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predict both 3-state and 8-state secondary structure using conditional neural fields from PSI-BLAST profiles: Webserver/downloadable: server download: 2011 GOR: Information theory/Bayesian inference: Many implementations: Basic GOR GOR V: 2002 (GOR V) Jpred: Multiple Neural network assignment from PSI-BLAST and HMMER profiles. Predicts ...
PSI Protein Classifier is a program generalizing the results of both successive and independent iterations of the PSI-BLAST program. PSI Protein Classifier determines belonging of the found by PSI-BLAST proteins to the known families. The unclassified proteins are grouped according to similarity.
PSI-blast based secondary structure PREDiction (PSIPRED) is a method used to investigate protein structure. It uses artificial neural network machine learning methods in its algorithm. [ 2 ] [ 3 ] [ 4 ] It is a server-side program, featuring a website serving as a front-end interface, which can predict a protein's secondary structure ( beta ...
The open-source software MMseqs is an alternative to BLAST/PSI-BLAST, which improves on current search tools over the full range of speed-sensitivity trade-off, achieving sensitivities better than PSI-BLAST at more than 400 times its speed. [27]
Of these PSI contributions over 20% represented new Pfam families, compared to the non-SG average of 5%. [12] Pfam families represent structurally distinct groups of proteins as predicted from sequenced genomes. Not targeting homologs of known structure was accomplished by using sequence comparison tools like BLAST and PSI-BLAST. [12]
CS-BLAST greatly improves alignment quality over the entire range of sequence identities and especially for difficult alignments in comparison to regular BLAST and PSI-BLAST. PSI-BLAST (Position-Specific Iterated BLAST) runs at about the same speed per iteration as regular BLAST, but is able to detect weaker sequence similarities that are still ...
Lipman is very well known for his seminal work on a series of sequence similarity algorithms, starting from the Wilbur-Lipman [13] algorithm in 1983, FASTA search [14] [15] in 1985, BLAST [16] in 1990, and Gapped BLAST and PSI-BLAST [17] in 1997. BLAST eventually became the most widely-used and highly-cited (over 160,000 citations as of 2021 ...
Psi is an ab initio computational chemistry package originally written by the research group of Henry F. Schaefer, III (University of Georgia). Utilizing Psi, one can perform a calculation on a molecular system with various kinds of methods such as Hartree-Fock , Post-Hartree–Fock electron correlation methods, and density functional theory .