Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
J R Soc Interface. 2009 Aug 6;6 Suppl 4:S477-91. doi: 10.1098/rsif.2008.0508.focus. Epub 2009 Mar 11.

Challenges in the computational design of proteins.

Author information

  • 1Laboratoire de Biochimie, Ecole Polytechnique, CNRS, Palaiseau, France.

Abstract

Protein design has many applications not only in biotechnology but also in basic science. It uses our current knowledge in structural biology to predict, by computer simulations, an amino acid sequence that would produce a protein with targeted properties. As in other examples of synthetic biology, this approach allows the testing of many hypotheses in biology. The recent development of automated computational methods to design proteins has enabled proteins to be designed that are very different from any known ones. Moreover, some of those methods mostly rely on a physical description of atomic interactions, which allows the designed sequences not to be biased towards known proteins. In this paper, we will describe the use of energy functions in computational protein design, the use of atomic models to evaluate the free energy in the unfolded and folded states, the exploration and optimization of amino acid sequences, the problem of negative design and the design of biomolecular function. We will also consider its use together with the experimental techniques such as directed evolution. We will end by discussing the challenges ahead in computational protein design and some of their future applications.

PMID:
19324680
[PubMed - indexed for MEDLINE]
PMCID:
PMC2843960
Free PMC Article

Images from this publication.See all images (6)Free text

Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Icon for HighWire Icon for PubMed Central
    Loading ...
    Write to the Help Desk