MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison

By Angel R. Ortiz, Charles E.M. Strauss, Osvaldo Olmea. Protein Science, 2002

531 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b6df329e1f595da06f198556b92ad3e04ce4511b

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Citations in the corpus

Using Multiple Microenvironments to Find Similar Ligand-Binding Sites: Application to Kinase Inhibitor Binding (2011, methodology): “…in binding ATP, ANP or ADP, we generate pairs of binding sites from functionally and structurally distant kinases by applying two rules: (1) two kinases are from different EC sub-subgroups; (2) the identity of structural alignment by MAMMOTH [36] between the two kinases is not higher than 30%.”
NEW TOOLS AND EXPANDED DATA ANALYSIS CAPABILITIES AT THE PROTEIN STRUCTURE PREDICTION CENTER (2007, methodology): “GDT plots, (4) alignment quality bar graphs, (5) comparison of models with”
Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre (2008, background): “40 Many pairs of proteins in the same SCOP superfamily are significantly structurally dissimilar.”
Protein structure prediction and analysis using the Robetta server (2004, unknown): “For de novo models, the Mammoth (21) structure-model comparison results are displayed for the top 10 matches with Z -scores > 4.5.”
The Protein Model Portal (2008, methodology): “The alignment between the target sequence and the template is inferred dynamically on-the-ﬂy by structural superposition of the ﬁnal model to the template structure using MAMMOTH [29].”
Detecting Remote Evolutionary Relationships among Proteins by Large-Scale Semantic Embedding (2011, methodology): “We then trained embeddings using ADDA as unlabeled data and SCOP as labeled data, where the labeled data was used in (i) an auxiliary classification task based on SCOP category labels or (ii) an auxiliary ranking task based either on SCOP category relationships or on MAMMOTH similarity scores.”
Comparative Protein Structure Modeling Using MODELLER (2016, methodology): “…of variants of profile-profile alignment methods that differ in the scoring functions they use (Pietrokovski, 1996; Rychlewski et al., 1998; Yona and Levitt, 2002; Panchenko, 2003; Sadreyev and Grishin, 2003; von Ohsen et al., 2003; Edgar, 2004; Marti-Renom et al., 2004; Zhou and Zhou, 2005).”
CASP11 Statistics and the Prediction Center Evaluation System (2016, background): “…alignment accuracy measures (AL0, AL4); results of the sequence-independent model-target comparisons (LGA_S, Mammoth,7 DALI11); RMSD (root mean square deviation); strereochemical correctness measure (Molprobity12); as well as measures based on local correctness of…”
MCQ4Structures to compute similarity of molecule structures (2013, methodology): “The global comparison methods [e.g. GDT_TS (Zemla 2003) or URMS (Ortiz et al. 2002)] aim to evaluate the overall proximity of objects, what makes them very useful for processing multiple structures.”