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Items: 1 to 20 of 40

1.
The bone-degrading enzyme machinery: From multi-component understanding to the treatment of residues from the meat industry
Laura Fernandez-Lopez, Sergio Sanchez-Carrillo, Antonio García-Moyano, Erik Borchert, David Almendral, Sandra Alonso, Isabel Cea-Rama, Noa Miguez, Øivind Larsen, Johannes Werner, Kira S. Makarova, Francisco J. Plou, Thomas G. Dahlgren, Julia Sanz-Aparicio, Ute Hentschel, Gro Elin Kjæreng Bjerga, Manuel Ferrer
Comput Struct Biotechnol J. 2021; 19: 6328–6342. Published online 2021 Nov 23. doi: 10.1016/j.csbj.2021.11.027
PMCID:
PMC8645421
AbstractArticlePDF–2.5M
2.
Functional Characterization and Structural Analysis of NADH Oxidase Mutants from Thermus thermophilus HB27: Role of Residues 166, 174, and 194 in the Catalytic Properties and Thermostability
Javier Rocha-Martin, Pedro A. Sánchez-Murcia, Fernando López-Gallego, Aurelio Hidalgo, José Berenguer, José M. Guisan
Microorganisms. 2019 Nov; 7(11): 515. Published online 2019 Oct 31. doi: 10.3390/microorganisms7110515
PMCID:
PMC6921046
AbstractArticlePDF–3.6M
3.
Correlative two-color two-photon (2C2P) excitation STED microscopy
Christoph Polzer, Stefan Ness, Mojtaba Mohseni, Thomas Kellerer, Markus Hilleringmann, Joachim Rädler, Thomas Hellerer
Biomed Opt Express. 2019 Sep 1; 10(9): 4516–4530. Published online 2019 Aug 7. doi: 10.1364/BOE.10.004516
PMCID:
PMC6757464
AbstractArticlePDF–3.2M
4.
TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs
Zhen Tan, Yinghan Fu, Gaurav Sharma, David H. Mathews
Nucleic Acids Res. 2017 Nov 16; 45(20): 11570–11581. Published online 2017 Sep 28. doi: 10.1093/nar/gkx815
PMCID:
PMC5714223
AbstractArticlePDF–1.2M
5.
Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics
Jasper J. Koehorst, Edoardo Saccenti, Peter J. Schaap, Vitor A. P. Martins dos Santos, Maria Suarez-Diez
Version 3. F1000Res. 2016; 5: 1987. Published online 2017 Jun 27. doi: 10.12688/f1000research.9416.3
PMCID:
PMC5031134
AbstractArticlePDF–5.2M
6.
Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment
Marc F. Lensink, Sameer Velankar, Andriy Kryshtafovych, Shen‐You Huang, Dina Schneidman‐Duhovny, Andrej Sali, Joan Segura, Narcis Fernandez‐Fuentes, Shruthi Viswanath, Ron Elber, Sergei Grudinin, Petr Popov, Emilie Neveu, Hasup Lee, Minkyung Baek, Sangwoo Park, Lim Heo, Gyu Rie Lee, Chaok Seok, Sanbo Qin, Huan‐Xiang Zhou, David W. Ritchie, Bernard Maigret, Marie‐Dominique Devignes, Anisah Ghoorah, Mieczyslaw Torchala, Raphaël A.G. Chaleil, Paul A. Bates, Efrat Ben‐Zeev, Miriam Eisenstein, Surendra S. Negi, Zhiping Weng, Thom Vreven, Brian G. Pierce, Tyler M. Borrman, Jinchao Yu, Françoise Ochsenbein, Raphaël Guerois, Anna Vangone, João P.G.L.M. Rodrigues, Gydo van Zundert, Mehdi Nellen, Li Xue, Ezgi Karaca, Adrien S.J. Melquiond, Koen