Self-consistent Knowledge-Based Approach to Protein Design

Author(s):  
Andrea Rossi ◽  
Cristian Micheletti ◽  
Flavio Seno ◽  
Amos Maritan
2001 ◽  
Vol 80 (1) ◽  
pp. 480-490 ◽  
Author(s):  
Andrea Rossi ◽  
Cristian Micheletti ◽  
Flavio Seno ◽  
Amos Maritan

2006 ◽  
Vol 16 (4) ◽  
pp. 508-513 ◽  
Author(s):  
Alan M Poole ◽  
Rama Ranganathan

2014 ◽  
Vol 10 (4) ◽  
Author(s):  
Jaume Bonet ◽  
Andras Fiser ◽  
Baldo Oliva ◽  
Narcis Fernandez-Fuentes

AbstractProtein structures are made up of periodic and aperiodic structural elements (i.e., α-helices, β-strands and loops). Despite the apparent lack of regular structure, loops have specific conformations and play a central role in the folding, dynamics, and function of proteins. In this article, we reviewed our previous works in the study of protein loops as local supersecondary structural motifs or Smotifs. We reexamined our works about the structural classification of loops (ArchDB) and its application to loop structure prediction (ArchPRED), including the assessment of the limits of knowledge-based loop structure prediction methods. We finalized this article by focusing on the modular nature of proteins and how the concept of Smotifs provides a convenient and practical approach to decompose proteins into strings of concatenated Smotifs and how can this be used in computational protein design and protein structure prediction.


2014 ◽  
Vol 30 (13) ◽  
pp. 1935-1936 ◽  
Author(s):  
Jaume Bonet ◽  
Joan Segura ◽  
Joan Planas-Iglesias ◽  
Baldomero Oliva ◽  
Narcis Fernandez-Fuentes

2008 ◽  
Vol 9 (4) ◽  
pp. 765-775 ◽  
Author(s):  
J. Shimada ◽  
A.V. Ishchenko ◽  
E.I. Shakhnovich

2002 ◽  
Vol 12 (4) ◽  
pp. 447-452 ◽  
Author(s):  
William P Russ ◽  
Rama Ranganathan

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