghma, AL, Dzhi@ Dr. Lukasz Kurgan, Ph.D., Associate professor at Alberta University, Edmonton, Canada, Lkurgan@ece.ulberta.ca Dr. Ali Akbar Owji, Ph.D., Associate professor at Biochemistry Department, Shiraz Medical School, Shiraz Universityof Medical Sciences, Shiraz, Iran, owjiaa@sums.ac.ir。

嗜肺军团菌mip基因重组质粒GFP-mip的构建及表达惠英华;曹秀琴;杨志伟【摘要】Objective To construct recombinant plasmid GFP - mip of Legionella pneumophila macrophage infectivity potentiator gene and observe its expression in the NIH3T3 cells. Methods The macrophage infectivity potentiator gene was amplified from DNA of Legionella pneumophila by polymerase chain reation ( PCR),then cloned into pEGFP - C1 vector. The recombinant plasmid was named as GFP - mip and was analyzed with restriction endonuclease XhoI and BarnHl digestion, PCR and DNA sequencing techniques. The NIH3T3 cell was transfected by recombinant plasmid GFP - mip with lipofection strategy. The stable expression products of macrophage infectivity petentiator gene were observed by the fluorescent microscope. Results 702bp mip gene was amplified . Under the fluorescent microscope, green fluorescent was observed in the cell cytoplasm and on the cell membrane. Conclusion The recombinant plasmid GFP - mip was constructed successfully and expressed in the NIH3T3 cells.%目的构建嗜肺军团菌mip基因的真核重组质粒GFP-mip,并观察其在NIH3T3细胞中的表达.方法以嗜肺军团菌DNA为模版,通过PCR扩增获得mip基因,将其定向克隆到绿色荧光质粒pEGFP-C1中,构建真核重组质粒GFP-mip.经限制性核酸内切酶XhoI和BamHI酶切鉴定、PCR和核酸序列分析后,通过脂质体法转染到NIH3T3细胞中,利用荧光显微镜观察重组质粒的稳定表达.结果扩增出了702bpmip基因,在细胞质和细胞膜观察到较强绿色荧光.结论成功构建了真核重组质粒GFP-mip,并在NIH3T3细胞中得到了表达.【期刊名称】《宁夏医科大学学报》【年(卷),期】2011(033)002【总页数】5页(P105-107,111,封2)【关键词】嗜肺军团菌;mip基因;GFP-mip;蛋白表达【作者】惠英华;曹秀琴;杨志伟【作者单位】宁夏医科大学基础医学院病原生物学与免疫学教研室,银川,750004;生育力保持省部级共建教育部重点实验室,银川,750004;宁夏医科大学基础医学院病原生物学与免疫学教研室,银川,750004【正文语种】中文【中图分类】R378军团病主要由嗜肺军团菌引起，其中1型感染率约占70%～90%[1]。

