Pepsin homologues in bacteria (2009)
Rawlings, Neil D, Bateman, Alex
Abstract Background Peptidase family A1, to which pepsin belongs, had been assumed to be restricted to eukaryotes. The tertiary structure of pepsin shows two lobes with similar folds and it has been...
Broadening Pfam Protein Sequence Annotations (2009)
Jaina Mistry, Penny Cogghill, Sean Eddy, Rob Finn, John Tate, Alex Bateman
Pfam is a database of conserved protein families or domains commonly used for genome annotation and sequence classification. It comprises two parts: (1) Pfam-A families, which are fully annotated and...
Sequence Analysis Prediction of both conserved and nonconserved microRNA targets in animals (2009)
Xiaowei Wang, Dr. Alex Bateman
Motivation: MicroRNAs (miRNAs) are involved in many diverse biological processes and they may potentially regulate the functions of thousands of genes. However, one major issue in miRNA studies is...
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...
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...
PromoterExplorer: An Effective Promoter Identification Method Based on the AdaBoost Algorithm (2008)
Xudong Xie, Shuanhu Wu, Kin-man Lam, Hong Yan, Alex Bateman
Motivation: Promoter prediction is important for the analysis of gene regulations. Although a number of promoter prediction algorithms have been reported in literature, significant improvement in...
in prokaryotes and ubiquitin signaling in eukaryotes (2008)
Kirill Borziak, Igor B. Zhulin, Dr. Alex Bateman
FIST: a sensory domain for diverse signal transduction pathways
Databases and ontologies AssociationDB: Web-based exploration of genomic association (2008)
Dominik Seelow, Katrin Hoffmann, Tom H. Lindner, Dr. Alex Bateman
Summary: Genome-wide association studies use hundreds of thousands of markers making it challenging to present and finally interpret the results. We developed a graphical, web-based solution for an...
Cedric Simillion, a Koen Janssens, b Lieven Sterckc,d and Yves Van de Peer c,d∗ (2008)
United Kingdom, Hogeschool Gent, Dr. Alex Bateman
genomic homology using genomic profiles
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 Wellcome Trust Genome Campus, (2008)
Daniel Haft, Smart Pfam Tigrfams, Alex Bateman, In Interpro, Alex Bateman
HMM-based databases
Evan Keibler, Manimozhiyan Arumugam, Michael Brent, Alex Bateman
Motivation: Hidden Markov models (HMMs) and generalized HMMs been successfully applied to many problems, but the standard Viterbi Algorithm for computing the most probable interpretation of an input...
Hierarchical and Multi-Resolution Representation of Protein Flexibility (2008)
Yong Zhao, Daniel Stoffler, Michel Sanner, Alex Bateman
Motivation: Conformational rearrangements during molecular interactions are observed in a wide range of biological systems. However, computational methods aiming at simulating and predicting...
Protein interactions in human genetic diseases (2008)
Schuster-Böckler, Benjamin, Bateman, Alex
Abstract We present a novel method that combines protein structure information with protein interaction data to identify residues that form part of an interaction interface. Our prediction method can...
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...
Large-scale screening for novel low-affinity extracellular protein interactions (2008)
Bushell, K. Mark, Söllner, Christian, Schuster-Boeckler, Benjamin, Bateman, Alex, Wright, Gavin J.
Extracellular protein–protein interactions are essential for both intercellular communication and cohesion within multicellular organisms. Approximately a fifth of human genes encode...
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...
Databases, data tombs and dust in the wind (2008)
Wren, Jonathan D., Bateman, Alex
Contact: jdwren@gmail.com As biomedical data accumulates, the need to store, share and organize it grows. Consequently, the number of Internet-accessible databases has been rapidly growing on an...
The RNA WikiProject: Community annotation of RNA families (2008)
Daub, Jennifer, Gardner, Paul P., Tate, John, Ramsköld, Daniel, Manske, Magnus, Scott, William G., ...
The online encyclopedia Wikipedia has become one of the most important online references in the world and has a substantial and growing scientific content. A search of Google with many RNA-related...
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...
Sean R. Eddy, Ewan Birney, Alex Bateman, Richard Durbin
Pfam contains multiple alignments and hidden Markov model based profiles (HMM-profiles) of complete protein domains. The definition of domain boundaries, family members, and alignment is done...
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...
Corin Yeats, Stephen Bentley, Alex Bateman
Background: Streptomyces coelicolor has long been considered a remarkable bacterium with a complex life-cycle, ubiquitous environmental distribution, linear chromosomes and plasmids, and a huge range...
