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754
The Pfam protein families database
- Nucleic Acids Res
, 2012
"... Pfam is a widely used database of protein families, currently containing more than 13 000 manually curated protein families as of release 26.0. Pfam is available via servers in the UK ..."
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Cited by 285 (9 self)
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Pfam is a widely used database of protein families, currently containing more than 13 000 manually curated protein families as of release 26.0. Pfam is available via servers in the UK
HMMER web server: interactive sequence similarity searching
- Nucleic Acids Research
, 2011
"... HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the soft-ware, HMMER3, have resulted in a 100-fold speed gai ..."
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HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the soft-ware, HMMER3, have resulted in a 100-fold speed gain relative to previous versions. It is now feasible to make efficient profile hidden Markov model (pro-file HMM) searches via the web. A HMMER web server
InterPro: the integrative protein signature database
, 2008
"... The InterPro database ..."
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Protein structure prediction on the Web: a case study using the Phyre server,
- Nat. Protoc.
, 2009
"... Abstract Determining the structure and function of a novel protein sequence is a cornerstone of many aspects of modern biology. Over the last three decades a number of state-of-the-art computational tools for structure prediction have been developed. It is critical that the broader biological commu ..."
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Cited by 246 (10 self)
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Abstract Determining the structure and function of a novel protein sequence is a cornerstone of many aspects of modern biology. Over the last three decades a number of state-of-the-art computational tools for structure prediction have been developed. It is critical that the broader biological community are aware of such tools and, more importantly, are capable of using them and interpreting their results in an informed way. This protocol provides a guide to interpreting the output of structure prediction servers in general and details one such tool in particular, the Phyre server. Phyre is widely used by the biological community with over 150 submissions per day and provides a simple interface to what can often seem an overwhelming wealth of data.
D: DrugBank 3.0: a comprehensive resource for ’omics’ research on drugs
- Nucleic Acids Res 2011, , Database Issue
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CDD: a conserved domain database for the functional annotation of proteins. Nucleic Acids Res
"... NCBI’s Conserved Domain Database (CDD) is a resource for the annotation of protein sequences with the location of conserved domain footprints, and functional sites inferred from these footprints. CDD includes manually curated domain models that make use of protein 3D structure to refine domain model ..."
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Cited by 147 (6 self)
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NCBI’s Conserved Domain Database (CDD) is a resource for the annotation of protein sequences with the location of conserved domain footprints, and functional sites inferred from these footprints. CDD includes manually curated domain models that make use of protein 3D structure to refine domain models and provide insights into sequence/ structure/function relationships. Manually curated models are organized hierarchically if they describe domain families that are clearly related by common descent. As CDD also imports domain family models from a variety of external sources, it is a partially re-dundant collection. To simplify protein annotation, redundant models and models describing homolo-gous families are clustered into superfamilies. By default, domain footprints are annotated with the corresponding superfamily designation, on top of which specific annotation may indicate high-confidence assignment of family membership. Pre-computed domain annotation is available for proteins in the Entrez/Protein dataset, and a novel interface, Batch CD-Search, allows the computation and download of annotation for large sets of protein queries. CDD can be accessed via
GtRNAdb: a database of transfer RNA genes detected in genomic sequence
- Nucleic Acids Res
, 2009
"... genomic sequence ..."
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MEROPS: the peptidase database
- Nucleic Acids Res
, 2004
"... Peptidases, their substrates and inhibitors are of great relevance to biology, medicine and biotech-nology. The MEROPS database ..."
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Cited by 129 (4 self)
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Peptidases, their substrates and inhibitors are of great relevance to biology, medicine and biotech-nology. The MEROPS database
REBASE-a database for DNA restriction and modification: enzymes, genes and genomes
- Nucleic Acids Res
, 2009
"... REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction–modification (R–M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, ..."
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Cited by 127 (12 self)
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REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction–modification (R–M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. Experimentally characterized homing endonucleases are also included. The fastest growing segment of REBASE contains the putative R–M systems found in the sequence databases. Comprehensive descriptions of the R–M content of all fully sequenced genomes are available including summary schematics. The contents of REBASE may be browsed from the web
A NEW GENERATION OF HOMOLOGY SEARCH TOOLS BASED ON PROBABILISTIC INFERENCE
, 2009
"... Many theoretical advances have been made in applying probabilistic inference methods to improve the power of sequence homology searches, yet the BLAST suite of programs is still the workhorse for most of the field. The main reason for this is practical: BLAST’s programs are about 100-fold faster tha ..."
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Many theoretical advances have been made in applying probabilistic inference methods to improve the power of sequence homology searches, yet the BLAST suite of programs is still the workhorse for most of the field. The main reason for this is practical: BLAST’s programs are about 100-fold faster than the fastest competing implementations of probabilistic inference methods. I describe recent work on the HMMER software suite for protein sequence analysis, which implements probabilistic inference using profile hidden Markov models. Our aim in HMMER3 is to achieve BLAST’s speed while further improving the power of probabilistic inference based methods. HMMER3 implements a new probabilistic model of local sequence alignment and a new heuristic acceleration algorithm. Combined with efficient vector-parallel implementations on modern processors, these improvements synergize. HMMER3 uses more powerful log-odds likelihood scores (scores summed over alignment uncertainty, rather than scoring a single optimal alignment); it calculates accurate expectation values (E-values) for those scores without simulation using a generalization of Karlin/Altschul theory; it computes posterior distributions over the ensemble of possible alignments and returns posterior probabilities (confidences) in each aligned residue; and it does all this at an overall speed comparable to BLAST. The HMMER project aims to usher in a new generation of more powerful homology search tools based on probabilistic inference methods.
