2000
DOI: 10.1093/nar/28.1.225
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PRINTS-S: the database formerly known as PRINTS

Abstract: The PRINTS database houses a collection of protein family fingerprints. These are groups of motifs that together are diagnostically more potent than single motifs by virtue of the biological context afforded by matching motif neighbours. Around 1200 fingerprints have now been created and stored in the database. The September 1999 release (version 24.0) encodes approximately 7200 motifs, covering a range of globular and membrane proteins, modular polypeptides and so on. In addition to its continued steady growt… Show more

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Cited by 207 publications
(104 citation statements)
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“…Members of the TetR family exhibit a high degree of sequence similarity at the DNA binding domain (see below). Interpro (258) assigns proteins to the TetR family based on PROSITE signature PS01081 (364), PRINTS motif PR00455 (15,16), and Pfam Hidden Markov Model (HMM) profile PF00440 (26,27). To establish a single criterion defining the TetR family, we decided to develop a conventional profile, because conventional profiles are easy to manage and their sensitivity is equivalent to that of HMM profiles.…”
Section: Defining the Tetr Family Tetr Family Profilementioning
confidence: 99%
“…Members of the TetR family exhibit a high degree of sequence similarity at the DNA binding domain (see below). Interpro (258) assigns proteins to the TetR family based on PROSITE signature PS01081 (364), PRINTS motif PR00455 (15,16), and Pfam Hidden Markov Model (HMM) profile PF00440 (26,27). To establish a single criterion defining the TetR family, we decided to develop a conventional profile, because conventional profiles are easy to manage and their sensitivity is equivalent to that of HMM profiles.…”
Section: Defining the Tetr Family Tetr Family Profilementioning
confidence: 99%
“…Currently, motif composition is often used to assign putative functions to novel protein sequences based on the known functions of other proteins that share one or more motifs with the novel protein. Several motif databases have been developed, including those that contain relatively short motifs, e.g., PROSITE R OSI T E [18]; or groups of motifs referred to as fingerprints, e.g., PRINTS R IN T S [3], or BLOCKS L O CK S [20]; or sequence patterns, often based on position-specific scoring matrices or hidden Markov models generated from multiple sequence alignments e.g., called profiles, PROSITE R OSI T E [18] or domains, e.g., Pfam [9]. Such motif databases or resources that integrate several databases, e.g., InterPro [2], MetaFam [36], can be queried using a protein sequence to obtain a list of motifs that are found in the sequence as well as the functions or structures associated with these motifs.…”
Section: Background and Introductionmentioning
confidence: 99%
“…More generally, it may be necessary to identify combinations of motifs that must present, or perhaps even absent in a sequence, in order to reliably assign it to a functional family. Indeed, in the PRINTS R IN T S database [3], the fingerprints used to assign proteins to functional families can be simple motifs or a combination of motifs. However, the process of identifying a fingerprint for each protein family of interest can be labor intensive and requires considerable domain knowledge.…”
Section: Background and Introductionmentioning
confidence: 99%
“…The PRINTS database [5] is in turn built on top of SWISS-PROT. PRINTS is a pattern database, gathering information about sets of related proteins (protein "families").…”
Section: Introductionmentioning
confidence: 99%
“…They are most commonly represented using two letter codes at the beginning of each line, although there are increasing moves toward use of relational [5] or XML based schema [3]. There is often additional structure expressed in other syntaxes.…”
mentioning
confidence: 99%