David J Studholme, Neil D Rawlings, Alan J Barrett, Alex Bateman, Alex Bateman
Background: We wished to compare two databases based on sequence similarity: one that aims to be comprehensive in its coverage of known sequences, and one that specialises in a relatively small...
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...
Alex Bateman, Ewan Birney, Richard Durbin, Sean R. Eddy
Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the WWW in the UK at
Bmc Bioinformatics, Alex Bateman
Background: Post transcriptional gene silencing (PTGS) is a recently discovered phenomenon that is an area of intense research interest. Components of the PTGS machinery are being discovered by...
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 (
Reuse of structural domain–domain interactions in protein networks (2007)
Schuster-Böckler, Benjamin, Bateman, Alex
Abstract Background Protein interactions are thought to be largely mediated by interactions between structural domains. Databases such as i Pfam relate interactions in protein structures to known...
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...
Bmc Bioinformatics, Benjamin Schuster-böckler, Alex Bateman
Reuse of structural domain–domain interactions in protein
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....
New developments in the interpro database (2007)
Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, ...
InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE,
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...
New developments in the InterPro database (2007)
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs,...
Metazoan Scc4 Homologs Link Sister Chromatid Cohesion to Cell and Axon Migration Guidance (2006)
Vlad C. Seitan, Peter Banks, Steve Laval, Nazia A. Majid, Dale Dorsett, Amer Rana, ...
A complex previously found only in yeast is described in metazoa, where it functions both in chromatid cohesion and in migration during development.
Metazoan Scc4 Homologs Link Sister Chromatid Cohesion to Cell and Axon Migration Guidance (2006)
Vlad C. Seitan, Peter Banks, Steve Laval, Nazia A. Majid, Dale Dorsett, Amer Rana, ...
Saccharomyces cerevisiae Scc2 binds Scc4 to form an essential complex that loads cohesin onto chromosomes. The prevalence of Scc2 orthologs in eukaryotes emphasizes a conserved role in regulating...
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...
ADP_EM: Fast exhaustive multi-resolution docking for highthroughput (2006)
José Ignacio Garzón, Julio Kovacs, Ruben Abagyan, Pablo Chacón, Alex Bateman
coverage.
miRBase: microRNA sequences, targets and gene nomenclature (2006)
Griffiths-Jones, Sam, Grocock, Russell J., Van Dongen, Stijn, Bateman, Alex, Enright, Anton J.
The miRBase database aims to provide integrated interfaces to comprehensive microRNA sequence data, annotation and predicted gene targets. miRBase takes over functionality from the microRNA Registry...
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...
InterPro, progress and status in 2005 (2005)
Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam,...
Benjamin Schuster-böckler, Alex Bateman
Summary: The availability of advanced profile–profile comparison tools, such as PRC or HHsearch demands sophisticated visualization tools not presently available. We introduce an approach built...
Rfam: annotating non-coding RNAs in complete genomes (2005)
Griffiths-Jones, Sam, Moxon, Simon, Marshall, Mhairi, Khanna, Ajay, Eddy, Sean R., Bateman, Alex
Rfam is a comprehensive collection of non-coding RNA (ncRNA) families, represented by multiple sequence alignments and profile stochastic context-free grammars. Rfam aims to facilitate the...
InterPro, progress and status in 2005 (2005)
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam,...
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...
Bateman, Alex, Holden, Matthew T. G., Yeats, Corin
Summary: Biofilms are complex microbial communities found at surfaces that are often associated with extracellular polysaccharides. Biofilm formation is a complex process that is being understood at...
Visualizing profile-profile alignment: pairwise HMM logos (2005)
Schuster-Böckler, Benjamin, Bateman, Alex
Summary: The availability of advanced profile–profile comparison tools, such as PRC or HHsearch demands sophisticated visualization tools not presently available. We introduce an approach built...
Visualizing profile-profile alignment: pairwise HMM Logos (2005)
Schuster-Böckler, Benjamin, Bateman, Alex
Summary: The availability of advanced profile-profile comparison tools such as PRC or HHsearch demands sophisticated visualisation tools not presently available. We introduce an approach built upon...
The Hotdog fold: wrapping up a superfamily of thioesterases and dehydratases (2004)
Dillon, Shane C, Bateman, Alex
Abstract Background The Hotdog fold was initially identified in the structure of Escherichia coli FabA and subsequently in 4-hydroxybenzoyl-CoA thioesterase from Pseudomonas sp. strain CBS. Since...
Enhanced protein domain discovery using taxonomy (2004)
Coin, Lachlan, Bateman, Alex, Durbin, Richard
Abstract Background It is well known that different species have different protein domain repertoires, and indeed that some protein domains are kingdom specific. This information has not yet been...
