Enhanced genome annotation using structural profiles in the program 3D-PSSM.

By Lawrence A. Kelley, Robert M. MacCallum, Michael J.E. Sternberg. Journal of Molecular Biology, 2000

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View Paper: https://www.semanticscholar.org/paper/c7d62ec86db7b8219c9da41e580000df15d07749

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Citations in the corpus

Identification of correct regions in protein models using structural, alignment, and consensus information (2006, methodology): “To limit the number of models, only the first ranked model from the following servers were used: PDB-BLAST, FFAS (Rychlewski et al. 2000), Sam-T99 (Karplus et al. 1998), mGenTHREADER (Jones 1999a), INBGU, FUGUE (Shi et al. 2001), 3D-PSSM ( Kelley et al. 2000 ), and Dali (Holm and Sander 1993).”
EVA: evaluation of protein structure prediction servers (2003, background): “... P Fitzjohn and BC Moreira (26,27) CPHModels http://www.cbs.dtu.dk/services/CPHmodels/ S Brunak et al. (28) ESyPred3D http://www.fundp.ac.be/urbm/bioinfo/esypred/ C Lambert (29) SDSC1 http://cl.sdsc.edu/hm.html IN Shindyalov and PE Bourne (24) SwissModel http://www.expasy.org/swissmod/ T Schwede,”
Sequence and structural analysis of BTB domain proteins (2005, methodology): “Cul1 was replaced by a homology model of Cul3 that was generated using the 3D-PSSM server [129].”
Rapid Protein Side-Chain Packing via Tree Decomposition (2005, methodology): “The former step is usually done using protein threading programs [1, 2, 3, 4, 5, 6, 7, 8, 9, 10] or sequence-based homology search tools such as PDB-BLAST [11].”
Comparative Protein Structure Modeling Using MODELLER (2007, methodology): “Commonly used threading programs are GenTHREADER (Jones, 1999; McGufﬁn and Jones, 2003), 3D-PSSM (Kelley et al., 2000), FUGUE (Shi et al., 2001 Zhou, 2005), and SAM-T02 multi-track HMM (Karchin et al., 2003; Karplus et al., 2003).”
Structures and mechanisms of glycosyltransferases. (2006, methodology): “aUsing 3D-PSSM program (Kelley et al., 2000).”
Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre (2008, methodology): “…analogy detection have been achieved in the past decade, beginning with sequence–structure threading1–3 and structural profiles,4,5 including the use of predicted secondary structure,6 tertiary structure profiles,7,8 hidden Markov models,9,10 and most recently profile–profile matching algorithms.”
JPred4: a protein secondary structure prediction server (2015, background): “…structure alone is not as useful as a full three-dimensional model, secondary structure predictions provide important constraints for fold-recognition techniques (13–17) as well as in homology modelling (18,19), ab initio (20–24) and constraint-based tertiary structure prediction methods (25–27).”
A mutation in the vesicle-trafficking protein VAPB causes late-onset spinal muscular atrophy and amyotrophic lateral sclerosis. (2004, methodology): “…for normal and mutant proteins, by use of the 3D-PSSM server and the UCLA-DOE fold recognition server (top solution score of 62), on the basis of the major sperm protein (MSP) structure of Ascaris suum (Protein Data Bank code 1MSP) (Bullock et al. 1996; Kelley et al. 2000; Mallick et al. 2002).”
Pcons5: combining consensus, structural evaluation and fold recognition scores (2005, methodology): “In total 10,974 protein models for these eleven servers were used: PDB–BLAST [23], FFAS [23], Sam-T99 [16], mGenTHREADER [14], INBGU [7], three FUGUE servers [25], 3D-PSSM [18], Orfeus [11] and Superfamily [13].”
Improvement of the GenTHREADER Method for Genomic Fold Recognition (2003, methodology): “A number of other automatic methods have been developed that are designed to enhance sequence based searching by incorporating structural information, for example, INBGU (Fischer, 2000), 3D-PSSM (Kelley et al., 2000), FUGUE (Shi et al.”
The β-Subunit of the Arabidopsis G Protein Negatively Regulates Auxin-Induced Cell Division and Affects Multiple Developmental Processes Online version contains Web-only data. Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.006148. (2003, positive): “The fold-recognition servers BIOINBGU (Fischer, 2000), 3D-PSSM (Kelley et al., 2000), GenTHREADER (Jones, 1999), and FUGUE (Shi et al., 2001) all identified the Arabidopsis sequence GPA1 as a G protein with 99% confidence, and all but 3D-PSSM identified the Arabidopsis sequence AGB1 as a G protein…”
IL-33, an interleukin-1-like cytokine that signals via the IL-1 receptor-related protein ST2 and induces T helper type 2-associated cytokines. (2005, methodology): “…of dog DVS-27 (Onda et al., 1999) (accession # BAA75891) was identiﬁed by this effort from GenBank, and its IL-1 family assignment was secured by Superfamily (Gough and Chothia, 2002) and 3D-PSSM (Kelley et al., 2000) fold recognition methods that matched ittoIL-1/FGF b -trefoilfold templates.”