FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties.

By Jiye Shi, Tom L. Blundell, Kenji Mizuguchi. Journal of Molecular Biology, 2001

1,306 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1c21ae097a3041b98e33ccc3ce8371f5e814a365

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. Yang Zhang
2. Andrej Sali
3. Ben M. Webb
4. Jinbo Xu
5. Liam J. McGuffin
6. Jianlin Cheng
7. Torsten Schwede
8. Björn Wallner

In Molecular Biology

1. Yang Zhang
2. Andrej Sali
3. Jinbo Xu
4. Ben M. Webb
5. Liam J. McGuffin
6. Jianlin Cheng
7. Sheng Wang
8. Arne Elofsson

Citations in the corpus

• Using HHsearch to tackle proteins of unknown function: A pilot study with PH domains (2016, background): “Profiles can implicitly encode aspects of secondary structure((7)), but some tools go further by explicitly including secondary structure((8-10)), either relying on solved structures or predicting secondary structural elements((11,12)).”
• Structural bioinformatics A machine learning information retrieval approach to protein fold recognition (2006, neutral): “…1993; Abagyan et al., 1994; Murzin and Bateman, 1997; Xu et al., 1998; Jones, 1999; Panchenko et al., 2000; David et al., 2000; Shi et al., 2001; Skolnick and Kihara, 2001; Xu et al., 2003; Kim et al., 2003) align query sequences with template structures and compute compatibility scores…”
• Alignment of protein sequences by their profiles (2004, methodology): “For example, the FUGUE program (Shi et al. 2001) aligns correctly ∼6% more C atoms within 3.”
• Als3 Is a Candida albicans Invasin That Binds to Cadherins and Induces Endocytosis by Host Cells (2007, methodology): “The domains presented were the consensus of folds identified by Composer [53], MatchMaker [54], GeneFold [55], Robetta [56], Fugue [57], and Swiss-Model [58].”
• Protein structure modeling with MODELLER. (2014, background): “The differences are usually in the form of the gap-penalty function (linear, affine, or variable)(16), the substitution matrix used to score the aligned residues (20x20 matrices derived from alignments with a given sequence identity, those derived from structural alignments, and those incorporating ”
• Comparative Protein Structure Modeling Using Modeller (2006, methodology): “Commonly used threading programs are GenTHREADER (Jones, 1999; McGuffin and Jones, 2003), 3D-PSSM (Kelley et al., 2000) FUGUE (Shi et al., 2001), SP3 (Zhou and Zhou, 2005), SAM-T08 multi-track HMM (Karchin et al., 2003; Karplus et al., 2003), and MUSTER (Wu and Zhang, 2008).”
• Improving protein fold recognition by random forest (2014, background): “…folds when there is little sequence similarity between a target and a template protein, such as PSI-BLAST [18], HMMER [19], SAM-T98 [20], SSHMM [21],THREADER [22], FUGUE [23], SPARKS [24], SP3 [25], HHpred [26], FOLDpro [5], SP4 [27], SP5 [28], RAPTOR [29], SPARKS-X [30], and BoostThreader [31].”
• Can correct protein models be identified? (2003, methodology): “Models from seven of these servers were used: PDB-BLAST (Rychlewski et al. 2000), FFAS (Rychlewski et al. 2000), Sam-T99 (Karplus et al. 1998), mGenTHREADER (Jones 1999a), INBGU (Fischer 2000), FUGUE (Shi et al. 2001), and 3D-PSSM (Kelley et al. 2000).”
• 3D-Jury: A Simple Approach to Improve Protein Structure Predictions (2003, methodology): “…the 3D-Jury system operating in the best-model-mode on a set of eight servers (ORFeus Pas et al., 2003; SamT02, Karplus et al., 2001; FFAS03, Rychlewski et al., 2000; mGenTHREADER, Jones, 1999; INBGU, Fischer, 2000; RAPTOR, Xu et al., 2003; FUGUE-2, Shi et al., 2001; 3D-PSSM, Kelley et al., 2000).”
• Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. (2009, methodology): “In particular, some methods for estimating protein structure are knowledge based and rely on collecting the statistics of protein geometry and contact patterns to create objective functions to be minimized in the search for correct conformations (Fischer and Eisenberg 1996; Jaroszewski et al. 1998; ”
• Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee (2006, methodology): “These PDB structures are used as templates to guide the alignment of the original sequences using structure-based sequence alignment methods like SAP or Fugue.”