Related papers: Variational approach to protein design and extract…
We propose a novel method for the determination of the effective interaction potential between the amino acids of a protein. The strategy is based on the combination of a new optimization procedure and a geometrical argument, which also…
The possibility of deriving the contact potentials between amino acids from their frequencies of occurence in proteins is discussed in evolutionary terms. This approach allows the use of traditional thermodynamics to describe such…
The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…
In this paper we introduce a novel method of deriving a pairwise potential for protein folding. The potential is obtained by optimization procedure, which simultaneously maximizes the energy gap for {\it all} proteins in the database. To…
We apply a new approach to the reverse protein folding problem. Our method uses a minimization function in the design process which is different from the energy function used for folding. For a lattice model, we show that this new approach…
We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. Using numerical simulations of all chains containing eight or ten monomers, we…
Recent advances in coarse-grained lattice and off-lattice protein models are reviewed. The sequence dependence of thermodynamical folding properties are investigated and evidence for non-randomness of the binary sequences of good folders…
We propose and discuss a novel strategy for protein design. The method is based on recent theoretical advancements which showed the importance to treat carefully the conformational free energy of designed sequences. In this work we show how…
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 of local interactions, native structure formation does not…
We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…
Understanding the principles of protein folding is a cornerstone of computational biology, with implications for drug design, bioengineering, and the understanding of fundamental biological processes. Lattice protein folding models offer a…
We present the results of a self-consistent, unified molecular dynamics study of simple model heteropolymers in the continuum with emphasis on folding, sequence design and the determination of the interaction parameters of the effective…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
These lectures will address two questions. Is there a simple variational principle underlying the existence of secondary motifs in the native state of proteins? Is there a general approach which can qualitatively capture the salient…
We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding,…
We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using…
Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…
Gate-based universal quantum computers form a rapidly evolving field of quantum computing hardware technology. In previous work, we presented a quantum algorithm for lattice protein folding on a cubic lattice, tailored for quantum…
A coarse-grained off-lattice model that is not biased in any way to the native state is proposed to fold proteins. To predict the native structure in a reasonable time, the model has included the essential effects of water in an effective…
A variational method for computing conformational properties of molecules with Lennard-Jones potentials for the monomer-monomer interactions is presented. The approach is tailored to deal with angular degrees of freedom, {\it rotors}, and…