Faculty Opinions recommendation of Three-dimensional structures of membrane proteins from genomic sequencing.

By José N. Onuchic. 2016

23 citations recorded by the source corpus.

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Citations in the corpus

Predicting multiple conformations via sequence clustering and AlphaFold2 (2023, positive): “As previous studies have identified evolutionary couplings corresponding to multiple states of domain-based conformational changes 15,16,20 , we speculate that clustering-based MSA preprocessing methods will offer improvements over existing methods 14 and, importantly, insights into the evolution…”
Large-Scale Conformational Transitions and Dimerization Are Encoded in the Amino-Acid Sequences of Hsp70 Chaperones (2015, unknown): “This technique not only can reliably predict the protein native structure [45,48–52], but it can also predict the presence of multiple conformers of the same proteins [44,48,53], homo-multimerization [44,48] and protein-protein interactions [54,55].”
Amino acid coevolution reveals three-dimensional structure and functional domains of insect odorant receptors (2015, unknown): “These EC clusters suggest these regions are under strong evolutionary constraint and are therefore predictive of functional importance 28 .”
Applications of sequence coevolution in membrane protein biochemistry (2017, unknown): “This is similar to structural modeling of soluble and membrane proteins in the original Marks et al. (2011) and Hopf et al. (2012) studies [11,40] of soluble and membrane proteins, which use the evolutionary couplings (as well as secondary structure prediction) as constraints in distance geometry…”
Systematic evaluation of CS‐Rosetta for membrane protein structure prediction with sparse NOE restraints (2017, unknown): “…of TMH trimers with recurrent sequence motifs that reveal consensus networks of inter-helical contacts,20 or are based on correlated mutations.21 ,22 The latter approach requires a large number of homologous sequences, which are available only for a limited number of targets, however.23…”
Protein structure determination by combining sparse NMR data with evolutionary couplings (2015, unknown): “Sequence fragments of less than 70% of the full length of the search protein were removed, and sequences with more than 70% identity were down-weighted, as previously described 6,8 .”