Iterated profile searches with PSI-BLAST--a tool for discovery in protein databases.

By Stephen F. Altschul, Eugene V. Koonin. 1998

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Citations in the corpus

Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences (2019, background): “To do well at this prediction task, the learned representations must encode the underlying factors that inﬂuence sequence variation in the data.”
A simple and fast secondary structure prediction method using hidden neural networks (2005, methodology): “All involved secondary structure prediction methods were tested on the same PSI-BLAST results to make the comparison as unbiased as possible.”
Evolution of proteins and proteomes: a phylogenetics approach (2005, methodology): “The sensitivity of such homology searches has been more than doubled (Park, et al 1998) by profi le-based methods such as PSI-BLAST (Altschul and Koonin 1998, Altschul, et al 1997) or hidden markov models (Baldi, et al 1994, Eddy 1998).”
Predicting protein contact map using evolutionary and physical constraints by integer programming (2013, methodology): “…using the following input features: EPAD (a context-specific distance-based statistical potential) (Zhao and Xu, 2012), PSIBLAST sequence profile (Altschul and Koonin, 1998), secondary structure predicted by PSIPRED (Jones, 1999), pairwise contact score and contrastive MI (CMI) derived from…”
Ortholog identification in the presence of domain architecture rearrangement (2011, background): “Each functional or structural domain can then be used as a starting point to identify homologs in sequence databases such as UniProt [62] using BLAST, PSI-BLAST [63] or related tools.”
CPHmodels-3.0—remote homology modeling using structure-guided sequence profiles (2010, methodology): “This includes a PsiBlast search against a reduced non-redundant protein sequence database (nr), proﬁle-proﬁle alignment including predicted local structure information obtained from NetSurfP (7), and a double-sided Z -score evaluation.”
Prediction of the human membrane proteome (2010, methodology): “Sequence proﬁles were assembled for each query sequence with the position speciﬁc iterative basic local alignment search tool [29] using the complete UniProtKB/ Swiss-Prot [30] sequence set (release 14.8) as database and allowing a maximum of two iterations with an e -value cut-off of 1e (cid:2) 5.”
Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction (2006, methodology): “Casbon and Saqi tested a profile-to-pro-file approach relying on a hybrid PSI-BLAST/HMM protocol [26].”
Bioinformatics Original Paper Integrating Multi-attribute Similarity Networks for Robust Representation of the Protein Space (unknown): “For sequence based components of the similarity network, we choose two widely used sequence comparison methods, PSI-Blast (Altschul and Koonin, 1998), and HMMer (Eddy, 1998) on the SUPERFAMILY database (Gough, 2002) (HMMer is referred to as HMM throughout the paper).”
Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms (2004, methodology): “Each protein sequence in SGD is used as a query for the PSI-BLAST (Position-Specific Iterated BLAST) program ( 4 ) against the most recent version of the nonredundant (nr) protein sequence data set (5) at NCBI (6).”
Scalable web services for the PSIPRED Protein Analysis Workbench (2013, methodology): “For each method, a list of the best scoring PDB chains is compiled, and a homology model is built for each. pGenTHREADER and HHSearch natively output models, whereas MODELLER (14) is used to build models against the PSIBLAST results.”
The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data (2004, methodology): “The sequence of each enzyme which has been manually annotated was taken from the PDB sequences repository held at EBI (pdb_aa.fasta, available from the MSD group FTP site at ftp://ftp.ebi.ac.uk/pub/databases/msd/) and subjected to PSI-BLAST (6) analysis (using a cut-off of <0.0005 for inclusion in t”