所有S C I生物期刊影响因子Ranking? Journal Title? Impact Factor带#者为EI亦收录者1. Biochemical Research Methods （生物化学研究方法）1 Current Opinion In Biotechnology2 Journal Of Chromatography A3 Bioconjugate Chemistry4 Methods In Enzymology5 Applied Immunohistochemistry6 Cytometry7 Acta Crystallographica Section D-Biological Crystallography8 Chromatographia9 Journal Of Immunological Methods10 Analytical Biochemistry#11 Journal Of Molecular Graphics & Modelling12 Biotechniques13 Journal Of Chromatographic Science14 Journal Of Virological Methods15 Journal Of Chromatography B16 Transgenic Research17 Protein Expression And Purification18 Journal Of Neuroscience Methods#19 Journal Of Liquid Chromatography & Related Technologies20 Biomedical Chromatography21 Molecular And Cellular Probes22 Journal Of Microbiological Methods23 Journal Of Labelled Compounds & Radiopharmaceuticals24 Genetic Analysis-Biomolecular Engineering25 Journal Of Biochemical And Biophysical Methods26 Biologicals27 Preparative Biochemistry & Biotechnology28 Hybridoma29 Journal Of Magnetic Resonance2. Biochemistry & Molecular Biology（生物化学与分子生物学）1 Annual Review Of Biochemistry2 Cell3 Nature Medicine4 Annual Review Of Cell And Developmental Biology5 Trends In Biochemical Sciences6 Annual Review Of Plant Physiology And Plant Molecular Biology7 Faseb Journal8 Embo Journal9 Critical Reviews In Biochemistry And Molecular Biology10 Advances In Enzymology And Related Areas Of Molecular Biology11 Nature Structural Biology12 Molecular And Cellular Biology13 Plant Cell14 Annual Review Of Biophysics And Biomolecular Structure15 Advances In Protein Chemistry16 Molecular Biology Of The Cell17 Human Molecular Genetics18 Structure19 Current Opinion In Structural Biology20 Reviews Of Physiology Biochemistry And Pharmacology21 Bioessays22 Journal Of Biological Chemistry23 Oncogene24 Vitamins And Hormones-Advances In Research And Applications25 Gene Therapy26 Rna-A Publication Of The Rna Society27 Progress In Nucleic Acid Research And Molecular Biology28 Chemistry & Biology29 Journal Of Molecular Biology30 Molecular Microbiology31 Cell Death And Differentiation32 Molecular Biology And Evolution33 Journal Of Biomolecular Nmr34 Mole35 Molecular Pharmacology36 Protein Science37 Biochemistry38 Progress In Lipid Research39 Natural Product Reports40 Natural Product Reports41 Journal Of Neurochemistry42 Nucleic Acids Research43 American Journal Of Respiratory Cell And Molecular Biology44 Proteins-Structure Function And Genetics45 Journal Of Lipid Research46 Cell Growth & Differentiation47 British Journal Of Pharmacology48 Biochemical Journal49 Free Radical Biology And Medicine50 Febs Letters51 Progress In Biophysics & Molecular Biology52 Molecular Plant-Microbe Interactions53 Molecular Phylogenetics And Evolution54 Journal Of Molecular Evolution55 European Journal Of Biochemistry56 European Journal Of Human Genetics57 Molecular Ecology58 Drug Discovery Today59 Journal Of Membrane Biology60 Journal Of Structural Biology61 Glycobiology62 Plant Molecular Biology63 Diagnostic Molecular 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Transduction Research128 Steroids129 Journal Of Interferon And Cytokine Research130 Cell Adhesion And Communication131 Biochimie132 Carbohydrate Research133 Transgenic Research134 Journal Of Photochemistry And Photobiology B-Biology135 Molecular And Cellular Biochemistry136 Journal Of Inorganic Biochemistry137 Protein Expression And Purification138 Journal Of Nutritional Biochemistry139 Neurochemical Research140 Folding & Design141 Bulletin De La Societe Chimique De France142 Anti-Cancer Drug Design143 Journal Of Chemical Ecology144 Journal Of Biomolecular Structure & Dynamics145 Cold Spring Harbor Symposia On Quantitative Biology146 Current Topics In Membranes147 Hemoglobin148 Prostaglandins Leukotrienes And Essential Fatty Acids149 Archives Of Insect Biochemistry And Physiology150 Canadian Journal Of Microbiology151 International Journal Of Biochemistry & Cell Biology152 Acta Chemica Scandinavica153 Biomedical Chromatography154 Phytochemistry155 International Journal Of Biological Macromolecules156 Mechanisms Of Ageing And Development157 Clinical Biochemistry158 Somatic Cell And Molecular Genetics159 Annals Of Clinical Biochemistry160 Cellular And Molecular Biology161 Molecular And Cellular Probes162 Fish Physiology And Biochemistry163 Journal Of Carbohydrate Chemistry164 Clinica Chimica Acta165 Journal Of Protein Chemistry166 Pesticide Biochemistry And Physiology167 Bioscience Reports#168 Bioelectrochemistry And Bioenergetics169 Biochemical Society Symposium170 Inflammation171 Journal Of Bioluminescence And Chemiluminescence172 Metal Ions In Biological Systems173 Biochemical And Molecular Medicine174 Comparative Biochemistry And Physiology B-Biochemistry & MolecularBiology175 Bioscience Biotechnology And Biochemistry176 Nucleosides & Nucleotides177 Zeitschrift Fur Naturforschung C-A Journal Of Biosciences#178 Biocatalysis And Biotransformation179 Biotechnology And Applied Biochemistry180 Cell Biochemistry And Function181 Biometals182 European Journal Of Clinical Chemistry And Clinical Biochemistry183 Comparative Biochemistry And Physiology C-Pharmacology Toxicology & Endocri 184 Amino Acids185 Biopharmaceutics & Drug Disposition186 Bioorganic Chemistry187 Process Biochemistry188 Journal Of Food Biochemistry189 Biochemical Society Transactions190 Journal Of Trace Elements In Medicine And Biology191 Biochemical Genetics192 Experimental And Clinical Immunogenetics193 Applied Biochemistry And Biotechnology194 Biological Trace Element Research195 Journal Of Enzyme Inhibition196 Journal De Chimie Physique Et De Physico-Chimie Biologique197 Journal Of Immunoassay198 Mediators Of Inflammation199 Journal Of Biochemical And Biophysical Methods200 Biochemistry And Molecular Biology International201 Biochemical Systematics And Ecology202 Molecular Biology203 Bioorganicheskaya Khimiya204 Preparative Biochemistry & Biotechnology205 Biogenic Amines206 Genes & Genetic Systems207 Research Communications In Molecular Pathology And Pharmacology208 Biochemistry-Moscow209 Molecules And Cells210 Biotherapy211 Biochemical Archives212 Physiological Chemistry And Physics And