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1

Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art

Rasna R Walia, Cornelia Caragea, Benjamin A Lewis, Fadi Towfic, Michael Terribilini, Yasser El-Manzalawy, Drena Dobbs, Vasant Honavar

Journal:

BMC Bioinformatics

Year:

2012

Language:

english

File:

PDF, 820 KB

english, 2012

2

Predicting linear B-cell epitopes using string kernels

Yasser EL-Manzalawy, Drena Dobbs, Vasant Honavar

Journal:

Journal of Molecular Recognition

Year:

2008

Language:

english

File:

PDF, 543 KB

english, 2008

3

Three-dimensional threading approach to protein structure recognition

Haibo Cao, Yungok Ihm, Cai-Zhuang Wang, James R. Morris, Mehmet Su, Drena Dobbs, Kai-Ming Ho

Journal:

Year:

2004

Language:

english

File:

PDF, 607 KB

english, 2004

4

Automated data-driven discovery of motif-based protein function classifiers

Xiangyun Wang, Diane Schroeder, Drena Dobbs, Vasant Honavar

Journal:

Information Sciences

Year:

2003

Language:

english

File:

PDF, 194 KB

english, 2003

5

HomPPI: a class of sequence homology based protein-protein interface prediction methods

Li C Xue, Drena Dobbs, Vasant Honavar

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 3.01 MB

english, 2011

6

ZFNGenome: A comprehensive resource for locating zinc finger nuclease target sites in model organisms

Deepak Reyon, Jessica R Kirkpatrick, Jeffry D Sander, Feng Zhang, Daniel F Voytas, J Keith Joung, Drena Dobbs, Clark R Coffman

Journal:

Year:

2011

Language:

english

File:

PDF, 1.03 MB

english, 2011

7

Identification of interface residues in protease-inhibitor and antigen-antibody complexes: a support vector machine approach

Changhui Yan, Vasant Honavar, Drena Dobbs

Journal:

Neural Computing and Applications

Year:

2004

Language:

english

File:

PDF, 1.57 MB

english, 2004

8

Characterization of Protein–Protein Interfaces

Changhui Yan, Feihong Wu, Robert L. Jernigan, Drena Dobbs, Vasant Honavar

Journal:

The Protein Journal

Year:

2008

Language:

english

File:

PDF, 966 KB

english, 2008

9

Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly

Wright, David A, Thibodeau-Beganny, Stacey, Sander, Jeffry D, Winfrey, Ronnie J, Hirsh, Andrew S, Eichtinger, Magdalena, Fu, Fengli, Porteus, Matthew H, Dobbs, Drena, Voytas, Daniel F

Journal:

Nature Protocols

Year:

2006

Language:

english

File:

PDF, 528 KB

english, 2006

10

Mixture of experts models to exploit global sequence similarity on biomolecular sequence labeling

Cornelia Caragea, Jivko Sinapov, Drena Dobbs, Vasant Honavar

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 683 KB

english, 2009

11

Predicting RNA-Protein Interactions Using Only Sequence Information

Usha K Muppirala, Vasant G Honavar, Drena Dobbs

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 405 KB

english, 2011

12

Predicting binding sites of hydrolase-inhibitor complexes by combining several methods

Taner Z Sen, Andrzej Kloczkowski, Robert L Jernigan, Changhui Yan, Vasant Honavar, Kai-Ming Ho, Cai-Zhuang Wang, Yungok Ihm, Haibo Cao, Xun Gu, Drena Dobbs

Journal:

BMC Bioinformatics

Year:

2004

Language:

english

File:

PDF, 790 KB

english, 2004

13

Predicting DNA-binding sites of proteins from amino acid sequence

Changhui Yan, Michael Terribilini, Feihong Wu, Robert L Jernigan, Drena Dobbs, Vasant Honavar

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 934 KB

english, 2006

14

Exploring inconsistencies in genome-wide protein function annotations: a machine learning approach

Carson Andorf, Drena Dobbs, Vasant Honavar

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 467 KB

english, 2007

15

Glycosylation site prediction using ensembles of Support Vector Machine classifiers

Cornelia Caragea, Jivko Sinapov, Adrian Silvescu, Drena Dobbs, Vasant Honavar

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 340 KB

english, 2007

16

Predicting protein-protein interface residues using local surface structural similarity

Rafael A Jordan, Yasser EL-Manzalawy, Drena Dobbs, Vasant Honavar

Journal:

BMC Bioinformatics

Year:

2012

Language:

english

File:

PDF, 1.93 MB

english, 2012

17

Visualization of Nucleosomal Substructure in Native Chromatin by Atomic Force Microscopy

Martin, Linda D., Vesenka, James P., Henderson, Eric, Dobbs, Drena L.

