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The bio.tools registry of software tools and data resources for the life sciences.
Ison J, Ienasescu H, Chmura P, Rydza E, Ménager H, Kalaš M, Schwämmle V, Grüning B, Beard N, Lopez R, Duvaud S, Stockinger H, Persson B, Vařeková RS, Raček T, Vondrášek J, Peterson H, Salumets A, Jonassen I, Hooft R, Nyrönen T, Valencia A, Capella S, Gelpí J, Zambelli F, Savakis B, Leskošek B, Rapacki K, Blanchet C, Jimenez R, Oliveira A, Vriend G, Collin O, van Helden J, Løngreen P, Brunak S. Ison J, et al. Among authors: hooft r. Genome Biol. 2019 Aug 12;20(1):164. doi: 10.1186/s13059-019-1772-6. Genome Biol. 2019. PMID: 31405382 Free PMC article.
Facilities that make the PDB data collection more powerful.
Lange J, Baakman C, Pistorius A, Krieger E, Hooft R, Joosten RP, Vriend G. Lange J, et al. Among authors: hooft r. Protein Sci. 2020 Jan;29(1):330-344. doi: 10.1002/pro.3788. Epub 2019 Dec 2. Protein Sci. 2020. PMID: 31724231 Free PMC article.
Top 10 metrics for life science software good practices.
Artaza H, Chue Hong N, Corpas M, Corpuz A, Hooft R, Jimenez RC, Leskošek B, Olivier BG, Stourac J, Svobodová Vařeková R, Van Parys T, Vaughan D. Artaza H, et al. Among authors: hooft r. F1000Res. 2016 Aug 16;5:ELIXIR-2000. doi: 10.12688/f1000research.9206.1. eCollection 2016. F1000Res. 2016. PMID: 27635232 Free PMC article.
Four simple recommendations to encourage best practices in research software.
Jiménez RC, Kuzak M, Alhamdoosh M, Barker M, Batut B, Borg M, Capella-Gutierrez S, Chue Hong N, Cook M, Corpas M, Flannery M, Garcia L, Gelpí JL, Gladman S, Goble C, González Ferreiro M, Gonzalez-Beltran A, Griffin PC, Grüning B, Hagberg J, Holub P, Hooft R, Ison J, Katz DS, Leskošek B, López Gómez F, Oliveira LJ, Mellor D, Mosbergen R, Mulder N, Perez-Riverol Y, Pergl R, Pichler H, Pope B, Sanz F, Schneider MV, Stodden V, Suchecki R, Svobodová Vařeková R, Talvik HA, Todorov I, Treloar A, Tyagi S, van Gompel M, Vaughan D, Via A, Wang X, Watson-Haigh NS, Crouch S. Jiménez RC, et al. Among authors: hooft r. F1000Res. 2017 Jun 13;6:ELIXIR-876. doi: 10.12688/f1000research.11407.1. eCollection 2017. F1000Res. 2017. PMID: 28751965 Free PMC article.
The PDBFINDER database: a summary of PDB, DSSP and HSSP information with added value.
Hooft RW, Sander C, Scharf M, Vriend G. Hooft RW, et al. Comput Appl Biosci. 1996 Dec;12(6):525-9. doi: 10.1093/bioinformatics/12.6.525. Comput Appl Biosci. 1996. PMID: 9021272
It is often desirable to make a selection from these files based on a criterion like R-factor, experimental method, length of the amino acid sequence, or the number of homologous sequences in SWISSPROT. ...AVAILABILITY: The latest version of the PDBFINDER database can be d …
It is often desirable to make a selection from these files based on a criterion like R-factor, experimental method, length of the ami …
Improving macromolecular electrostatics calculations.
Nielsen JE, Andersen KV, Honig B, Hooft RW, Klebe G, Vriend G, Wade RC. Nielsen JE, et al. Among authors: hooft rw. Protein Eng. 1999 Aug;12(8):657-62. doi: 10.1093/protein/12.8.657. Protein Eng. 1999. PMID: 10469826
29 results