Medical Nmr213 General Physiology And Biophysics214 Magnesium-Bulletin215 Archives Of Physiology And Biochemistry216 Cellular And Molecular Life Sciences217 Journal Of Peptide Research3. Biology（生物学）1 Faseb Journal2 Bioessays3 Plant Journal4 Biological Reviews Of The Cambridge Philosophical Society5 Quarterly Review Of Biology6 Molecular Phylogenetics And Evolution7 Proceedings Of The Royal Society Of London Series B-Biological Sciences8 Philosophical Transactions Of The Royal Society Of London Series B-Biological Sciences9 Life Sciences10 Molecular And Biochemical Parasitology11 Bioscience12 Journal Of Biological Rhythms13 Journal Of Experimental Biology14 Cladistics-The International Journal Of The Willi Hennig Society15 Journal Of Evolutionary Biology16 Conservation Biology17 Evolutionary Ecology18 Chemico-Biological Interactions19 Journal Of Theoretical Biology20 Polar Biology21 Cold Spring Harbor Symposia On Quantitative Biology22 Microscopy Research And Technique23 Proceedings Of The Japan Academy Series B-Physical And Biological Sciences24 Biological Journal Of The Linnean Society25 Human Biology26 Biological Bulletin27 Zeitschrift Fur Naturforschung C-A Journal Of Biosciences28 Origins Of Life And Evolution Of The Biosphere29 Comptes Rendus De L Academie Des Sciences Serie Iii-Sciences De La Vie-Life30 Biometals31 Annals Of Human Biology32 Biological Rhythm Research33 Biologicals34 Biosystems35 Archives Italiennes De Biologie36 Biotropica37 Folia Biologica38 Annals Of Applied Biology39 Brazilian Journal Of Medical And Biological Research40 Journal Of Biosciences41 Zhurnal Obshchei Biologii42 Journal Of The History Of Biology43 Science In China Series C-Life Sciences44 Proceedings Of The Biological Society Of Washington45 Acta Biotheoretica46 Growth Development And Aging47 Acta Biologica Hungarica48 Izvestiya Akademii Nauk Seriya Biologicheskaya49 Cellular And Molecular Life Sciences50 Theory In Biosciences4. Biology,? Miscellaneous （生物学－其他）1 Trends In Ecology & Evolution2 Molecular Biology And Evolution3 Systematic Biology4 Molecular Phylogenetics And Evolution5 Journal Of Molecular Evolution6 American Naturalist7 Evolution8 Chemical Senses9 Radiation Research10 Evolutionary Biology11 Journal Of Biological Rhythms12 Computer Applications In The Biosciences13 Paleobiology14 International Journal Of Radiation Biology15 Cladistics-The International Journal Of The Willi Hennig Society16 Journal Of Evolutionary Biology17 Conservation Biology18 Theoretical Population Biology19 Biometrika20 Journal Of Theoretical Biology21 American Journal Of Physical Anthropology22 Polar Biology23 Yearbook Of Physical Anthropology24 Cryobiology25 Journal Of Eukaryotic Microbiology26 Development Genes And Evolution27 Bioelectromagnetics28 Journal Of Human Evolution29 Archiv Fur Protistenkunde30 Biological Conservation#31 Bioelectrochemistry And Bioenergetics32 Bulletin Of Mathematical Biology33 Bulletin Of The American Museum Of Natural History34 Metal Ions In Biological Systems35 Human Biology36 Journal Of Radiation Research37 Biometrics38 Journal Of Mathematical Biology39 Origins Of Life And Evolution Of The Biosphere40 Chronobiology International41 Genetics Selection Evolution42 Annals Of Human Biology43 Mathematical Biosciences44 Journal Of Thermal Biology45 Radiation And Environmental Biophysics46 European Journal Of Protistology47 Electro- And Magnetobiology48 Biological Rhythm Research49 Computers In Biology And Medicine50 Biochemical Systematics And Ecology51 Journal Of Natural History52 Cryo-Letters53 Fluoride54 Acta Protozoologica55 Annals Of Applied Biology56 American Midland Naturalist57 Perspectives In Biology And Medicine58 Journal Of The History Of Biology59 Ima Journal Of Mathematics Applied In Medicine And Biology60 Growth Development And Aging61 Natural History62 Biology And Environment-Proceedings Of The Royal Irish Academy5. 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期刊名参考文献格式AAA Style Guide Abad, A., et al.1998 Seventy-two hour epirubicin infusion plusquinidine in unresectable and metastatic adenocarcinomaof the pancreas: a phase II trial. Am J Clin Oncol21(2):151-4.Academy Mannagement Rev Abad, A., Massuti, B., Blanco, E., Carrato, A., Maurel, J., Cervantes, A., Aranda, E., Anton, A., Vicent, J. M.,Dorta, J., Garcia de Paredes, M. L., & Ariza, A. 1998.Seventy-two hour epirubicin infusion plus quinidine inunresectable and metastatic adenocarcinoma of thepancreas: a phase II trial. Am J Clin Oncol, 21(2):151-154.Accounting Review Abad, A., B. Massuti, E. Blanco, A. Carrato, J. Maurel, A.Cervantes, E. Aranda, A. Anton, J. M. Vicent, J. Dorta,M. L. Garcia de Paredes, and A. Ariza. 1998.Seventy-two hour epirubicin infusion plus quinidine inunresectable and metastatic adenocarcinoma of thepancreas: a phase II trial. Am J Clin Oncol21(2):151-154.Accounts ChemicalRes(1) Abad, A.; Massuti, B.; Blanco, E.; Carrato, A.; Maurel, J.; Cervantes, A.; Aranda, E.; Anton, A.; Vicent, J. M.; Dorta, J.; Garcia de Paredes, M. L.; Ariza, A.: Seventy-two hour epirubicin infusion plus quinidine in unresectable and metastatic adenocarcinoma of the pancreas: a phase II trial. American journal of clinical oncology1998, 21, 151-4.Acta Biomaterialia [1] Abad A, Massuti B, Blanco E, Carrato A, Maurel J, Cervantes A, et al. Seventy-two hour epirubicin infusion plus quinidine in unresectable and metastatic adenocarcinoma of the pancreas: a phase II trial. American journal of clinical oncology 1998;21:151-4.Addiction 1. A BAD, A., M ASSUTI, B., B LANCO, E. et al. (1998)Seventy-two hour epirubicin infusion plus quinidine inunresectable and metastatic adenocarcinoma of thepancreas: a phase II trial, Am J Clin Oncol, 21, 151-4.Adv Agronomy Abad, A., Massuti, B., Blanco, E., Carrato, A., Maurel, J., Cervantes, A., Aranda, E., Anton, A., Vicent, J. M.,Dorta, J., Garcia de Paredes, M. L., and Ariza, A. (1998).Seventy-two hour epirubicin infusion plus quinidine in unresectable and metastatic adenocarcinoma of the pancreas: a phase II trial. Am J Clin Oncol21, 151-4.Adv Drug Delivery Rev [1] A. Abad, B. Massuti, E. Blanco, A. Carrato, J. Maurel, A. Cervantes, E. Aranda, A. Anton, J.M. Vicent, J. Dorta, M.L. Garcia de