InterPro: the integrative protein signature database (2009)
Hunter, Sarah, Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
The InterPro database (http://www.ebi.ac.uk/interpro/) integrates together predictive models or ‘signatures’ representing protein domains, families and functional sites from multiple, diverse...
Rfam: updates to the RNA families database (2009)
Gardner, Paul P., Daub, Jennifer, Tate, John G., Nawrocki, Eric P., Kolbe, Diana L., Lindgreen, Stinus, ...
Rfam is a collection of RNA sequence families, represented by multiple sequence alignments and covariance models (CMs). The primary aim of Rfam is to annotate new members of known RNA families on...
DASMI: exchanging, annotating and assessing molecular interaction data (2009)
Blankenburg, Hagen, Finn, Robert D., Prlic, Andreas, Jenkinson, Andrew M., Ramírez, Fidel, Emig, Dorothea, ...
Motivation: Ever increasing amounts of biological interaction data are being accumulated worldwide, but they are currently not readily accessible to the biologist at a single site. New techniques are...
Bateman, Alex, Finn, Robert D., Sims, Peter J., Wiedmer, Therese, Biegert, Andreas, Söding, Johannes
Motivation: Phospholipid scramblases (PLSCRs) constitute a family of cytoplasmic membrane-associated proteins that were identified based upon their capacity to mediate a Ca2+-dependent bidirectional...
Integrating biological data – the Distributed Annotation System (2008)
Jenkinson, Andrew M, Albrecht, Mario, Birney, Ewan, Blankenburg, Hagen, Down, Thomas, Finn, Robert D, ...
Abstract Background The Distributed Annotation System (DAS) is a widely adopted protocol for dynamically integrating a wide range of biological data from geographically diverse sources. DAS continues...
A Unified View of Protein Sequence and Structure Using the Distributed Annotation System (2008)
Andreas Prlic, Thomas Down, Alex Bateman, Tim Hubbard, Christine Orengo, Mark Dibley, ...
The eFamily project aims to improve integration between protein sequence and structure data. One of the technologies being used to achieve this is the Distributed Annotation System (DAS). DAS is a...
The Pfam protein families database (2008)
Robert D. Finn, John Tate, Jaina Mistry, Penny C. Coggill, Stephen John Sammut, Hans-rudolf Hotz, ...
Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. The current release of Pfam (22.0) contains 9318...
Integrating biological data - the Distributed {Annotation} {System} (2008)
Jenkinson, Andrew M., Albrecht, Mario, Birney, Ewan, Blankenburg, Hagen, Down, Thomas, Finn, Robert D., ...
Experience using web services for biological sequence analysis (2008)
Stockinger, Heinz, Attwood, Teresa, Chohan, Shahid Nadeem, Côté, Richard, Cudré-Mauroux, Philippe, Falquet, Laurent, ...
Programmatic access to data and tools through the web using so-called web services has an important role to play in bioinformatics. In this article, we discuss the most popular approaches based on...
The Pfam protein families database (2008)
Finn, Robert D., Tate, John, Mistry, Jaina, Coggill, Penny C., Sammut, Stephen John, Hotz, Hans-Rudolf, ...
Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. The current release of Pfam (22.0) contains 9318...
Pfam 10 years on: 10 000 families and still growing (2008)
Sammut, Stephen John, Finn, Robert D., Bateman, Alex
Classifications of proteins into groups of related sequences are in some respects like a periodic table for biology, allowing us to understand the underlying molecular biology of any organism. Pfam...
Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. (2007)
Alex Bateman, Ewan Birney, Richard Durbin, Sean R. Eddy, Robert D. Finn, Erik L. L
Pfam is a collection of multiple alignments and profile hidden Markov models of protein domain families. Release 3.1 is a major update of the Pfam database and contains 1313 families which are...
Alex Bateman, Ewan Birney, Richard Durbin, Sean R. Eddy, Robert D. Finn
Pfam is a collection of multiple alignments and profile hidden Markov models of protein domain families. Release 3.1 is a major update of the Pfam database and contains 1313 families which are...
Integrating sequence and structural biology with DAS (2007)
Prlić, Andreas, Down, Thomas A, Kulesha, Eugene, Finn, Robert D, Kähäri, Andreas, Hubbard, Tim JP
Abstract Background The Distributed Annotation System (DAS) is a network protocol for exchanging biological data. It is frequently used to share annotations of genomes and protein sequence. Results...