Visscher, Panagiotis L. Kastritis, Alexandre M.J.J. Bonvin, Xianjin Xu, Liming Qiu, Chengfei Yan, Jilong Li, Zhiwei Ma, Jianlin Cheng, Xiaoqin Zou, Yang Shen, Lenna X. Peterson, Hyung‐Rae Kim, Amit Roy, Xusi Han, Juan Esquivel‐Rodriguez, Daisuke Kihara, Xiaofeng Yu, Neil J. Bruce, Jonathan C. Fuller, Rebecca C. Wade, Ivan Anishchenko, Petras J. Kundrotas, Ilya A. Vakser, Kenichiro Imai, Kazunori Yamada, Toshiyuki Oda, Tsukasa Nakamura, Kentaro Tomii, Chiara Pallara, Miguel Romero‐Durana, Brian Jiménez‐García, Iain H. Moal, Juan Férnandez‐Recio, Jong Young Joung, Jong Yun Kim, Keehyoung Joo, Jooyoung Lee, Dima Kozakov, Sandor Vajda, Scott Mottarella, David R. Hall, Dmitri Beglov, Artem Mamonov, Bing Xia, Tanggis Bohnuud, Carlos A. Del Carpio, Eichiro Ichiishi, Nicholas Marze, Daisuke Kuroda, Shourya S. Roy Burman, Jeffrey J. Gray, Edrisse Chermak, Luigi Cavallo, Romina Oliva, Andrey Tovchigrechko, Shoshana J. Wodak
Proteins. 2016 Sep; 84(Suppl Suppl 1): 323–348. Published online 2016 Jun 1. doi: 10.1002/prot.25007
PMCID:
PMC5030136
AbstractArticlePDF–1.1M
7.
Genome-wide gene order distances support clustering the gram-positive bacteria
Christopher H. House, Matteo Pellegrini, Sorel T. Fitz-Gibbon
Front Microbiol. 2014; 5: 785. Published online 2015 Jan 20. doi: 10.3389/fmicb.2014.00785
PMCID:
PMC4299520
AbstractArticlePDF–8.7M
8.
Host-to-host variation of ecological interactions in polymicrobial infections
Sayak Mukherjee, Kristin E. Weimer, Sang-Cheol Seok, Will C. Ray, C. Jayaprakash, Veronica J. Vieland, W. Edward Swords, Jayajit Das
Phys Biol. Author manuscript; available in PMC 2015 Dec 4.
Published in final edited form as: Phys Biol. 2014; 12(1): 016003. Published online 2014 Dec 4. doi: 10.1088/1478-3975/12/1/016003
PMCID:
PMC4269105
AbstractArticlePDF–1.3M
9.
J-UNIO protocol used for NMR structure determination of the 206-residue protein NP_346487.1 from Streptococcus pneumoniae TIGR4
Kristaps Jaudzems, Bill Pedrini, Michael Geralt, Pedro Serrano, Kurt Wüthrich
J Biomol NMR. Author manuscript; available in PMC 2016 Jan 1.
Published in final edited form as: J Biomol NMR. 2015 Jan; 61(1): 65–72. Published online 2014 Nov 27. doi: 10.1007/s10858-014-9886-3
PMCID:
PMC4304919
AbstractArticlePDF–1.2M
10.
Evolution of tryptophan biosynthetic pathway in microbial genomes: a comparative genetic study
V. K. Priya, Susmita Sarkar, Somdatta Sinha
Syst Synth Biol. 2014 Mar; 8(1): 59–72. Published online 2013 Oct 19. doi: 10.1007/s11693-013-9127-1
PMCID:
PMC3933628
AbstractArticlePDF–1.2M
11.
A subgraph isomorphism algorithm and its application to biochemical data
Vincenzo Bonnici, Rosalba Giugno, Alfredo Pulvirenti, Dennis Shasha, Alfredo Ferro
BMC Bioinformatics. 2013; 14(Suppl 7): S13. Published online 2013 Apr 22. doi: 10.1186/1471-2105-14-S7-S13
PMCID:
PMC3633016
AbstractArticlePDF–1.0M
12.