Paredes, A. Ariza, Seventy-two hour epirubicin infusion plus quinidine in unresectable and metastatic adenocarcinoma of the pancreas: a phase II trial, American journal of clinical oncology, 21 (1998) 151-154.Adv Nursing Science 1. Abad A, Massuti B, Blanco E, et al. Seventy-two hourepirubicin infusion plus quinidine in unresectable andmetastatic adenocarcinoma of the pancreas: a phase IItrial. American journal of clinical oncology. Apr1998;21(2):151-154.Adv Skin Wound Care 1.Abad A, Massuti B, Blanco E, et al. Seventy-two hourepirubicin infusion plus quinidine in unresectable andmetastatic adenocarcinoma of the pancreas: a phase IItrial. American journal of clinical oncology. Apr1998;21(2):151-154.Agri Forest Meteorology Abad, A. et al., 1998. Seventy-two hour epirubicin infusion plus quinidine in unresectable and metastatic adenocarcinomaof the pancreas: a phase II trial. Am J Clin Oncol, 21(2):151-4.AIDS 1. Abad A, Massuti B, Blanco E, Carrato A, Maurel J,Cervantes A, et al. Seventy-two hour epirubicin infusionplus quinidine in unresectable and metastaticadenocarcinoma of the pancreas: a phase II trial. Am JClin Oncol 1998,21:151-154.AIDS and Behavior 1. Abad A, Massuti B, Blanco E, et al. Seventy-two hourepirubicin infusion plus quinidine in unresectable andmetastatic adenocarcinoma of the pancreas: a phase IItrial. American journal of clinical oncology. Apr1998;21(2):151-154.Ann Nuclear Part Sci 1. Abad A, Massuti B, Blanco E, Carrato A, Maurel J, et al.1998. American journal of clinical oncology 21:151-4 Abad, A., B. Massuti, et al. (1998). "Seventy-two hourAuthor-Date epirubicin infusion plus quinidine in unresectable andmetastatic adenocarcinoma of the pancreas: a phase IItrial." Am J Clin Oncol 21(2): 151-154.BBA-Reviews onCancer [1] A. Abad, B. Massuti, E. Blanco, A. Carrato, J. Maurel, A. Cervantes, E. Aranda, A. Anton, J.M. Vicent, J. Dorta, M.L. Garcia de Paredes, A. Ariza, Seventy-two hour epirubicin infusion plus quinidine in unresectable and metastatic adenocarcinoma of the pancreas: a phase II trial, American journal of clinical oncology, 21 (1998) 151-154.Biochemical Biophysical Res [1] A. Abad, B. Massuti, E. Blanco, A. Carrato, J. Maurel, A. Cervantes, E. Aranda, A. Anton, J.M. Vicent, J. Dorta, M.L. Garcia de Paredes, A. Ariza, Seventy-two hour epirubicin infusion plus quinidine in unresectable and metastatic adenocarcinoma of the pancreas: a phase II trial, Am J Clin Oncol 21 (1998) 151-154.Biochemistry 1. Abad, A., Massuti, B., Blanco, E., Carrato, A., Maurel,J., Cervantes, A., Aranda, E., Anton, A., Vicent, J. M.,Dorta, J., Garcia de Paredes, M. L., and Ariza, A. (1998)Seventy-two hour epirubicin infusion plus quinidine inunresectable and metastatic adenocarcinoma of thepancreas: a phase II trial, American journal of clinicaloncology21, 151-154.BMC Biotechnology 1. Abad A, Massuti B, Blanco E, Carrato A, Maurel J,Cervantes A, Aranda E, Anton A, Vicent JM, Dorta J etal: Seventy-two hour epirubicin infusion plusquinidine in unresectable and metastaticadenocarcinoma of the pancreas: a phase II trial.American journal of clinical oncology 1998,21(2):151-154.BMC Cell Biology 1. Abad A, Massuti B, Blanco E, Carrato A, Maurel J,Cervantes A, Aranda E, Anton A, Vicent JM, Dorta J etal: Seventy-two hour epirubicin infusion plusquinidine in unresectable and metastaticadenocarcinoma of the pancreas: a phase II trial.American journal of clinical oncology 1998,21(2):151-154.BMC EvolutionaryBiology 1. Abad A, Massuti B, Blanco E, Carrato A, Maurel J,Cervantes A, Aranda E, Anton A, Vicent JM, Dorta J etal: Seventy-two hour epirubicin infusion plusquinidine in unresectable and metastaticadenocarcinoma of the pancreas: a phase II trial. American journal of clinical oncology 1998, 21(2):151-154.BMC Structural Biology 1. Abad A, Massuti B, Blanco E, Carrato A, Maurel J,Cervantes A, Aranda E, Anton A, Vicent JM, Dorta J etal: Seventy-two hour epirubicin infusion plusquinidine in unresectable and metastaticadenocarcinoma of the pancreas: a phase II trial.American journal of clinical oncology 1998,21(2):151-154.Cancer Cell Abad, A., Massuti, B., Blanco, E., Carrato, A., Maurel, J., Cervantes, A., Aranda, E., Anton, A., Vicent, J. M., Dorta, J., et al. (1998). Seventy-two hour epirubicin infusion plus quinidine in unresectable and metastatic adenocarcinoma of the pancreas: a phase II trial. American journal of clinical oncology21, 151-154.Cancer Cell International 1. Abad A, Massuti B, Blanco E, Carrato A, Maurel J,Cervantes A, Aranda E, Anton A, Vicent JM, Dorta J etal: Seventy-two hour epirubicin infusion plusquinidine in unresectable and metastaticadenocarcinoma of the pancreas: a phase II trial.American journal of clinical oncology 1998,21(2):151-154.Cell Abad, A., Massuti, B., Blanco, E., Carrato, A., Maurel, J., Cervantes, A., Aranda, E., Anton, A., Vicent, J.M., Dorta, J., et al. (1998). Seventy-two hour epirubicin infusion plus quinidine in unresectable and metastatic adenocarcinoma of the pancreas: a phase II trial. American journal of clinical oncology21, 151-154.Cell and Chromosome 1. Abad A, Massuti B, Blanco E, Carrato A, Maurel J,Cervantes A, Aranda E, Anton A, Vicent JM, Dorta J etal: Seventy-two hour epirubicin infusion plusquinidine in unresectable and metastaticadenocarcinoma of the pancreas: a phase II trial.American journal of clinical oncology 1998,21(2):151-154.Chemical Society Reviews 1. A. Abad, B. Massuti, E. Blanco, A. Carrato, J. Maurel, A. Cervantes, E. Aranda, A. Anton, J. M. Vicent, J. Dorta, M. L.Garcia de Paredes and A. Ariza, American journal of clinical oncology, 1998, 21, 151-154.Computational Intelligence A BAD, A., B. M ASSUTI, E. B LANCO, A. C ARRA TO, J. M AUREL, A.C ERV ANTES, E. A RANDA, A. A NTON, J. M. V ICENT, J.D ORTA, M. L. G ARCIA DE P AREDES and A. A RIZA. 1998.Seventy-Two Hour Epirubicin Infusion Plus Quinidine inUnresectable and Metastatic Adenocarcinoma of thePancreas: A Phase Ii Trial. Am J Clin Oncol, 21:151-4.Current OpinionLipid [1] Abad A, Massuti B, Blanco E et al.Seventy-two hour epirubicin infusion plus quinidine in unresectable and metastatic adenocarcinoma of the pancreas: a phase II trial. American journal of clinical oncology 1998; 21:151-154.。

