An HMM model for coiled-coil domains and a comparison with PSSM-based predictions

By Mauro Delorenzi, Terence P. Speed. Bioinform., 2002

478 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/9f33ae0160e3aa0c7fe9f645b9e9b2a92966f9cb

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In Molecular Biology

Citations in the corpus

Structural validation and assessment of AlphaFold2 predictions for centrosomal and centriolar proteins and their complexes (2022, methodology): “The secondary structure and coiled-coil regions were predicted using PsiPred 55 , Jpred 56 , and Marcoil 57 , Deepcoil 58 and Pcoils 59,60 .”
Automated inference of molecular mechanisms of disease from amino acid substitutions (2009, background): “, 2001), coiled-coil structure (Delorenzi and Speed, 2002), stability (Capriotti et al.”
Performance of mutation pathogenicity prediction methods on missense variants (2011, methodology): “…by the method PHD [Rost, 1996], transmembrane helix prediction by TMHMM [Krogh et al., 2001], coiled-coil structure prediction by MARCOIL [Delorenzi and Speed, 2002], stability prediction by I-Mutant 2.0 [Capriotti et al., 2005], B-factor prediction [Radivojac et al., 2004], and disorder…”
The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis (2016, methodology): “These highly accessed tools include both internal developments, such as CS-BLAST (6), HHblits (7) and PCOILS (8), and external tools, e.g. BLASTClust (9), Modeller (10) and MARCOIL (11) (Table 2).”
Multicoil2: Predicting Coiled Coils and Their Oligomerization States from Sequence in the Twilight Zone (2011, methodology): “For example, Marcoil [12,13] uses explicit knowledge of coiled coils to train a single HMM to efficiently search for a variable-length subsequence with a large value for a coiled-coil propensity statistic.”
An HMM posterior decoder for sequence feature prediction that includes homology information (2005, background): “The applications include transmembrane topology predictors (Sonnhammer et al., 1998; Tusnady and Simon, 1998), signal peptide predictors (Nielsen and Krogh, 1998), coil–coil protein predictors ( Delorenzi and Speed, 2002 ), gene predictors (Krogh et al., 1994b; Burge and Karlin, 1997), secondary str”
Paircoil2: improved prediction of coiled coils from sequence (2006, methodology): “We compared the performance of the programs Paircoil2, Paircoil, COILS, Multicoil and MARCOIL on individual coiled–coil families in the coiled–coil dataset used for training.”
A Unified Multitask Architecture for Predicting Local Protein Properties (2012, methodology): “Subsequent methods achieved improved accuracy by including correlations among residues [36–38] or by using hidden Markov models [39].”
Comparative analysis of coiled-coil prediction methods. (2006, methodology): “A further increase in informational input was achieved by Marcoil (Delorenzi and Speed, 2002), which calculates”