The evolutionary rate of antibacterial drug targets
Arkadiusz Gladki, Szymon Kaczanowski, Pawel Szczesny, Piotr Zielenkiewicz
BMC Bioinformatics. 2013; 14: 36. Published online 2013 Feb 1. doi: 10.1186/1471-2105-14-36
PMCID:
PMC3598507
AbstractArticlePDF–559K
13.
Diversified Carbohydrate-Binding Lectins from Marine Resources
Tomohisa Ogawa, Mizuki Watanabe, Takako Naganuma, Koji Muramoto
J Amino Acids. 2011; 2011: 838914. Published online 2011 Nov 15. doi: 10.4061/2011/838914
PMCID:
PMC3269628
AbstractArticlePDF–3.6M
14.
Complete Genome Sequence and Comparative Analysis of the Fish Pathogen Lactococcus garvieae
Hidetoshi Morita, Hidehiro Toh, Kenshiro Oshima, Mariko Yoshizaki, Michiko Kawanishi, Kohei Nakaya, Takehito Suzuki, Eiji Miyauchi, Yasuo Ishii, Soichi Tanabe, Masaru Murakami, Masahira Hattori
PLoS One. 2011; 6(8): e23184. Published online 2011 Aug 4. doi: 10.1371/journal.pone.0023184
PMCID:
PMC3150408
AbstractArticlePDF–432K
15.
Recombinant expression and functional analysis of proteases from Streptococcus pneumoniae, Bacillus anthracis, and Yersinia pestis
Keehwan Kwon, Jeremy Hasseman, Saeeda Latham, Carissa Grose, Yu Do, Robert D Fleischmann, Rembert Pieper, Scott N Peterson
BMC Biochem. 2011; 12: 17. Published online 2011 May 5. doi: 10.1186/1471-2091-12-17
PMCID:
PMC3113736
AbstractArticlePDF–1.8M
16.
Proteinortho: Detection of (Co-)orthologs in large-scale analysis
Marcus Lechner, Sven Findeiß, Lydia Steiner, Manja Marz, Peter F Stadler, Sonja J Prohaska
BMC Bioinformatics. 2011; 12: 124. Published online 2011 Apr 28. doi: 10.1186/1471-2105-12-124
PMCID:
PMC3114741
AbstractArticlePDF–473K
17.
A novel scoring function for discriminating hyperthermophilic and mesophilic proteins with application to predicting relative thermostability of protein mutants
Yunqi Li, C Russell Middaugh, Jianwen Fang
BMC Bioinformatics. 2010; 11: 62. Published online 2010 Jan 28. doi: 10.1186/1471-2105-11-62
PMCID:
PMC3098108
AbstractArticlePDF–1.3M
18.
Computational prediction of essential genes in an unculturable endosymbiotic bacterium, Wolbachia of Brugia malayi
Alexander G Holman, Paul J Davis, Jeremy M Foster, Clotilde KS Carlow, Sanjay Kumar
BMC Microbiol. 2009; 9: 243. Published online 2009 Nov 28. doi: 10.1186/1471-2180-9-243
PMCID:
PMC2794283
AbstractArticlePDF–1.0M
19.
Sequence and structural analysis of the Asp-box motif and Asp-box beta-propellers; a widespread propeller-type characteristic of the Vps10 domain family and several glycoside hydrolase families
Esben M Quistgaard, Søren S Thirup
BMC Struct Biol. 2009; 9: 46. Published online 2009 Jul 13. doi: 10.1186/1472-6807-9-46
PMCID:
PMC2716378
AbstractArticlePDF–2.5M
20.
The presence of the pilus locus is a clonal property among pneumococcal invasive isolates
Sandra I Aguiar, Isa Serrano, Francisco R Pinto, José Melo-Cristino, Mario Ramirez
BMC Microbiol. 2008; 8: 41. Published online 2008 Feb 28. doi: 10.1186/1471-2180-8-41
PMCID:
PMC2270847
AbstractArticlePDF–477K

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