基于序列及结构特征的固有无序蛋白—核酸相互作用位点预测分析王洪波;郭珍珍;于家峰;王吉华【摘要】固有无序蛋白是一类具有柔性结构的蛋白质,许多情况下通过与其它物质相互作用形成稳定结构来发挥重要生物功能.本文分别利用基于序列特征和结构特征的蛋白质结合位点预测程序对固有无序蛋白有序区和无序区与核酸分子的结合位点进行了预测分析.结果发现,基于结构特征的结合位点预测方法整体上要优于基于序列特征的预测方法,表明无序区尽管缺少稳定空间结构,结构特征依然在固有无序蛋白结合位点中发挥了重要作用.因此,可以为今后固有无序蛋白序列特征及结构特征的提取提供可靠依据.【期刊名称】《德州学院学报》【年(卷),期】2014(030)002【总页数】5页(P6-10)【关键词】固有无序蛋白;序列特征;结构特征;结合位点预测【作者】王洪波;郭珍珍;于家峰;王吉华【作者单位】山东省功能大分子生物物理重点实验室,德州学院生物物理研究所,山东德州 253023;德州学院物理与电子信息学院,山东德州 2530023;山东师范大学生命科学学院,济南 250014;山东省功能大分子生物物理重点实验室,德州学院生物物理研究所,山东德州 253023;山东省功能大分子生物物理重点实验室,德州学院生物物理研究所,山东德州 253023;山东省功能大分子生物物理重点实验室,德州学院生物物理研究所,山东德州 253023;德州学院物理与电子信息学院,山东德州2530023【正文语种】中文【中图分类】Q511 引言固有无序蛋白（IDPs）是指在生理条件下不具有稳定的三维结构，但能够正常行使功能的一类蛋白质，它的发现是对蛋白质序列－结构－功能传统观念的挑战［1，2］.由于IDPs在生物体内广泛存在，且具有重要功能，参与细胞中多种生理和病理活动［3，4］，受到越来越多的关注.IDPs可以通过与核酸相互作用行使功能，相互作用时的结合位点的研究变得具有重要的生物学意义.对于蛋白质结合位点有很多蛋白质结合位点预测软件可以进行预测，这些预测软件主要基于蛋白质的序列特征或者结构特征［5］对蛋白质结合位点进行预测.由于固有无序蛋白的序列分为有序区和无序区［6］，且研究表明无序区在序列特征上明显区别于有序区，因而人们在对IDPs的结合位点进行预测时更加关注IDPs的序列信息，例如根据IDPs 序列的氨基酸组成特征进行结合位点的预测［7］.但是由于无序区没有稳定的三维结构，基于IDPs结构特征的结合位点预测算法还少有报道，也少有软件考虑到无序区和有序区的区别分别进行预测.本文主要收集能够与核酸（DNA和RNA）结合的固有无序蛋白，分别利用基于序列特征和结构特征的蛋白质结合位点预测程序，对其有序区和无序区与核酸分子的结合位点进行预测分析，从而挖掘适合对固有无序蛋白结合位点进行预测的特征，为结合残基预测算法的进一步发展提供帮助以及数据支持.2 材料和方法2.1 数据集Disprot［8］是专门收集固有无序蛋白的数据库，本文统计所用的6.01版本含有684条固有无序蛋白以Disprot为基础，从PDB［9］中提取结构由X射线晶体衍射方法测得的固有无序蛋白与DNA、RNA复合物结构，且分辨率不低于3.5埃.然后利用在线去冗余软件PISCES［10］，相似度阈值设为25%，对得到的与复合物对应的固有无序蛋白序列去冗余，构建出IDPs－DNA25和IDPs－RNA11两个数据集.然后根据DisProt中提供的有序区与无序区的信息，构建有序区－DNA21、无序区－DNA12、有序区－RNA5、无序区－RNA9四个数据子集.通常按照距离阈值法［11，12］定义固有无序蛋白结合复合物的结合残基，即IDPs序列的氨基酸残基，其原子与作用物中的任何一个原子间的距离不大于3.5埃，就认为这个氨基酸为结合残基，否则为非结合残基.根据这种方法，在两个大数据集中分别得到372、240个结合残基和4770、1418个非结合残基.本文即以这些结合残基为基础对预测算法的结果进行比对统计.2.2 预测算法根据构建的IDPs－DNA和IDPs－RNA数据集的不同，分别选择四种蛋白质结合位点预测算法针对每一个数据集进行预测，而且每四种预测算法中分别含有两个以序列特征为基础的预测算法以及两个以结构特征为基础的预测算法（见表1）.表1 蛋白质－DNA以及蛋白质－RNA结合残基预测算法DBS－PSSM［13］Sequence－based；neural network based；evolutionary information 序列特征蛋白质－DNA BindN＋［14］ Sequence－based；biochemical feature；evolutionary information；SVMs 序列特征DISPLAR［15］ Structural and physical properties；3Dstructure based 结构特征DBD－Threader［5］Threading－based method；fold similarity and DNA－binding propensity；protein templates结构特征Pprint［16］ PSSM；orthogonal binary vectorinformation 序列特征序列特征SPOT2［18］ Structural based；structural alignment；结构特征RNABindR V2.0［19］Structural information；SVM；PSSM 结构特征SPOT1［17］ Sequence－based；protein templates蛋白质－RNA2.3 评价预测结果的参数对于以上预测算法得到的预测结果，采用通用的评价参数［14］Accuracy （Acc）、Sensitivity（Se）、Specificity（Sp）、Strength（St）、F－measure（Fm）和MCC进行评价.Acc指总的预测正确的氨基酸的比例.TP表示正确预测的结合残基的数目；TN表示正确预测的非结合残基的数目；FP表示错误预测的结合残基的数目；FN表示错误预测的非结合残基的数目.Se和Sp分别表示结合残基中预测正确的比例和非结合残基中预测正确的比例.Strength、F－measure和MCC属于综合指标，是对敏感性和特异性的权衡.其中MCC取值在－1到1之间，相对于Se和Sp来说，是一个更加严谨的标准，过高和过低的预测都是会导致MCC值的降低.如果MCC＝1是一个最优的预测，若MCC＝－1则是一个完全相反的预测.3 结果和讨论3.1 蛋白质－DNA结合位点预测算法结果分析DBS－PSSM和BindN＋都以序列特征为基础，两种方法都采用了进化保守性信息，BindN＋与DBS－PSSM相比还增加了结合残基的理化信息.DBD－Threader 是选取了一些已知结合位点的蛋白质结合复合物作为模版与未知蛋白复合物的结构进行比对，从而预测出结合位点.DISPLAR是采用蛋白质结构上和物理上的特性进行结合位点的预测.从图1的预测结果可以看到：1）在蛋白质－DNA结合位点预测方面有序区的预测结果和无序区的预测结果存在明显差异，这表明由于无序区在结构和序列上都不同于有序区，预测软件所基于的序列和结构特征并不一定符合无序区结合位点的特征.2）对有序区来说，四种预测方法的结果差别不大，说明有序区序列、结构和结合位点具有一定的保守性，符合一般蛋白质的特性，较符合结合位点预测软件所基于的特征.但是BindN＋、DBS－PSSM和DBD－Threader的MCC值较小，还有很大的提升空间.3）从无序区结果来看，DBD－Threader和DISPLAR显著优于BindN＋和DBS－PSSM.而且BindN＋和DBS－PSSM的MCC值都不到0.3，说明无序区在序列特征上不同于有序区，对于无序区一般以进化保守性信息等序列特征为基础的预测算法不太适合无序区；尽管无序区没有稳定的三维结构，但结构上也具有二级结构等特征，而且结构特征在无序区的结合位点方面依然起到重要作用，以结构特征为基础的预测软件相比取得的效果较好.图1 比较4种蛋白质－DNA结合位点预测软件对与DNA相互作用的无序区和有序区的预测结果3.2 蛋白质－RNA结合位点预测算法结果分析SPOT算法是对不同类型的蛋白质设计模板，在预测时将未知蛋白与模板蛋白先进行匹配，然后再预测.Pprint算法是通过PSI－BLAST比对一些有结合位点的蛋白质得到的序列信息进行预测.RNABindR V2.0根据自己数据库内的三个具有结合位点的蛋白质数据集得到的结构信息进行预测.