Journal:

Year:

1995

Language:

english

File:

PDF, 2.72 MB

english, 1995

18

Xenopus laevis Ovarian DNA Helicase I: A 3' to 5' Helicase That Unwinds Short Duplexes

Poll, E. H. A., Harrison, Jeff, Umthun, Angela, Dobbs, Drena L., Benbow, Robert M.

Journal:

Year:

1994

Language:

english

File:

PDF, 1.86 MB

english, 1994

19

A single-stranded DNA binding protein that specifically recognizes cis-acting sequences in the replication origin and transcriptional promoter region of Tetrahymena rDNA

Hou, Zhen, Umthun, Angela R., Dobbs, Drena L.

Journal:

Year:

1995

Language:

english

File:

PDF, 3.89 MB

english, 1995

20

Predicting MHC-II Binding Affinity Using Multiple Instance Regression

EL-Manzalawy, Yasser, Dobbs, Drena, Honavar, Vasant

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2011

Language:

english

File:

PDF, 1.42 MB

english, 2011

21

[IEEE 2007 IEEE International Conference on Bioinformatics and Biomedicine Workshops - San Jose, CA, USA (2007.11.2-2007.11.4)] 2007 IEEE International Conference on Bioinformatics and Biomedicine Workshops - Structural characterization of RNA-binding sites of proteins: Preliminary results

Towfic, Fadi, Gemperline, David C., Caragea, Cornelia, Feihong Wu,, Dobbs, Drena, Honavar, Vasant

Year:

2007

Language:

english

File:

PDF, 732 KB

english, 2007

22

[IEEE 2008 IEEE International Conference on Bioinformatics and Biomedicine - Philadelphia, PA, USA (2008.11.3-2008.11.5)] 2008 IEEE International Conference on Bioinformatics and Biomedicine - Using Global Sequence Similarity to Enhance Biological Sequence Labeling

Caragea, Cornelia, Sinapov, Jivko, Dobbs, Drena, Honavar, Vasant

Year:

2008

Language:

english

File:

PDF, 634 KB

english, 2008

23

[IEEE 2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007) - Fremont, CA, USA (2007.11.2-2007.11.4)] 2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007) - Analysis of Protein Protein Dimeric Interfaces

Wu, Feihong, Towfic, Fadi, Dobbs, Drena, Honavar, Vasant

Year:

2007

Language:

english

File:

PDF, 256 KB

english, 2007

24

[IEEE 2007 IEEE 7th International Symposium on BioInformatics and BioEngineering - Boston, MA, USA (2007.10.14-2007.10.17)] 2007 IEEE 7th International Symposium on BioInformatics and BioEngineering - Assessing the Performance of Macromolecular Sequence Classifiers

Caragea, Cornelia, Sinapov, Jivko, Honavar, Vasant, Dobbs, Drena

Year:

2007

Language:

english

File:

PDF, 1.48 MB

english, 2007

25

[ACM Press the 2nd ACM Conference - Chicago, Illinois (2011.08.01-2011.08.03)] Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine - BCB '11 - Improving protein-RNA interface prediction by combining sequence homology based method with a naive Bayes classifier

Xue, Li C., Walia, Rasna, El-Manzalawy, Yasser, Dobbs, Drena, Honavar, Vasant

Year:

2011

Language:

english

File:

PDF, 556 KB

english, 2011

26

DockRank: Ranking docked conformations using partner-specific sequence homology-based protein interface prediction

Xue, Li C., Jordan, Rafael A., Yasser, EL-Manzalawy, Dobbs, Drena, Honavar, Vasant

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 778 KB

english, 2014

27

Codability criterion for picking proteinlike structures from random three-dimensional configurations

Cao, Hai-Bo, Wang, Cai-Zhuang, Dobbs, Drena, Ihm, Yungok, Ho, Kai-Ming

Journal:

Physical Review E

Year:

2006

Language:

english

File:

PDF, 140 KB

english, 2006

28

G-Quadruplex (G4) Motifs in the Maize (Zea mays L.) Genome Are Enriched at Specific Locations in Thousands of Genes Coupled to Energy Status, Hypoxia, Low Sugar, and Nutrient Deprivation

Andorf, Carson M., Kopylov, Mykhailo, Dobbs, Drena, Koch, Karen E., Stroupe, M. Elizabeth, Lawrence, Carolyn J., Bass, Hank W.

