Protein design: A perspective from simple tractable models
arXiv:cond-mat/9804199
Abstract
We review the recent progress in computational approaches to protein design which builds on advances in statistical-mechanical protein folding theory. In particular, we evaluate the degeneracy of the protein code (i.e. how many sequences fold into a given conformation) and outline a simple condition for ''designability`` in a protein model. From this point of view we discuss several popular protein models that were used for sequence design by several authors. We evaluate the strengths and weaknesses of popular approaches based on stochastic optimization in sequence space and discuss possible ways to improve them to bring them closer to experiment. We also discuss how sequence design affects folding and point out to some features of proteins that can be deigned ''in'' or designed ''out''}
12 pages three figures
References in corpus (8)
- Why Do Proteins Look Like Proteins?
- Chain length scaling of protein folding time
- Reply to Comment on "Criterion that Determines the Foldability of Proteins"
- A New Algorithm for Protein Design
- Is Heteropolymer Freezing Well Described by the Random Energy Model?
- Freezing Transition of Random Heteropolymers Consisting of an Arbitrary Set of Monomers
- Cooperativity of Protein Folding and the Random-Field Ising Model
- Elusive Unfoldability: Learning a Contact Potential to Fold Crambin
Cited by in corpus (11)
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- Size and structure of the sequence space of repeat proteins
- Testing simplified protein models of the hPin1 WW domain
- Interplay between pleiotropy and secondary selection determines rise and fall of mutators in stress response
- The Hypercube of Life: How Protein Stability Imposes Limits on Organism Complexity and Speed of Molecular Evolution
- Permutation glass
- Thermodynamics of protein folding: a random matrix formulation
- Thermal Adaptation in Viruses and Bacteria
- All-atom ab initio folding of a diverse set of proteins
- Protein Structure and Evolutionary History Determine Sequence Space Topology
- The Marginal Stability of Proteins: How Jiggling and Wiggling of Atoms are Connected to Neutral Evolution