从图2中可以看出：1）在蛋白质－RNA结合位点预测方面有序区跟无序区的预测结果也存在明显差异，有序区结果的差异性也小于无序区的预测结果.2）Pprint 和RNABindR V2.0对有序区和无序区结合残基的预测结果都不理想，MCC值都很低，尤其是对无序区的预测结果可靠性不高，两种算法有待改进.3）SPOT的两种算法取得的结果都较好.在有序区中SPOT1和SPOT2结果相差不大，而在无序区中，SPOT2的结果明显好于SPOT1，再次说明无序区的结构特征在结合位点方面起到重要的作用，对无序区进行结合位点的预测时，结构特征相比更有作用.图2 比较4种蛋白质－RNA结合位点预测软件对与RNA相互作用的无序区和有序区的预测结果为了对基于序列特征以及结构特征的蛋白质结合位点预测软件的结果进行量化比较，本文做了蛋白质－DNA以及蛋白质－RNA结合残基预测算法结果的六个参数的平均值（表2），从中可以看出以结构特征为基础的预测算法要明显优于以序列特征为基础的预测算法.表2 蛋白质－DNA以及蛋白质－RNA结合残基预测算法结果的六个参数的平均值序列特征 82 44 85 65 57 0.2312无序区蛋白质－DNA有序区结构特征 89 79 90 85 84 0.5297序列特征 84 66 85 76 74 0.3250结构特征 92 5294 73 66 0.4036序列特征 68 79 65 72 70 0.3958无序区蛋白质－RNA有序区结构特征 74 87 70 79 76 0.5344序列特征 88 82 88 82 85 0.4850结构特征 84 86 84 81 85 0.49724 结论分别利用基于序列特征以及基于结构特征的蛋白质结合位点预测算法对固有无序蛋白与核酸相互作用位点进行了预测分析，发现两种类型的算法对有序区和无序区的预测结果有差异，而且两类算法对有序区的预测结果相差不大，表明这些算法基于的特征在一定程度上都符合有序区的特征.但在无序区的结合位点预测方面，基于结构特征的结合位点预测方法整体上要优于基于序列特征的预测方法，表明无序区尽管缺少稳定空间结构，但结构特征依然在固有无序蛋白结合位点中发挥重要作用；对无序区结合位点预测时，应适当考虑结构特征的影响.因此，本文可以为今后固有无序蛋白序列特征及结构特征提取提供可靠依据.随着实验技术的发展以及数据库内的IDPs数量的增多，可以发现更多固有无序蛋白结合位点的特征，促进IDPs结合位点预测算法的发展以及固有无序蛋白的研究，进而为关于固有无序蛋白的疾病的药物开发等提供帮助.参考文献：［1］Uversky VN，Dunker AK.Understanding protein non－folding ［J］.Biochimica et Biophysica Acta（BBA）－Proteins and Proteomics，2010，1804（6）：1231－1264.［2］黄永棋，刘志，荣鄢.天然无序蛋白质：序列－结构－功能的新关系［J］.物理化学学报，2010，26.［3］曹赞霞，王吉华.促进或抑制α－synuclein蛋白异常聚集的相互作用蛋白质［J］.生物物理学报，2010，26（9）.［4］郭珍珍，朱玉风，王吉华.固有无序蛋白质－DNA复合物结合位点处核苷酸偏好性分析［J］.德州学院学报，2013，29（2）：50－53.［5］Gao M，Skolnick J.A threading－based method for the prediction of DNA－binding proteins with application to the human genome［J］.PLoS computational biology，2009，5（11）：e1000567.［6］Fukuchi S，Hosoda K，Homma K，etal.Binary classification of protein molecules into intrinsically disordered and ordered segments［J］.BMC structural biology，2011，11（1）：29.［7］Goodman R C，Beaty T L.Prediction of Binding Sites on Intrinsically Disordered Proteins［J］.Biophysical Journal，2011，100（3Supplement 1）.［8］Sickmeier M，Hamilton JA，LeGall T，.DisProt：the database ofdisordered proteins［J］.Nucleic acids research，2007，35（suppl 1）：D786－D793.［9］Bernstein FC，Koetzle TF，Williams GJ..The protein data bank ［J］.European Journal of Biochemistry，1977，80（2）：319－324. ［10］Wang G，Dunbrack RL，Jr..PISCES：aprotein sequence culling server［J］.Bioinformatics，2003，19（12）：1589－1591.［11］Ofran Y，Rost B.Predicted protein－protein interaction sites from local sequence information［J］.FEBS Lett，2003，544（1－3）：236－239. ［12］Wu J，Liu H，Duan X..Prediction of DNA－binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature.Bioinformatics，2009，25（1）：30－35.［13］Ahmad S，Sarai A.PSSM－based prediction of DNA binding sites in proteins［J］.BMC bioinformatics，2005，6（1）：33.［14］Wang L，Huang C，Yang MQ.BindN＋for accurate prediction of DNA and RNA－binding residues from protein sequence features［J］.BMC Syst Biol，2010，4 Suppl 1：S3.［15］Tjong H，Zhou HX.DISPLAR：an accurate method for predicting DNA－binding sites on protein surfaces［J］.Nucleic Acids Res，2007，35（5）：1465－1477.［16］Kumar M，Gromiha M M，Raghava G P S.Prediction of RNA binding sites in a protein using SVM and PSSM profile［J］.Proteins：Structure，Function，and Bioinformatics，2008，71（1）：189－194.［17］Zhao H，Yang Y，Zhou Y.Highly accurate and high－resolution function prediction of RNA binding proteins by fold recognition andbinding affinity prediction［J］.RNA Biol，2011，8（6）：988－996. ［18］Zhao H，Yang Y，Zhou Y.Structure－based predic－tion of RNA－binding domains and RNA－binding sites and application to structural genomics targets［J］.Nucleic acids research，2011，39（8）：3017－3025.［19］Terribilini M，Sander J D，Lee J H，et al.RNABindR：a server for analyzing and predicting RNA－binding sites in proteins［J］.Nucleic acids research，2007，35（suppl 2）：W578－W584.。