Novel protein domains and motifs in the marine planctomycete Rhodopirellula baltica (2004)
Studholme, David J., Fuerst, John A., Bateman, Alex
The planctomycetes are a phylum of bacteria that have a unique cell compartmentalisation and yeast-like budding cell division and peptidoglycan-less proteinaceous cell walls. We wished to further our...
Novel protein domains and motifs in the marine planctomycete Rhodopirellula baltica (2004)
Studholme, David J., Fuerst, John A., Bateman, Alex
The planctomycetes are a phylum of bacteria that have a unique cell compartmentalisation and yeast-like budding cell division and peptidoglycan-less proteinaceous cell walls. We wished to further our...
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...
The Pfam protein families database (2004)
Alex Bateman, Ewan Birney, Lorenzo Cerruti, Richard Durbin, Laurence Etwiller, Sean R. Eddy, ...
Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at
Research article Enhanced protein domain discovery using taxonomy (2004)
Bmc Bioinformatics, Lachlan Coin, Alex Bateman, Richard Durbin
Background: It is well known that different species have different protein domain repertoires, and indeed that some protein domains are kingdom specific. This information has not yet been...
The G5 domain: a potential N-acetylglucosamine recognition domain involved (2004)
in biofilm formation
Bmc Bioinformatics, Shane C Dillon, Alex Bateman, Shane C Dillon, Alex Bateman
The Hotdog fold: wrapping up a superfamily of thioesterases and
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...
Bateman, Alex, Holden, Matthew T. G., Yeats, Corin
Summary: Biofilms are complex microbial communities found at surfaces that are often associated with extracellular polysaccharides. Biofilm formation is a complex process that is only recently being...
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...
Bateman, Alex, Holden, Matthew T. G., Yeats, Corin
Summary: Biofilms are complex microbial communities found at surfaces that are often associated with extracellular polysaccharides. Biofilm formation is a complex process that is only recently being...
The TROVE module: A common element in Telomerase, Ro and Vault ribonucleoproteins (2003)
Bateman, Alex, Kickhoefer, Valerie
Abstract Background Ribonucleoproteins carry out a variety of important tasks in the cell. In this study we show that a number of these contain a novel module, that we speculate mediates RNA-binding....
A comparison of Pfam and MEROPS: Two databases, one comprehensive, and one specialised. (2003)
Studholme, David J, Rawlings, Neil D, Barrett, Alan J, Bateman, Alex
Abstract Background We wished to compare two databases based on sequence similarity: one that aims to be comprehensive in its coverage of known sequences, and one that specialises in a relatively...
Yeats, Corin, Bentley, Stephen, Bateman, Alex
Abstract Background Streptomyces coelicolor has long been considered a remarkable bacterium with a complex life-cycle, ubiquitous environmental distribution, linear chromosomes and plasmids, and a...
The InterPro Database, 2003 brings increased coverage and new features (2003)
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Barrell, Daniel, Bateman, Alex, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one...
Rfam: An RNA family database (2003)
Sam Griffiths-Jones, Alex Bateman, Mhairi Marshall, Ajay Khanna, Sean R. Eddy, Sean R
Rfam is a collection of multiple sequence alignments and covariance models representing non-coding RNA families. Rfam is available on the web in the UK at http://www.sanger.ac.uk/Software/Rfam/ and...
The InterPro Database, 2003 brings increased coverage and new features (2003)
Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Daniel Barrell, Alex Bateman, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one...
Alex Bateman, Valerie Kickhoefer, Open Access, Y Rnavrnatelomerase Rnavparptepro
Background: Ribonucleoproteins carry out a variety of important tasks in the cell. In this study we show that a number of these contain a novel module, that we speculate mediates RNA-binding....
The InterPro Database, 2003 brings increased coverage and new features (2003)
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Barrell, Daniel, Bateman, Alex, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one...
Rfam: an RNA family database (2003)
Griffiths-Jones, Sam, Bateman, Alex, Marshall, Mhairi, Khanna, Ajay, Eddy, Sean R.
Rfam is a collection of multiple sequence alignments and covariance models representing non-coding RNA families. Rfam is available on the web in the UK at http://www.sanger.ac.uk/Software/Rfam/ and...
Membrane-bound progesterone receptors contain a cytochrome b5-like ligand-binding domain (2002)
Mifsud, William, Bateman, Alex
Abstract Background Membrane-associated progesterone receptors (MAPRs) are thought to mediate a number of rapid cellular effects not involving changes in gene expression. They do not show sequence...
The SGS3 protein involved in PTGS finds a family (2002)
Abstract Background Post transcriptional gene silencing (PTGS) is a recently discovered phenomenon that is an area of intense research interest. Components of the PTGS machinery are being discovered...
