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Select item 97036921.

MP4: a machine learning based classification tool for prediction and functional annotation of pathogenic proteins from metagenomic and genomic datasets

Ankit Gupta, Aditya S. Malwe, Gopal N. Srivastava, Parikshit Thoudam, Keshav Hibare, Vineet K. Sharma

BMC Bioinformatics. 2022; 23: 507. Published online 2022 Nov 28. doi: 10.1186/s12859-022-05061-7

PMCID:: PMC9703692

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Select item 81130372.

Peroxiredoxins wear many hats: Factors that fashion their peroxide sensing personalities

Jesalyn Bolduc, Katarina Koruza, Ting Luo, Julia Malo Pueyo, Trung Nghia Vo, Daria Ezeriņa, Joris Messens

Redox Biol. 2021 Jun; 42: 101959. Published online 2021 Apr 20. doi: 10.1016/j.redox.2021.101959

PMCID:: PMC8113037

Article PDF–2.9M

Select item 52065363.

Conservation of coevolving protein interfaces bridges prokaryote–eukaryote homologies in the twilight zone

Juan Rodriguez-Rivas, Simone Marsili, David Juan, Alfonso Valencia

Proc Natl Acad Sci U S A. 2016 Dec 27; 113(52): 15018–15023. Published online 2016 Dec 13. doi: 10.1073/pnas.1611861114

PMCID:: PMC5206536

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Select item 49138814.

The bacterial DnaA-trio replication origin element specifies ssDNA initiator binding

Tomas T. Richardson, Omar Harran, Heath Murray

Nature. Author manuscript; available in PMC 2016 Dec 8.

Published in final edited form as: Nature. 2016 Jun 8; 534(7607): 412–416. Published online 2016 Jun 8. doi: 10.1038/nature17962

Correction in:: Nature. 2016 Jun 29; 536(7617): 488.

PMCID:: PMC4913881

Article PDF–3.9M

Select item 43755315.

Homozygous SLC6A17 Mutations Cause Autosomal-Recessive Intellectual Disability with Progressive Tremor, Speech Impairment, and Behavioral Problems

Zafar Iqbal, Marjolein H. Willemsen, Marie-Amélie Papon, Luciana Musante, Marco Benevento, Hao Hu, Hanka Venselaar, Willemijn M. Wissink-Lindhout, Anneke T. Vulto-van Silfhout, Lisenka E.L.M. Vissers, Arjan P.M. de Brouwer, Sylviane Marouillat, Thomas F. Wienker, Hans Hilger Ropers, Kimia Kahrizi, Nael Nadif Kasri, Hossein Najmabadi, Frédéric Laumonnier, Tjitske Kleefstra, Hans van Bokhoven

Am J Hum Genet. 2015 Mar 5; 96(3): 386–396. doi: 10.1016/j.ajhg.2015.01.010

PMCID:: PMC4375531

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Select item 42995206.

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

Article PDF–8.7M

Select item 41479107.

Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane)

Gabriel Studer, Marco Biasini, Torsten Schwede

Bioinformatics. 2014 Sep 1; 30(17): i505–i511. Published online 2014 Aug 22. doi: 10.1093/bioinformatics/btu457

PMCID:: PMC4147910

Article PDF–480K

Select item 40826298.

Genome-wide identification of pathogenicity factors of the free-living amoeba Naegleria fowleri

Denise C Zysset-Burri, Norbert Müller, Christian Beuret, Manfred Heller, Nadia Schürch, Bruno Gottstein, Matthias Wittwer

BMC Genomics. 2014; 15(1): 496. Published online 2014 Jun 19. doi: 10.1186/1471-2164-15-496

PMCID:: PMC4082629

Article PDF–682K

Select item 40347699.

Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information

Sergey Ovchinnikov, Hetunandan Kamisetty, David Baker

eLife. 2014; 3: e02030. Published online 2014 May 1. doi: 10.7554/eLife.02030

PMCID:: PMC4034769

Article PDF–5.6M

Select item 362718610.

The Structural Biology of Enzymes Involved in Natural Product Glycosylation

Shanteri Singh, George N. Phillips, Jr., Jon S. Thorson

Nat Prod Rep. Author manuscript; available in PMC 2013 Oct 12.

Published in final edited form as: Nat Prod Rep. 2012 Oct; 29(10): 1201–1237. Published online 2012 Jun 12. doi: 10.1039/c2np20039b

PMCID:: PMC3627186

Article PDF–17M

Select item 332973811.