当你了解这些事儿，投BMC就不会被退回希希公主Biomed Central简称为BMC，是一家世界领先的科技期刊出版集团，出版范围覆盖生物医学、生命科学、医学教育、公共卫生、化学、工程、环境、材料科学、数学等多学科。

BMC出版集团Guideline中目前有182份,其中直接以BMC命名的杂志有67份，影响因子最高的是Genome biology（IF2015:11.313），BMC命名的杂志中目前影响因子最高的是BMC Medicine（IF2015:8.005）。

开放获取（Open Access，简称OA）服务是其主要特色。

BMC在2008年被著名的Spring 出版集团收购，但是BMC系列的杂志在2014年前都采用自己的投稿系统Biomed Central系统，在2015年慢慢过渡到采用Spring的投稿系统Editorial Manager投稿，而投稿的一些格式还是沿用了BMC自己的特色。

BMC系列的杂志投稿时，杂志社很注重格式，如果不完全按照杂志社的稿约准备文稿的话，基本上都会被杂志社退回要求修改了再投。

下面我们就来聊一聊BMC杂志投稿需要注意的一些细节格式问题。

武汉美捷登生物科技有限公司电话：400-640-2600（周一至周六08:30 - 20:00）内地总部地址：武汉市江岸区中山大道岳飞街21号金源世界中心D座1201-1203室网上稿件处理系统：:8080/电邮：Main text 五部分结构，分别是Background、三部分结构，分别是Background,涉及人体试验的话，还需要有病人或者监护人的知情同意书。

这些内容在正文的方法部分需要进行陈述。

如果有这些证明文件，可以这样表述：The experimental protocol was established, according to the ethical guidelines of the Helsinki Declaration and was approved by the Human Ethics Committee of XXX(单位伦理委员会的名字). Written informed consent was obtained from individual or guardian participants.Consent for publication:同意发表声明如果本文中任何个人或者任何人的某数据需要得到他人的同意才能发表的话，都需要先取得他人的同意后，再在这里声明。

海南省转基因木瓜非法种植调查报告1.调查背景绿色和平于2009年2月至3月间，随机对超市所销售木瓜的转基因成分检测发现：国产木瓜均为转基因木瓜。

根据农业部转基因生物安全管理办公室公布的信息[1]，农业部于2006年批准了华南农业大学研发的抗木瓜环斑病毒转基因木瓜，而该品种只被允许在广东省商业化种植，审批号为农基安证字（2006）第001号，有效期为2006年7月20日至2011年7月20日。

所以，如果这些转基因木瓜确实来自于广东省以外的地区，那么就意味存在非法种植的情况。

因此，绿色和平决定在海南的木瓜种植基地进行实地采样并做转基因成分检测，以了解是否存在转基因木瓜的非法种植情况。

2.调查结果绿色和平于2009年2月至3月间，在北京、上海、广东和香港四个地区购买了木瓜样品，送至独立的国际权威检测机构进行转基因成分检测。

结果显示，各地所销售的国产木瓜均为转基因木瓜，仅有沃尔玛超市北京知春路分店所销售的菲律宾进口木瓜为非转基因木瓜。

详细情况见下表1。

表1：京沪穗港四地木瓜转基因成分检测结果检测结果采样地点采样时间原产地（据商品标签或超市员工介绍）易初莲花，广州三元里店2009-02-14 广东阳性华润万家，深圳华强北店2009-02-15 广东阳性沃尔玛，深圳华侨城店2009-02-15 广东阳性沃尔玛，北京知春路分店2009-03-05 菲律宾进口阴性易初莲花，上海船厂路店2009-03-21 福建阳性沃尔玛，上海五角场店2009-03-21 海南阳性易初莲花，北京成府路店2009-03-24 海南阳性华润万家，北京知春路分店2009-03-24 不确定阳性沃尔玛，北京知春路分店2009-03-24 海南阳性自由市场，香港马鞍山2009-03-26 中国内地阳性百佳超市，香港马鞍山分店2009-03-26 中国内地阳性自由市场，香港旺角2009-03-26 中国内地阳性百佳超市，香港旺角分店2009-03-26 中国内地阳性注：检测结果“阳性”表示该样品含转基因成分为了解广东省以外地区是否存在非法种植转基因木瓜的情况，绿色和平于2009年4月，在海南三亚市与海南乐东黎族自治县的农场进行实地取样，送至独立的国际权威检测机构进行转基因成分检测。