Journal:

Journal of Genetics and Genomics

Year:

2014

Language:

english

File:

PDF, 9.03 MB

english, 2014

29

[IEEE 2008 IEEE International Conference on Bioinformatics and Biomedicine - Philadelphia, PA, USA (2008.11.3-2008.11.5)] 2008 IEEE International Conference on Bioinformatics and Biomedicine - Predicting Protective Linear B-Cell Epitopes Using Evolutionary Information

EL-Manzalawy, Yasser, Dobbs, Drena, Honavar, Vasant

Year:

2008

Language:

english

File:

PDF, 130 KB

english, 2008

30

Proteomic Differentiation Between Murine Retinal and Brain-Derived Progenitor Cells

Dunn-Thomas, Tyra E., Dobbs, Drena L., Sakaguchi, Donald S., Young, Michael J., Honovar, Vasant G., Greenlee, M. Heather West

Journal:

Stem Cells and Development

Year:

2008

Language:

english

File:

PDF, 199 KB

english, 2008

31

Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization step

Kamil Steczkiewicz, Michael T. Zimmermann, Mateusz Kurcinski, Benjamin A. Lewis, Drena Dobbs, Andrzej Kloczkowski, Robert L. Jernigan, Andrzej Kolinski and Krzysztof Ginalski

Journal:

Proceedings of the National Academy of Sciences

Year:

2011

Language:

english

File:

PDF, 1.43 MB

english, 2011

32

Modular sequence elements associated with origin regions in eukaryotic chromosomal DNA

Dobbs, Drena L., Shaiu, Wen-Ling, Benbow, Robert M.

Journal:

Nucleic Acids Research

Year:

1994

Language:

english

File:

PDF, 5.67 MB

english, 1994

33

Computational modeling suggests dimerization of equine infectious anemia virus Rev is required for RNA binding

Umunnakwe, Chijioke N, Loyd, Hyelee, Cornick, Kinsey, Chavez, Jerald R, Dobbs, Drena, Carpenter, Susan

Journal:

Year:

2014

Language:

english

File:

PDF, 1.77 MB

english, 2014

34

Identification of DNA-binding proteins that recognize a Conserved Type I repeat sequence in the replication origin region of Tetrahymena rDNA

Umthun, Angela R., Hou, Zhen, Sibenaller, Zita A., Shaiu, Wen-Ling, Dobbs, Drena L.

Journal:

Nucleic Acids Research

Year:

1994

Language:

english

File:

PDF, 9.83 MB

english, 1994

35

[ACM Press the 2nd ACM Conference - Chicago, Illinois (2011.08.01-2011.08.03)] Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine - BCB '11 - Ranking docked models of protein-protein complexes using predicted partner-specific protein-protein interfaces

Xue, Li C., Jordan, Rafael A., El-Manzalawy, Yasser, Dobbs, Drena, Honavar, Vasant

Year:

2011

Language:

english

File:

PDF, 672 KB

english, 2011

36

[ACM Press the 5th ACM Conference - Newport Beach, California (2014.09.20-2014.09.23)] Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics - BCB '14 - An analysis of conformational changes upon RNA-protein binding

Sankar, Kannan, Walia, Rasna R., Mann, Carla M., Jernigan, Robert L., Honavar, Vasant G., Dobbs, Drena

Year:

2014

Language:

english

File:

PDF, 357 KB

english, 2014

37

[ACM Press the ACM Conference - Orlando, Florida (2012.10.07-2012.10.10)] Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine - BCB '12 - Predicting protective bacterial antigens using random forest classifiers

El-Manzalawy, Yasser, Dobbs, Drena, Honavar, Vasant

Year:

2012

Language:

english

File:

PDF, 173 KB

english, 2012

38

Molecular and Biological Characterization of Equine Infectious Anemia Virus Rev

Carpenter, Susan, Dobbs, Drena

Journal:

Current HIV Research

Year:

2010

Language:

english

File:

PDF, 134 KB

english, 2010

39

Computational prediction of protein interfaces: A review of data driven methods

Xue, Li C., Dobbs, Drena, Bonvin, Alexandre M.J.J., Honavar, Vasant

Journal:

Year:

2015

Language:

english

File:

PDF, 1.26 MB

english, 2015

40

High frequency targeted mutagenesis inArabidopsis thalianausing zinc finger nucleases

