How far divergent evolution goes in proteins.

By Alexey G. Murzin. 1998

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Citations in the corpus

ECOD: An Evolutionary Classification of Protein Domains (2014, background): “The homology level (H) groups together domains with common ancestry as suggested by high sequence-structure scores, functional similarity, shared unusual features [25], and literature.”
PROMALS: towards accurate multiple sequence alignments of distantly related proteins (2007, background): “(Murzin, 1998), aligning distantly related sequences is an important task.”
Mh1 domain of Smad is a degraded homing endonuclease. (2001, background): “The overall fold resemblance, signi®cant local structural match near the core of both molecules assembled around Zn2, local sequence similarity in the zinc-binding site region combined with functional similarity in DNA-binding modes strongly suggest that I-PpoI and MH1 shared a common ancestor and ”
Prediction of protein function from protein sequence and structure (2003, background): “Murzin (1998) and Grishin (2001) have discussed how far divergence can push the relationships between homology, structure and sequence divergence, and functional change.”
Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable data sets. (2008, background): “Moreover, the alignment includes unusual structural features such as β-bulges that are regarded as evidence for homology.(8) Thus, we believe that they are most likely homologous.”
Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. (1998, background): “In these cases, the superfamilies are kept separate until the subsequent discovery of intermediate structures provides strong support for their merger (see Murzin (1998) for a description of such cases).”
Protein sequence comparison and fold recognition: progress and good-practice benchmarking. (2011, unknown): “the limit of detectable sequence similarity [3, 4].”
Emergence of Protein Fold Families through Rational Design (2006, background): “Understanding the evolution of proteins is an intriguing but challenging problem in molecular biology [1–12], which in many regards is vital to the progress in the field.”
Evolution of function in protein superfamilies, from a structural perspective. (2001, background): “Typical members act on a coenzyme A thioester, so the identi®cation of ClpP protease as an evolutionary relative was unexpected (Murzin, 1998).”
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment (2011, methodology): “For HHblits, we selected the template HMMs from the clustered UniProt that contained the SCOP template sequence.”