S C I以及S S C I收录的O p e n A c c e s s J o u r n a l开源刊物清单公司标准化编码 [QQX96QT-XQQB89Q8-NQQJ6Q8-MQM9N]The Thomson Reuters Links Open Access Journal Title List Journals starting with AANDISSN NAME EISSN 1085-3375Abstract and Applied Analysis1012-8255Academia-Revista Latinoamericana deAdministracion0001-5113ACTA ADRIATICA0717-5906Acta Bioethica0325-2957ACTA BIOQUIMICA CLINICA LATINOAMERICANA0102-3306Acta Botanica Brasilica0365-0588ACTA BOTANICA CROATICA0187-7151Acta Botanica MexicanaJournals starting with BANDISSN NAME EISSN1224-2780 Balkan Journal of Geometry and Its Applications1311-0160Balkan Journal of Medical Genetics0067-3064Baltica1028-2092Bangladesh Journal of Plant Taxonomy1744-9081Behavioral and Brain Functions1860-5397Beilstein Journal of Organic Chemistry0006-0887BIBLICA0327-9545BIOCELL1330-0962Biochemia Medica1726-BiogeosciencesJournals starting with CANDISSN NAME EISSN 0007-9235CA-A CANCER JOURNAL FOR CLINICIANS0366-5232CALDASIA0008-0845CALIFORNIA AGRICULTURE0318-6431 CANADIAN JOURNAL OF SOCIOLOGY-CAHIERS CANADIENS DE SOCIOLOGIE1475-2840Cardiovascular Diabetology1476-7120Cardiovascular Ultrasound0008-6452CARIBBEAN JOURNAL OF SCIENCE1931-7913CBE-Life Sciences Education0386-7196CELL STRUCTURE AND FUNCTION1538-6279CENTRO JOURNAL0862-5468CERAMICS-SILIKATY0104-7760Cerne0011-3891CURRENT SCIENCE1212-1975Czech Journal of Genetics and Plant Breeding Results returned: 55ANDISSN NAME EISSN 0011-5258DADOS-REVISTA DE CIENCIAS SOCIAIS1560-8115DARU-JOURNAL OF FACULTY OF PHARMACY1435-9871Demographic Research1641-1307Dendrobiology1866-0452Deutsches Arzteblatt International1305-3825Diagnostic and Interventional Radiology1746-1596Diagnostic Pathology1026-0226DISCRETE DYNAMICS IN NATURE AND SOCIETY1340-2838DNA RESEARCH1431-0643Documenta Mathematica1347-4367Drug Metabolism and Pharmacokinetics0012-7086DUKE LAW JOURNAL0012-7361Dyna0012-7353Dyna-ColombiaResults returned: 14ANDISSN NAME EISSN 1794-6190Earth Sciences Research Journal1708-3087ECOLOGY AND SOCIETY1864-6042Economics-The Open Access Open-Assessment E-Journal1436-4522EDUCATIONAL TECHNOLOGY & SOCIETYJournals starting with FANDISSN NAME EISSN FIBRES & TEXTILES IN EASTERN EUROPE1230-36660354-Filomat5180Filozofska Istrazivanja0351-47060090-FISHERY BULLETIN0656Fixed Point Theory and Applications1687-1820FLORIDA ENTOMOLOGIST0015-4040TitleJournals starting with GANDISSN NAME EISSN Gaceta Sanitaria0213-9111GAYANA BOTANICA0016-53011341-GENES & GENETIC SYSTEMS7568GENETICS AND MOLECULAR BIOLOGY1415-4757GENETICS AND MOLECULAR RESEARCH1676-5680Genetika-Belgrade0534-00121467-GEOCHEMICAL TRANSACTIONS4866Geodetski Vestnik0351-02711280-GEODIVERSITAS96590016-Geofisica Internacional71690352-Geofizika36591695-6133GEOLOGICA ACTA1811-4598GEOLOGICAL SURVEY OF DENMARK AND GREENLANDBULLETIN1405-1079Gestion y Politica Publica0017-1557GOLD BULLETIN0017-3495GRASAS Y ACEITESResults returned: 16TitleJournals starting with HANDISSN NAME EISSN1027-5606HYDROLOGY AND EARTH SYSTEM SCIENCES1433-5158HYLEResults returned: 16TitleJournals starting with IANDISSN NAME EISSN 1139-7241Iberica0120-0062Ideas y Valores0377-2063IETE JOURNAL OF RESEARCHJournals starting with JANDISSN NAME EISSN 1344-6304JAPANESE JOURNAL OF INFECTIOUS DISEASES0304-1042JAPANESE JOURNAL OF RELIGIOUS STUDIES1460-7425 JASSS-THE JOURNAL OF ARTIFICIAL SOCIETIES AND SOCIAL SIMULATION1806-3713Jornal Brasileiro de Pneumologia0021-7557Jornal de Pediatria1583-0039 JOURNAL FOR THE STUDY OF RELIGIONS AND IDEOLOGIES1680-5593Journal of Animal and Veterinary Advances1214-0287Journal of Applied Biomedicine1526-9914Journal of Applied Clinical Medical Physics0916-7250JOURNAL OF VETERINARY MEDICAL SCIENCE1534-7362JOURNAL OF VISION1930-2975Judgment and Decision Making1176-5119Junctures-The Journal for Thematic DialogueResults returned: 83Journals starting with KANDISSN NAME EISSN 1731-5530Kardiochirurgia i Torakochirurgia Polska0022-9032Kardiologia Polska1017-KLINIK PSIKOFARMAKOLOJI BULTENI-BULLETIN OF7833 CLINICAL PSYCHOPHARMACOLOGY0023-4001KOREAN JOURNAL OF PARASITOLOGY1229-6929KOREAN JOURNAL OF RADIOLOGY1340-6116Kyushu Journal of MathematicsResults returned: 6Journals starting with LANDISSN NAME EISSN 1094-3501LANGUAGE LEARNING & TECHNOLOGY0327-LATIN AMERICAN APPLIED RESEARCHJournals starting with LANDISSN NAME EISSN 1094-3501LANGUAGE LEARNING & TECHNOLOGY0327-0793LATIN AMERICAN APPLIED RESEARCH1679-7817 Latin American Journal of Solids and Structures0023-9186LAW AND CONTEMPORARY PROBLEMS0305-7518LEPROSY REVIEW0862-8432Linguistica Pragensia0868-4731Linguistica Uralica1433-8351Living Reviews in Relativity1846-5412Ljetopis Socijalnog Rada1860-5974Logical Methods in Computer Science Results returned: 10Journals starting with MANDISSN NAME EISSN1857-5552 Macedonian Journal of Chemistry and Chemical engineering0717-3644Maderas-Ciencia y Tecnologia1905-7873 Maejo International Journal of Science and Technology0718-0209Magallania1475-2875MALARIA JOURNAL0104-Mana-Estudos de Antropologia SocialJournals starting with NANDISSN NAME EISSN Nanoscale Research Letters1931-7573NATURAL HAZARDS AND EARTH SYSTEM SCIENCES1561-8633NEOPLASIA1522-8002Neotropical Ichthyology1679-6225Neural Development1749-8104NEURAL PLASTICITY0792-8483NEUROCIRUGIA1130-14730470-NEUROLOGIA MEDICO-CHIRURGICAResults returned: 21Journals starting with OANDISSN NAME EISSN 1812-0784Ocean Science0078-3234OCEANOLOGIA1294-4475OIL & GAS SCIENCE AND TECHNOLOGY-REVUE DE LINSTITUT FRANCAIS DU PETROLE0078-5466OPTICA APPLICATA1094-4087OPTICS EXPRESS1750-1172Orphanet Journal of Rare Diseases0030-6126OSAKA JOURNAL OF MATHEMATICSResults returned: 7Journals starting with PANDISSN NAME EISSN 1533-3159Pain Physician0556-3321PAKISTAN JOURNAL OF BOTANY0253-8318PAKISTAN VETERINARY JOURNAL。

Nature Communications 10.742，综合：一区，12.124Nucleic Acid Research 8.808，生物：一区；10.162Scientific Reports 5.078，综合类：二区，4.259Methods 3.221，生物，二区，3.802BMC Systems Biology 2.853，生物：3区，2.003Journal of Biomedical informatics 2.482，医学：3区；2.753Journal of Computational Biology 1.670，生物：四区；1.0320.931，生物：四区；0.800 Journal of Bioinformatics and Computational Biology 0.931Journal of Theoretical Biology1.833 生物、数学与计算生物学三区Journal of Mathematical Biology 1.786 生物4区数学与计算生物学3区Bioinformatics (IF: 4.328)BMC Bioinformatics (IF: 3.781)，生物：三区；2.448BMC Biology (IF: 4.734)，生物：一区；6.779Briefings in Bioinformatics (IF: 4.627)，生物：一区；5.134Journal of Computational Biology (IF: 1.563)，生物：四区；1.032PLoS Computational Biology (IF: 5.895)，生物：二区，2.542 Mathematical Biosciences (IF: 1.148)，生物：四区；1.246Journal of Biomedical Informatics (IF: 1.924)，医学：三区；2.753，生物：三区；2.781Molecular Biosystems ( IF: 4.236)，生物：三区；Frontiers in Genetics 4.151 生物二区生物：二区，微生物3区Microbial Ecology 3.614 生物：二区，微生物Frontiers in Microbiology4.019生物、微生物2区Frontiers in Cellular and Infection Microbiology3.520医学、微生物2区Research in Microbiology 2.372 生物、微生物3区。