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PROTDES: CHARMM toolbox for computational protein design.

Suárez M, Tortosa P, Jaramillo A - Syst Synth Biol (2009)

Bottom Line: PROTDES allows the integration of molecular dynamics within the protein design.Our software allows CHARMM users to perform protein design calculations and to create their own procedures for protein design using their own energy functions.We show this by implementing three different energy functions based on different solvent treatments: surface area accessibility, generalized Born using molecular volume and an effective energy function.

View Article: PubMed Central - PubMed

Affiliation: Biochemistry Laboratory, CNRS-UMR 7654, Ecole Polytechnique, 91128, Palaiseau, France, Maria.Suarez@polytechnique.edu.

ABSTRACT
We present an open-source software able to automatically mutate any residue positions and find the best aminoacids in an arbitrary protein structure without requiring pairwise approximations. Our software, PROTDES, is based on CHARMM and it searches automatically for mutations optimizing a protein folding free energy. PROTDES allows the integration of molecular dynamics within the protein design. We have implemented an heuristic optimization algorithm that iteratively searches the best aminoacids and their conformations for an arbitrary set of positions within a structure. Our software allows CHARMM users to perform protein design calculations and to create their own procedures for protein design using their own energy functions. We show this by implementing three different energy functions based on different solvent treatments: surface area accessibility, generalized Born using molecular volume and an effective energy function. PROTDES, a tutorial, parameter sets, configuration tools and examples are freely available at http://soft.synth-bio.org/protdes.html .

No MeSH data available.


Structure of the highest binding predicted peptide, using the ASA solvation, in the HLA-A2 binding pocket. The peptide is represented by a stick model and the HLA-A2 molecule is represented by its molecular surface. Figure generated using the Pymol (DeLano 2002) viewer software
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Fig2: Structure of the highest binding predicted peptide, using the ASA solvation, in the HLA-A2 binding pocket. The peptide is represented by a stick model and the HLA-A2 molecule is represented by its molecular surface. Figure generated using the Pymol (DeLano 2002) viewer software

Mentions: Figure 2 is a graphical representation of the results obtained with PROTDES using the ASA model with 200 iterations. The calculation was performed in a 2.13GHz CPU and each complete run of PROTDES took around 40 min.Fig. 2


PROTDES: CHARMM toolbox for computational protein design.

Suárez M, Tortosa P, Jaramillo A - Syst Synth Biol (2009)

Structure of the highest binding predicted peptide, using the ASA solvation, in the HLA-A2 binding pocket. The peptide is represented by a stick model and the HLA-A2 molecule is represented by its molecular surface. Figure generated using the Pymol (DeLano 2002) viewer software
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2735645&req=5

Fig2: Structure of the highest binding predicted peptide, using the ASA solvation, in the HLA-A2 binding pocket. The peptide is represented by a stick model and the HLA-A2 molecule is represented by its molecular surface. Figure generated using the Pymol (DeLano 2002) viewer software
Mentions: Figure 2 is a graphical representation of the results obtained with PROTDES using the ASA model with 200 iterations. The calculation was performed in a 2.13GHz CPU and each complete run of PROTDES took around 40 min.Fig. 2

Bottom Line: PROTDES allows the integration of molecular dynamics within the protein design.Our software allows CHARMM users to perform protein design calculations and to create their own procedures for protein design using their own energy functions.We show this by implementing three different energy functions based on different solvent treatments: surface area accessibility, generalized Born using molecular volume and an effective energy function.

View Article: PubMed Central - PubMed

Affiliation: Biochemistry Laboratory, CNRS-UMR 7654, Ecole Polytechnique, 91128, Palaiseau, France, Maria.Suarez@polytechnique.edu.

ABSTRACT
We present an open-source software able to automatically mutate any residue positions and find the best aminoacids in an arbitrary protein structure without requiring pairwise approximations. Our software, PROTDES, is based on CHARMM and it searches automatically for mutations optimizing a protein folding free energy. PROTDES allows the integration of molecular dynamics within the protein design. We have implemented an heuristic optimization algorithm that iteratively searches the best aminoacids and their conformations for an arbitrary set of positions within a structure. Our software allows CHARMM users to perform protein design calculations and to create their own procedures for protein design using their own energy functions. We show this by implementing three different energy functions based on different solvent treatments: surface area accessibility, generalized Born using molecular volume and an effective energy function. PROTDES, a tutorial, parameter sets, configuration tools and examples are freely available at http://soft.synth-bio.org/protdes.html .

No MeSH data available.