Predicting active site residue annotations in the Pfam database (2007)
Mistry, Jaina, Bateman, Alex, Finn, Robert D
Abstract Background Approximately 5% of Pfam families are enzymatic, but only a small fraction of the sequences within these families (
ProServer: a simple, extensible Perl DAS server (2007)
Finn, Robert D., Stalker, James W., Jackson, David K., Kulesha, Eugene, Clements, Jody, Pettett, Roger
Summary: The increasing size and complexity of biological databases has led to a growing trend to federate rather than duplicate them. In order to share data between federated databases, protocols...
SCOOP: a simple method for identification of novel protein superfamily relationships (2007)
Bateman, Alex, Finn, Robert D.
Motivation: Profile searches of sequence databases are a sensitive way to detect sequence relationships. Sophisticated profile–profile comparison algorithms that have been recently introduced...
Details on the system requirements and installation of ProServer can (2007)
Robert D. Finn, James W. Stalker, David K. Jackson, Eugene Kulesha, Jody Clements, Roger Pettett
Summary: The increasing size and complexity of biological databases has led to a growing trend to federate rather than duplicate them. In order to share data between federated databases, protocols...
BMC Bioinformatics Database Predicting active site residue annotations in the Pfam database (2007)
Jaina Mistry, Alex Bateman, Robert D Finn
Background: Approximately 5 % of Pfam families are enzymatic, but only a small fraction of the sequences within these families (<0.5%) have had the residues responsible for catalysis determined....
BMC Bioinformatics Research article Integrating sequence and structural biology with DAS (2007)
Andreas Prlić, Thomas A Down, Eugene Kulesha, Robert D Finn, Andreas Kähäri, Tim Jp Hubbard
Background: The Distributed Annotation System (DAS) is a network protocol for exchanging biological data. It is frequently used to share annotations of genomes and protein sequence. Results: Here we...
SCOOP: A simple method for identification of novel protein superfamily relationships (2007)
Bateman, Alex, Finn, Robert D.
Motivation: Profile searches of sequence databases are a sensitive way to detect sequence relationships. Sophisticated profile-profile comparison algorithms that have been recently introduced...
Pfam: clans, web tools and services (2006)
Robert D. Finn, Jaina Mistry, Benjamin Schuster-böckler, Sam Griffiths-jones, Volker Hollich, Timo Lassmann, ...
Pfam is a database of protein families that currently contains 7973 entries (release 18.0). A recent development in Pfam has enabled the grouping of related families into clans. Pfam clans are...
Motivation: Profile searches of sequence databases are a sensitive way to detect sequence relationships. Sophisticated profile–profile comparison algorithms that have been recently introduced...
Pfam: clans, web tools and services (2006)
Finn, Robert D., Mistry, Jaina, Schuster-Böckler, Benjamin, Griffiths-Jones, Sam, Hollich, Volker, Lassmann, Timo, ...
Pfam is a database of protein families that currently contains 7973 entries (release 18.0). A recent development in Pfam has enabled the grouping of related families into clans. Pfam clans are...
Finn, Robert D., Marshall, Mhairi, Bateman, Alex
Summary: There are many resources that contain information about binary interactions between proteins. However, protein interactions are defined by only a subset of residues in any protein. We have...
Robert D Finn, Mhairi Marshall, Alex Bateman
Summary: There are many resources that contain information about binary interactions between proteins. However, protein interactions are defined by only a subset of residues in any protein. We have...
Finn, Robert D., Marshall, Mhairi, Bateman, Alex
Summary: There are many resources that contain information about binary interactions between proteins. However, protein interactions are defined by only a subset of residues in any protein. We have...
The Pfam protein families database (2004)
Bateman, Alex, Coin, Lachlan, Durbin, Richard, Finn, Robert D., Hollich, Volker, Griffiths-Jones, Sam, ...
Pfam is a large collection of protein families and domains. Over the past 2 years the number of families in Pfam has doubled and now stands at 6190 (version 10.0). Methodology improvements for...
Finn, Robert D., Marshall, Mhairi, Bateman, Alex
Summary: There are many resources that contain information about binary interactions between proteins. However, protein interactions are defined by only a subset of residues in any protein. We have...
Escherichia coli RNA polymerase core and holoenzyme structures
Finn, Robert D., Orlova, Elena V., Gowen, Brent, Buck, Martin, Van Heel, Marin
Multisubunit RNA polymerase is an essential enzyme for regulated gene expression. Here we report two Escherichia coli RNA polymerase structures: an 11.0 Å structure of the core RNA polymerase and...