The Pfam Protein Families Database (2002)
Alex Bateman, Ewan Birney, Lorenzo Cerruti, Richard Durbin, Laurence Etwiller, Sean R. Eddy, ...
Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in...
Mulder, Nicola J., Apweiler, Rolf, Attwood, Terri K., Bairoch, Amos, Bateman, Alex, ...
The exponential increase in the submission of nucleotide sequences to the nucleotide sequence database by genome sequencing centres has resulted in a need for rapid, automatic methods for...
HMM-based databases in InterPro (2002)
Bateman, Alex, Haft, Daniel H.
Protein family databases are an important resource for protein annotation and understanding protein evolution and function. In recent years hidden Markov models (HMMs) have become one of the key...
The Pfam Protein Families Database (2002)
Bateman, Alex, Birney, Ewan, Cerruti, Lorenzo, Durbin, Richard, Etwiller, Laurence, Eddy, Sean R., ...
Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at...
Griffiths-Jones, Sam, Bateman, Alex
Motivation: The best quality multiple sequence alignments are generally considered to derive from structural superposition. However, no previous work has studied the relative performance of profile...
QuickTree: building huge Neighbour-Joining trees of protein sequences (2002)
Howe, Kevin, Bateman, Alex, Durbin, Richard
Summary: We have written a fast implementation of the popular Neighbor-Joining tree building algorithm. QuickTree allows the reconstruction of phylogenies for very large protein families (including...
The Pfam Protein Families Database (2000)
Alex Bateman, Ewan Birney, Richard Durbin, Sean R. Eddy, Kevin L. Howe, Erik Sonnhammer, ...
Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in...
The Pfam Protein Families Database (2000)
Bateman, Alex, Birney, Ewan, Durbin, Richard, Eddy, Sean R., Howe, Kevin L., Sonnhammer, Erik L. L.
Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the WWW in the UK at...
Pfam: Multiple Sequence Alignments and HMM-Profiles of Protein Domains (1998)
Sean R. Eddy, Ewan Birney, Alex Bateman, Richard Durbin
Pfam contains multiple alignments and hidden Markov model based profiles (HMM-profiles) of complete protein domains. The definition of domain boundaries, family members and alignment is done...
The Pfam Protein Families Database
Bateman, Alex, Birney, Ewan, Cerruti, Lorenzo, Durbin, Richard, Etwiller, Laurence, Eddy, Sean R., ...
Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in...
The Pfam Protein Families Database
Bateman, Alex, Birney, Ewan, Durbin, Richard, Eddy, Sean R., Howe, Kevin L., Sonnhammer, Erik L. L.
Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the WWW in the UK at http://www.sanger.ac.uk/Software/Pfam/ , in Sweden at...
Membrane-bound progesterone receptors contain a cytochrome b5-like ligand-binding domain
Mifsud, William, Bateman, Alex
Membrane-associated progesterone receptors are thought to mediate a number of rapid cellular effects not involving changes in gene expression. These receptors are here identified as distant homologs...
A comparison of Pfam and MEROPS: Two databases, one comprehensive, and one specialised.
Studholme, David J, Rawlings, Neil D, Barrett, Alan J, Bateman, Alex
Griffiths-Jones, Sam, Bateman, Alex, Marshall, Mhairi, Khanna, Ajay, Eddy, Sean R.
Rfam is a collection of multiple sequence alignments and covariance models representing non-coding RNA families. Rfam is available on the web in the UK at http://www.sanger.ac.uk/Software/Rfam/ and...
The InterPro Database, 2003 brings increased coverage and new features
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Barrell, Daniel, Bateman, Alex, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one...
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...
Rfam: annotating non-coding RNAs in complete genomes
Griffiths-Jones, Sam, Moxon, Simon, Marshall, Mhairi, Khanna, Ajay, Eddy, Sean R., Bateman, Alex
Rfam is a comprehensive collection of non-coding RNA (ncRNA) families, represented by multiple sequence alignments and profile stochastic context-free grammars. Rfam aims to facilitate the...
InterPro, progress and status in 2005
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam,...
miRBase: microRNA sequences, targets and gene nomenclature
Griffiths-Jones, Sam, Grocock, Russell J., Van Dongen, Stijn, Bateman, Alex, Enright, Anton J.
The miRBase database aims to provide integrated interfaces to comprehensive microRNA sequence data, annotation and predicted gene targets. miRBase takes over functionality from the microRNA Registry...
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...