Feng Zhang, Morgan L. Maeder, Erica Unger-Wallace, Justin P. Hoshaw, Deepak Reyon, Michelle Christian, Xiaohong Li, Christopher J. Pierick, Drena Dobbs, Thomas Peterson, J. Keith Joung, Daniel F. Voyt

Journal:

Proceedings of the National Academy of Sciences

Year:

2010

Language:

english

File:

PDF, 1.39 MB

english, 2010

41

A Proteomic Analysis of Maize Chloroplast Biogenesis

Patricia M. Lonosky, Xiaosi Zhang, Vasant G. Honavar, Drena L. Dobbs, Aigen Fu and Steve R. Rodermel

Journal:

PLANT PHYSIOLOGY

Year:

2004

Language:

english

File:

PDF, 2.49 MB

english, 2004

42

[WORLD SCIENTIFIC Proceedings of the Pacific Symposium - Kohala Coast, Hawaii, USA (4 – 8 January 2016)] Biocomputing 2016 - A MOTIF-BASED METHOD FOR PREDICTING INTERFACIAL RESIDUES IN BOTH THE RNA AND PROTEIN COMPONENTS OF PROTEIN-RNA COMPLEXES

MUPPIRALA, USHA, LEWIS, BENJAMIN A, MANN, CARLA M., DOBBS, DRENA

Language:

english

File:

PDF, 4.24 MB

english

43

Template-based protein–protein docking exploiting pairwise interfacial residue restraints

Xue, Li C, Rodrigues, João P.G.L.M., Dobbs, Drena, Honavar, Vasant, Bonvin, Alexandre M.J.J.

Journal:

Briefings in Bioinformatics

Year:

2016

Language:

english

File:

PDF, 644 KB

english, 2016

44

A Plasmodium -like virulence effector of the soybean cyst nematode suppresses plant innate immunity

Noon, Jason B., Qi, Mingsheng, Sill, Danielle N., Muppirala, Usha, Eves-van den Akker, Sebastian, Maier, Thomas R., Dobbs, Drena, Mitchum, Melissa G., Hewezi, Tarek, Baum, Thomas J.

Journal:

New Phytologist

Year:

2016

Language:

english

File:

PDF, 3.00 MB

english, 2016

45

Struct-NB: predicting protein-RNA binding sites using structural features

Towfic, Fadi, Caragea, Cornelia, Gemperline, David C., Dobbs, Drena, Honavar, Vasant

Journal:

International Journal of Data Mining and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 2.13 MB

english, 2010

46

[WORLD SCIENTIFIC Proceedings of the Pacific Symposium - Maui, Hawaii (3 – 7 January 2006)] Biocomputing 2006 - IDENTIFYING INTERACTION SITES IN “RECALCITRANT” PROTEINS: PREDICTED PROTEIN AND RNA BINDING SITES IN REV PROTEINS OF HIV-1 AND EIAV AGREE WITH EXPERIMENTAL DATA

TERRIBILINI, MICHAEL, LEE, JAE-HYUNG, YAN, CHANGHUI, JERNIGAN, ROBERT L., CARPENTER, SUSAN, HONAVAR, VASANT, DOBBS, DRENA

Language:

english

File:

PDF, 802 KB

english

47

[PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO. Proceedings of the CSB 2008 Conference - Stanford University, USA (26 – 29 August 2008)] Computational Systems Bioinformatics - PREDICTING FLEXIBLE LENGTH LINEAR B-CELL EPITOPES

EL-Manzalawy, Yasser, Dobbs, Drena, Honavar, Vasant

Language:

english

File:

PDF, 394 KB

english

48

Identification of a homogenous structural basis for oligomerization by retroviral Rev-like proteins

Umunnakwe, Chijioke N., Dorman, Karin S., Dobbs, Drena, Carpenter, Susan

Journal:

Year:

2017

Language:

english

File:

PDF, 1.62 MB

english, 2017

49

Analysis of the EIAV Rev-Responsive Element (RRE) Reveals a Conserved RNA Motif Required for High Affinity Rev Binding in Both HIV-1 and EIAV

Lee, Jae-Hyung, Culver, Gloria, Carpenter, Susan, Dobbs, Drena, Jin, Dong-Yan

Journal:

Year:

2008

Language:

english

File:

PDF, 660 KB

english, 2008

50

On Evaluating MHC-II Binding Peptide Prediction Methods

EL-Manzalawy, Yasser, Dobbs, Drena, Honavar, Vasant, Bajic, Vladimir B.

Journal:

Year:

2008

Language:

english

File:

PDF, 359 KB

english, 2008