9 papers
Design of Sequences with Good Folding Properties in Coarse-Grained Protein Models
Anders Irbäck, Carsten Peterson, Frank Potthast +1
Background: Designing amino acid sequences that are stable in a given target structure amounts to maximizing a conditional probability. A straightforward approach to accomplish thi…
A Minimal Off-Lattice Model for Alpha-helical Proteins
Frank Potthast
A minimal off-lattice model for alpha-helical proteins is presented. It is based on hydrophobicity forces and sequence independent local interactions. The latter are chosen so as t…
Monte Carlo Procedure for Protein Design
Anders Irbäck, Carsten Peterson, Frank Potthast +1
A new method for sequence optimization in protein models is presented. The approach, which has inherited its basic philosophy from recent work by Deutsch and Kurosky [Phys. Rev. Le…
Local Interactions and Protein Folding: A 3D Off-Lattice Approach
Anders Irbäck, Carsten Peterson, Frank Potthast +1
The thermodynamic behavior of a three-dimensional off-lattice model for protein folding is probed. The model has only two types of residues, hydrophobic and hydrophilic. In absence…
Identification of Amino Acid Sequences with Good Folding Properties in an Off-Lattice Model
Anders Irbäck, Carsten Peterson, Frank Potthast
Folding properties of a two-dimensional toy protein model containing only two amino-acid types, hydrophobic and hydrophilic, respectively, are analyzed. An efficient Monte Carlo pr…
Binary Assignments of Amino Acids from Pattern Conservation
Anders Irbäck, Frank Potthast
We develop a simple optimization procedure for assigning binary values to the amino acids. The binary values are determined by a maximization of the degree of pattern conservation…