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Protein design on computers. Five new proteins: Shpilka, grendel, fingerclasp, leather, and aida
Author(s) -
Sander Chris,
Vriend Gerrit,
Bazan Fernando,
Horovitz Am,
Nakamura Haruki,
Ribas Luis,
Finkelstein Alexei V.,
Lockhart Andrew,
Merkl Rainer,
Perry L. Jeanne,
Emery Stephen C.,
Gaboriaud Christine,
Marks Cara,
Moult John,
Verlinde Christophe,
Eberhard Marc,
Elofsson Arne,
Hubbard Tim J. P.,
Regan Lynne,
Banks Jay,
Jappelli Roberto,
Lesk Arthur M.,
Tramontano Anna
Publication year - 1992
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.340120203
Subject(s) - protein design , domain (mathematical analysis) , set (abstract data type) , computer science , sequence (biology) , computational biology , protein structure , biochemistry , biology , programming language , mathematics , mathematical analysis
What is the current state of the art in protein design? This question was approached in a recent two‐week protein design workshop sponsored by EMBO and held at the EMBL in Heidelberg. The goals were to test available design tools and to explore new design strategies. Five novel proteins were designed: Shpilka, a sandwich of two four‐stranded β‐sheets, a scaffold on which to explore variations in loop topology; Grendel, a four‐helical membrane anchor, ready for fusion to water‐soluble functional domains; Fingerclasp, a dimer of interdigitating β–β–α units, the simplest variant of the “handshake” structural class; Aida, an antibody binding surface intended to be specific for flavodoxin; Leather—a minimal NAD binding domain, extracted from a larger protein. Each design is available as a set of three‐dimensional coordinates, the corresponding amino acid sequence and a set of analytical results. The designs are placed in the public domain for scrutiny, improvement, and possible experimental verification.