Related papers: How to derive a protein folding potential? A new a…
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…
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…
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 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…
This paper presents a novel Differential Evolution algorithm for protein folding optimization that is applied to a three-dimensional AB off-lattice model. The proposed algorithm includes two new mechanisms. A local search is used to improve…
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…
An effective potential function is critical for protein structure prediction and folding simulation. Simplified protein models such as those requiring only $C_\alpha$ or backbone atoms are attractive because they enable efficient search of…
The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction,…
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…
A computational method is developed to work on an inverse equilibrium problem with an interest towards applications with protein folding. In general, we are given a set of equilibrium confgiurations and want to derive the most probable…
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…
Potential functions are critical for computational studies of protein structure prediction, folding, and sequence design. A class of widely used potentials for coarse grained models of proteins are contact potentials in the form of weighted…
Inverse protein folding -- the task of predicting a protein sequence from its backbone atom coordinates -- has surfaced as an important problem in the "top down", de novo design of proteins. Contemporary approaches have cast this problem as…
Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here a novel protein model capable of simultaneously provide quantitative protein design and…
Predicting protein secondary structure using lattice model is one of the most studied computational problem in bioinformatics. Here secondary structure or three dimensional structure of protein is predicted from its amino acid sequence.…
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…
We investigate the extent to which the commonly used standard pairwise contact potential can be used to identify the native fold of a protein. Ideally one would hope that a universal energy function exists, for which the native folds of all…
An effective potential function is critical for protein structure prediction and folding simulation. For simplified models of proteins where coordinates of only $C_\alpha$ atoms need to be specified, an accurate potential function is…
This work addresses the question of whether it is possible to define simple pair-wise interaction terms to approximate free energies of proteins or polymers. Rather than ask how reliable a potential of mean force is, one can ask how…