Nucleic Acids Research, 2006, Vol. 34, Database issue D3–D5 doi:10.1093/nar/gkj162 The Molecular Biology Database Collection: 2006 update Michael Y. Galperin* National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA Received October 28, 2005; Revised and Accepted November 1, 2005 ABSTRACT The NAR Molecular Biology Database Collection is a public online resource that contains links to all databases described in this issue of Nucleic Acids Research. In addition, this collection lists databases that have been featured in previous issues of NAR, as well as selected other databases that are freely available to the public and may be useful to the molecular biologist. The 2006 update includes 858 databases, 139 more than the previous one. The data- bases come with brief summaries, many of which have been updated recently. Each database is assigned a stable accession number that does not change if the database moves to a new location and its URL, authors’ names or the contact person address are updated. The complete database list and summaries are available online at the Nucleic Acids Research website http://nar.oxfordjournals.org/. COMMENTARY This is the 13th annual database issue of Nucleic Acids Research, and the ﬁrst one that goes entirely paperless. The list of molecular biology databases keeps getting bigger, and despite negative connotations sometimes connected to this growth, the databases are getting better and even more diverse. The current release of the Nucleic Acids Research online Molecular Biology Database Collection (Supplementary Table 1) includes 92 new databases, ﬁrst described in this issue, and 49 additional new databases, featured in Bioinform- atics, BMC Bioinformatics and other journals. These include ﬁrst ever databases from Ireland, Portugal and United Arab Emirates (1–3) and a variety of other databases maintained all over the world. Meanwhile, existing databases show remarkable resilience: out of 719 databases featured in the last year’s release (4), only 2 were no longer maintained because their authors graduated, retired or changed focus, and one more has shifted to restricted access. In contrast, three databases, ABCdb, EID and KDBI, that were considered dead last year and had been crossed off the list, have now been resurrected. In each case, their authors have moved to new work places and were able to resume maintenance of their databases. As promised last year, their accession numbers have not been re-used and these databases are now listed under the same entry numbers, 157, 32 and 138, respectively, that they had in previous releases. These numbers can be used to gain access to updated summaries of these databases on the NAR website, e.g. http://www. oxfordjournals.org/nar/database/summary/157. Similarly, PUMA2 (5), which replaced the WIT2 database, has kept its number 118 in list. After 12 years of database issues and 8 years of the accom- panying web supplement, it was interesting to check if they are really having an impact. In other words, how many people really care about them and use them? To evaluate the impact of the NAR database issues, I have used a tool that, despite all complaints and caveats, is commonly utilized for evaluating research productivity, namely the Science Citation Index produced by the Institute for Scientiﬁc Information. If data- bases are put on the web for the beneﬁt of the research com- munity, the frequency with which people use (and cite) a given database could serve as an indication of whether this database serves a useful purpose. An inspection of the citation ﬁgures for the 141 papers published 2 years ago in the 2004 NAR Database Issue (all citation data are as of October 15, 2005) revealed a very encouraging trend. Most of the papers were well—or very well—cited. Only ﬁve papers have not been cited at all and the same number of database descriptions — ﬁve—have been cited >100 times, becoming, in ISI parlance, instant ‘citation classics’. Whatever the caveats, the fact that the paper describing the Pfam domain database [http://www. sanger.ac.uk/Software/Pfam/, NAR Collection entry no. 210, Ref. (6)] has been cited 375 times in <2 years deﬁnitely indic- ates that this database is widely used by the research com- munity. Indeed, comparing a protein sequence against Pfam has become standard practice in sequence analysis, particu- larly in genome annotation. It is probably no coincidence that the ﬁrst author of the Pfam paper also serves as the Editor of *To whom correspondence should be addressed. Tel: +1 301 435 5910; Fax: +1 301 435 7794; Email: galperin@ncbi.nlm.nih.gov The Author 2006. Published by Oxford University Press. All rights reserved. The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org