The Pfam protein families database
Bateman, Alex, Coin, Lachlan, Durbin, Richard, Finn, Robert D., Hollich, Volker, Griffiths-Jones, Sam, ...
Pfam is a large collection of protein families and domains. Over the past 2 years the number of families in Pfam has doubled and now stands at 6190 (version 10.0). Methodology improvements for...
Pfam: clans, web tools and services
Finn, Robert D., Mistry, Jaina, Schuster-Böckler, Benjamin, Griffiths-Jones, Sam, Hollich, Volker, Lassmann, Timo, ...
Pfam is a database of protein families that currently contains 7973 entries (release 18.0). A recent development in Pfam has enabled the grouping of related families into clans. Pfam clans are...
Escherichia coli RNA polymerase core and holoenzyme structures
Finn, Robert D., Orlova, Elena V., Gowen, Brent, Buck, Martin, Van Heel, Marin
Multisubunit RNA polymerase is an essential enzyme for regulated gene expression. Here we report two Escherichia coli RNA polymerase structures: an 11.0 Å structure of the core RNA polymerase and...
The Pfam protein families database
Bateman, Alex, Coin, Lachlan, Durbin, Richard, Finn, Robert D., Hollich, Volker, Griffiths-Jones, Sam, ...
Pfam is a large collection of protein families and domains. Over the past 2 years the number of families in Pfam has doubled and now stands at 6190 (version 10.0). Methodology improvements for...
Pfam: clans, web tools and services
Finn, Robert D., Mistry, Jaina, Schuster-Böckler, Benjamin, Griffiths-Jones, Sam, Hollich, Volker, Lassmann, Timo, ...
Pfam is a database of protein families that currently contains 7973 entries (release 18.0). A recent development in Pfam has enabled the grouping of related families into clans. Pfam clans are...
Integrating sequence and structural biology with DAS
Prlić, Andreas, Down, Thomas A, Kulesha, Eugene, Finn, Robert D, Kähäri, Andreas, Hubbard, Tim JP
The Pfam protein families database
Finn, Robert D., Tate, John, Mistry, Jaina, Coggill, Penny C., Sammut, Stephen John, Hotz, Hans-Rudolf, ...
Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. The current release of Pfam (22.0) contains 9318...
Integrating biological data – the Distributed Annotation System
Jenkinson, Andrew M, Albrecht, Mario, Birney, Ewan, Blankenburg, Hagen, Down, Thomas, Finn, Robert D, ...
Modifier Effects between Regulatory and Protein-Coding Variation
Dimas, Antigone S., Stranger, Barbara E., Beazley, Claude, Finn, Robert D., Ingle, Catherine E., Forrest, Matthew S., ...
Genome-wide associations have shown a lot of promise in dissecting the genetics of complex traits in humans with single variants, yet a large fraction of the genetic effects is still unaccounted for....
Finn, Robert D., McLaughlin, Lesley A., Ronseaux, Sebastien, Rosewell, Ian, Houston, J. Brian, Henderson, Colin J., ...
In vitro, cytochrome b5 modulates the rate of cytochrome P450-dependent mono-oxygenation reactions. However, the role of this enzyme in determining drug pharmacokinetics in vivo and the consequential...
Bateman, Alex, Finn, Robert D., Sims, Peter J., Wiedmer, Therese, Biegert, Andreas, Söding, Johannes
Motivation: Phospholipid scramblases (PLSCRs) constitute a family of cytoplasmic membrane-associated proteins that were identified based upon their capacity to mediate a Ca2+-dependent bidirectional...
Rfam: updates to the RNA families database
Gardner, Paul P., Daub, Jennifer, Tate, John G., Nawrocki, Eric P., Kolbe, Diana L., Lindgreen, Stinus, ...
Rfam is a collection of RNA sequence families, represented by multiple sequence alignments and covariance models (CMs). The primary aim of Rfam is to annotate new members of known RNA families on...
InterPro: the integrative protein signature database
Hunter, Sarah, Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
The InterPro database (http://www.ebi.ac.uk/interpro/) integrates together predictive models or ‘signatures’ representing protein domains, families and functional sites from multiple, diverse...
DASMI: exchanging, annotating and assessing molecular interaction data
Blankenburg, Hagen, Finn, Robert D., Prlić, Andreas, Jenkinson, Andrew M., Ramírez, Fidel, Emig, Dorothea, ...
Motivation: Ever increasing amounts of biological interaction data are being accumulated worldwide, but they are currently not readily accessible to the biologist at a single site. New techniques are...