The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling

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Evaluating Protein Transfer Learning with TAPE (2019, background): “If good alignments are found, information from the alignments is either directly sufficient for the task at hand, or can be fed into downstream models for further use [24].”
Memoir: template-based structure prediction for membrane proteins (2013, neutral): “To illustrate Memoir’s use, models of the transmembrane domains of 15 membrane proteins were built using Memoir, HHpred and Swiss-Model’s automated mode (Table 1).”
Engineering Phage Host-Range and Suppressing Bacterial Resistance through Phage Tail Fiber Mutagenesis (2019, methodology): “(A) Three-dimensional structure of the tail fiber tip domain of phage T3 as modeled by SWISS-MODEL.”
Class of multiple sequence alignment algorithm affects genomic analysis. (2013, background): “MSAs are used regularly to, for example, estimate phylogenies (Felsenstein 2003), compare gene function between species (Eisen 1998), estimate protein structures (Arnold et al. 2006), and classify and annotate proteins (Finn et al. 2009) and ncRNAs (Gardner et al. 2011).”
Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin (2013, methodology): “To elucidate the structural mechanisms that are responsible for the additive and epistatic effects of the various α- and β-chain mutations on Hb-O2 affinity, we used the crystal structure of the LL-L rHb (PDB ID, 4h2l) to build a structural model for HH-H using MODELLER 9V11 (38) and SWISS-MODEL (39”