Variational approach to protein design and extraction of interaction potentials

Abstract

We present and discuss a novel approach to the direct and inverse protein folding problem. The proposed strategy is based on a variational approach that allows the simultaneous extraction of amino acid interactions and the low-temperature free energy of sequences of amino acids. The knowledge-based technique is simple and straightforward to implement even for realistic off-lattice proteins because it does not entail threading-like procedures. Its validity is assessed in the context of a lattice model by means of a variety of stringent checks.

5 pages, 3 figures

References in corpus (2)

• Protein design in a lattice model of hydrophobic and polar amino acids
• Steric constraints in model proteins

Cited by in corpus (5)

• Geometric and Statistical Properties of the Mean-Field HP Model, the LS Model and Real Protein Sequences
• Equilibrium properties of realistic random heteropolymers and their relevance for globular and naturally unfolded proteins
• A novel iterative strategy for protein design
• Iterative derivation of effective potentials to sample the conformational space of proteins at atomistic scale
• Determination of optimal effective interactions between amino acids in globular proteins