Enhanced protein domain discovery by using language modeling techniques from speech recognition
Coin, Lachlan, Bateman, Alex, Durbin, Richard
Most modern speech recognition uses probabilistic models to interpret a sequence of sounds. Hidden Markov models, in particular, are used to recognize words. The same techniques have been adapted to...
Metazoan Scc4 Homologs Link Sister Chromatid Cohesion to Cell and Axon Migration Guidance
Seitan, Vlad C, Banks, Peter, Laval, Steve, Majid, Nazia A, Dorsett, Dale, Rana, Amer, ...
Saccharomyces cerevisiae Scc2 binds Scc4 to form an essential complex that loads cohesin onto chromosomes. The prevalence of Scc2 orthologs in eukaryotes emphasizes a conserved role in regulating...
The Pfam Protein Families Database
Bateman, Alex, Birney, Ewan, Cerruti, Lorenzo, Durbin, Richard, Etwiller, Laurence, Eddy, Sean R., ...
Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in...
The Pfam Protein Families Database
Bateman, Alex, Birney, Ewan, Durbin, Richard, Eddy, Sean R., Howe, Kevin L., Sonnhammer, Erik L. L.
Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the WWW in the UK at http://www.sanger.ac.uk/Software/Pfam/ , in Sweden at...
Membrane-bound progesterone receptors contain a cytochrome b5-like ligand-binding domain
Mifsud, William, Bateman, Alex
Membrane-associated progesterone receptors are thought to mediate a number of rapid cellular effects not involving changes in gene expression. These receptors are here identified as distant homologs...
A comparison of Pfam and MEROPS: Two databases, one comprehensive, and one specialised.
Studholme, David J, Rawlings, Neil D, Barrett, Alan J, Bateman, Alex
Griffiths-Jones, Sam, Bateman, Alex, Marshall, Mhairi, Khanna, Ajay, Eddy, Sean R.
Rfam is a collection of multiple sequence alignments and covariance models representing non-coding RNA families. Rfam is available on the web in the UK at http://www.sanger.ac.uk/Software/Rfam/ and...
The InterPro Database, 2003 brings increased coverage and new features
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Barrell, Daniel, Bateman, Alex, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one...
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...
Enhanced protein domain discovery by using language modeling techniques from speech recognition
Coin, Lachlan, Bateman, Alex, Durbin, Richard
Most modern speech recognition uses probabilistic models to interpret a sequence of sounds. Hidden Markov models, in particular, are used to recognize words. The same techniques have been adapted to...
Rfam: annotating non-coding RNAs in complete genomes
Griffiths-Jones, Sam, Moxon, Simon, Marshall, Mhairi, Khanna, Ajay, Eddy, Sean R., Bateman, Alex
Rfam is a comprehensive collection of non-coding RNA (ncRNA) families, represented by multiple sequence alignments and profile stochastic context-free grammars. Rfam aims to facilitate the...
InterPro, progress and status in 2005
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam,...
miRBase: microRNA sequences, targets and gene nomenclature
Griffiths-Jones, Sam, Grocock, Russell J., Van Dongen, Stijn, Bateman, Alex, Enright, Anton J.
The miRBase database aims to provide integrated interfaces to comprehensive microRNA sequence data, annotation and predicted gene targets. miRBase takes over functionality from the microRNA Registry...
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...
Metazoan Scc4 Homologs Link Sister Chromatid Cohesion to Cell and Axon Migration Guidance
Seitan, Vlad C, Banks, Peter, Laval, Steve, Majid, Nazia A, Dorsett, Dale, Rana, Amer, ...
Saccharomyces cerevisiae Scc2 binds Scc4 to form an essential complex that loads cohesin onto chromosomes. The prevalence of Scc2 orthologs in eukaryotes emphasizes a conserved role in regulating...
New developments in the InterPro database
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs,...
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...
Protein interactions in human genetic diseases
Schuster-Böckler, Benjamin, Bateman, Alex
A method is presented to identify residues that form part of an interaction interface, leading to the prediction that 1,428 OMIM mutations are related to an interaction defect.
Large-scale screening for novel low-affinity extracellular protein interactions
Bushell, K. Mark, Söllner, Christian, Schuster-Boeckler, Benjamin, Bateman, Alex, Wright, Gavin J.
Extracellular protein–protein interactions are essential for both intercellular communication and cohesion within multicellular organisms. Approximately a fifth of human genes encode...
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...
The RNA WikiProject: Community annotation of RNA families
Daub, Jennifer, Gardner, Paul P., Tate, John, Ramsköld, Daniel, Manske, Magnus, Scott, William G., ...
The online encyclopedia Wikipedia has become one of the most important online references in the world and has a substantial and growing scientific content. A search of Google with many RNA-related...