We are producing a database of expert-curated protein domain alignments, describing sequence and 3D-structure conservation within protein families and capturing the known functional diversity within these families. These multiple sequence alignments are used to generate position-specific score matrices (PSSMs), that may in turn be used in NCBI's web-based protein classification resources. Links to the Conserved Domain Database (CDD) are made by default from NCBI?s BLAST resource, www.ncbi.nlm.nih.gov/BLAST/, and from protein records in NCBI?s PubMed/Entrez browser, www.ncbi.nlm.nih.gov/entrez/query.fcgi. Further information about CDD and these search services is available at www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml. These information services may be used to identify conserved domains within a protein sequence. Curated domain models summarize the known functions of family members, using relevant citations from PubMed when possible. They also provide site-specific functional annotation, via sequence and structure alignments and via evidence-based interaction-site features. The CDD alignment curation project differs from earlier efforts, upon which it builds, in two fundamental ways: (i) 3D-structure information is used in a quantitative way, whenever possible, to guide alignments, and (ii) an explicit hierarchy of families and subfamilies, related by descent from a common ancestor, reflects the evolutionary history of each domain. When a 3D structure is known within a domain family, this information is used to define a conserved 3D core structure, a set of un-gapped blocks that must be identified in all representative sequences included in the alignment. Representative sequences are aligned to this core structure using threading or structure-based alignment algorithms or, when multiple structures are known, by structure-structure alignment. These procedures assure high alignment accuracy, as needed for accurate transfer of annotation to new family members identified by searching. Explicit hierarchies identify major gene duplication events in the molecular evolution of each family. Our basic strategy is to use domain-sequence clustering methods together with known domain architecture and phylogeny to identify what appear to be ancient orthology groups. These define explicitly annotated """"""""children"""""""" of the overall """"""""parent"""""""" alignment, and in turn provide more specific functional annotation. The CDD project employs a high level of automation, to produce structure-based alignments, to identify candidate orthology groups, to update CDD alignments with new sequences and structures, and to """"""""publish"""""""" the results to web servers. These algorithms and associated software required are described under another project, """"""""Alignment Tools for the Conserved Domain Database,"""""""" LM000045-12. This project describes human-expert curation of CDD alignments. The role of the CDD curators is multifaceted. They first of all must survey relevant scientific literature, to produce concise summaries of the known functions of each domain family and to choose citations useful to users of NCBI?s web-based classification resources. Curators must also examine the results of automated sequence and structure comparison to infer the location of conserved core blocks, an iterative process that requires judgment with respect to elimination of incomplete or erroneous sequence and structure data. Curators must also identify apparent orthology groups, based on the consensus of results from alternative molecular evolution and clustering methods. The curator group has so far produced about 1000 curated CDD families which are now available via NCBI's protein classification servers.
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