HD-RNAS: An Automated Hierarchical Database of RNA Structures

Shubhra Sankar Ray, Sukanya Halder, Stephanie Kaypee, Dhananjay Bhattacharyya

Front Genet. 2012; 3: 59. Published online 2012 Apr 18. doi: 10.3389/fgene.2012.00059

PMCID:: PMC3329738

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Select item 297464212.

Distribution Analysis of Hydrogenases in Surface Waters of Marine and Freshwater Environments

Martin Barz, Christian Beimgraben, Torsten Staller, Frauke Germer, Friederike Opitz, Claudia Marquardt, Christoph Schwarz, Kirstin Gutekunst, Klaus Heinrich Vanselow, Ruth Schmitz, Julie LaRoche, Rüdiger Schulz, Jens Appel

PLoS One. 2010; 5(11): e13846. Published online 2010 Nov 5. doi: 10.1371/journal.pone.0013846

PMCID:: PMC2974642

Article PDF–850K

Select item 296312313.

Functional Promiscuity of Homologues of the Bacterial ArsA ATPases

Rostislav Castillo, Milton H. Saier, Jr.

Int J Microbiol. 2010; 2010: 187373. Published online 2010 Oct 20. doi: 10.1155/2010/187373

PMCID:: PMC2963123

Article PDF–1.5M

Select item 261419614.

Minimum Contradiction Matrices in Whole Genome Phylogenies

Marc Thuillard

Evol Bioinform Online. 2008; 4: 237–247. Published online 2008 Jul 21. doi: 10.4137/ebo.s909

PMCID:: PMC2614196

Article PDF–498K

Select item 193323415.

CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats

Ibtissem Grissa, Gilles Vergnaud, Christine Pourcel

Nucleic Acids Res. 2007 Jul; 35(Web Server issue): W52–W57. Published online 2007 May 30. doi: 10.1093/nar/gkm360

PMCID:: PMC1933234

Article PDF–553K

Select item 224261516.

Comparative analysis and “expression space” coverage of the production of prokaryotic membrane proteins for structural genomics

Sachin Surade, Markus Klein, Peggy C. Stolt-Bergner, Cornelia Muenke, Ankita Roy, Hartmut Michel

Protein Sci. 2006 Sep; 15(9): 2178–2189. doi: 10.1110/ps.062312706

PMCID:: PMC2242615

Article PDF–359K

Select item 117973117.

Uracil content of 16S rRNA of thermophilic and psychrophilic prokaryotes correlates inversely with their optimal growth temperatures

Amit N. Khachane, Kenneth N. Timmis, Vítor A. P. Martins dos Santos

Nucleic Acids Res. 2005; 33(13): 4016–4022. Published online 2005 Jul 19. doi: 10.1093/nar/gki714

PMCID:: PMC1179731

Article PDF–341K

Select item 1032590918.

Single-stranded DNA recruitment mechanism in replication origin unwinding by DnaA initiator protein and HU, an evolutionary ubiquitous nucleoid protein

Ryusei Yoshida, Shogo Ozaki, Hironori Kawakami, Tsutomu Katayama

Nucleic Acids Res. 2023 Jul 7; 51(12): 6286–6306. Published online 2023 May 13. doi: 10.1093/nar/gkad389

PMCID:: PMC10325909

Article PDF–2.4M

Select item 991317419.

Potent Inhibition of Macropinocytosis by Niclosamide in Cancer Cells: A Novel Mechanism for the Anticancer Efficacy for the Antihelminthic

Souad R. Sennoune, Gunadharini Dharmalingam Nandagopal, Sabarish Ramachandran, Marilyn Mathew, Sathish Sivaprakasam, Valeria Jaramillo-Martinez, Yangzom D. Bhutia, Vadivel Ganapathy

Cancers (Basel) 2023 Feb; 15(3): 759. Published online 2023 Jan 26. doi: 10.3390/cancers15030759

PMCID:: PMC9913174

Article PDF–3.4M

Select item 889682620.

Cellular assays identify barriers impeding iron-sulfur enzyme activity in a non-native prokaryotic host

Francesca D'Angelo, Elena Fernández-Fueyo, Pierre Simon Garcia, Helena Shomar, Martin Pelosse, Rita Rebelo Manuel, Ferhat Büke, Siyi Liu, Niels van den Broek, Nicolas Duraffourg, Carol de Ram, Martin Pabst, Emmanuelle Bouveret, Simonetta Gribaldo, Béatrice Py, Sandrine Ollagnier de Choudens, Frédéric Barras, Gregory Bokinsky

eLife. 2022; 11: e70936. Published online 2022 Mar 4. doi: 10.7554/eLife.70936

PMCID:: PMC8896826

Article PDF–2.7M

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