Improvement of the GenTHREADER Method for Genomic Fold Recognition

By Liam J. McGuffin, David T. Jones. Bioinform., 2003

370 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/0b0e10bbce5952fd2d41424f51185543e7e20ba9

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In Molecular Biology

Citations in the corpus

Pfam 10 years on: 10 000 families and still growing (2008, methodology): “For example secondary structure prediction has been used for this purpose [30, 31] as well as fold recognition methods such as threading [32].”
Comparative Protein Structure Modeling Using MODELLER (2007, methodology): “…on structural features such as solvent exposure, secondary structure type, and hydrogen-bonding properties (Shi et al., 2001; Karchin et al., 2003; McGufﬁn and Jones, 2003; Zhou and Zhou, 2005), or on statistical potentials for residue interactions implied by the alignment (Sippl, 1990; Bowie et…”
The Genomic Threading Database (2004, methodology): “The Genomic Threading Database (GTD) is a resource of accurately annotated proteomes of key organisms made using the GenTHREADER method for genomic scale fold recognition (Jones, 1999a; McGufﬁn and Jones, 2003).”
Improving sequence-based fold recognition by using 3D model quality assessment (2005, background): “Often the term model quality is used to designate the class of programs that use the experimental structure to evaluate a generated model’s native-like structural quality.”
High-throughput production of human proteins for crystallization: The SGC experience (2010, background): “…on bioinformatic prediction of structured domains, primarily on structure-informed sequence alignments with proteins of known structure (GenThreader McGuffin and Jones, 2003), prediction of secondary structures and intrinsically disordered regions (PsiPred, DisorPred, FoldIndex (Jones, 1999;…”
Automated tertiary structure prediction with accurate local model quality assessment using the intfold‐ts method (2011, methodology): “12 Following this study, we also investigated the use of energy-based scores for general model evaluation, with the program MODCHECK, which was found to provide significant added value to numerous sequence based fold recognition servers.”
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).”
Protein structure prediction servers at University College London (2005, methodology): “In 2003, the GenTHREADER method was improved through the incorporation of additional structural information which resulted in the detection of more remote homologs and higher overall quality of the predicted models (9).”
Comparative Protein Structure Modeling Using MODELLER (2016, methodology): “…on structural features such as solvent exposure, secondary structure type, and hydrogen-bonding properties (Shi et al., 2001; Karchin et al., 2003; McGufﬁn and Jones, 2003; Zhou and Zhou, 2005) or on statistical potentials for residue interactions implied by the alignment (Sippl, 1990; Bowie et…”