Characterizing the conformations of protein in the transition state ensemble (TSE) is important for studying protein folding. A promising approach pioneered by Vendruscolo et al40 to study TSE is to generate conformations that satisfy all constraints imposed by the experimentally measured φ-values that provide information about the native-likeness of the transition states. Faisca et al12 genera...

In this paper we propose a robotics-inspired method to enhance sampling of native-like conformations when employing only aminoacid sequence information for a protein at hand. Computing such conformations, essential to associating structural and functional information with gene sequences, is challenging due to the highdimensionality and the rugged energy surface of the protein conformational spa...

We describe a fast and accurate protocol, LoopBuilder, for the prediction of loop conformations in proteins. The procedure includes extensive sampling of backbone conformations, side chain addition, the use of a statistical potential to select a subset of these conformations, and, finally, an energy minimization and ranking with an all-atom force field. We find that the Direct Tweak algorithm u...

MOTIVATION Conformational searches in molecular docking are a time-consuming process with wide range of applications. Favorable conformations of the ligands that successfully bind with receptors are sought to form stable ligand-receptor complexes. Usually a large number of conformations are generated and their binding energies are examined. We propose adding a geometric screening phase before a...

Nondeterministic conformational search techniques, such as Genetic Algorithms (GAs) are promising for solving protein structure prediction (PSP) problem. The crossover operator of a GA can underpin the formation of potential conformations by exchanging and sharing potential sub-conformations, which is promising for solving PSP. However, the usual nature of an optimum PSP conformation being comp...

Shapes of a single, long DNA molecule condensed in a confinement of a virus capsid are described as conformations optimizing a model free energy functional accounting for the interplay between the bending energy of the DNA and the surface energy of the DNA bundled in a "rope". The rope is formed by bundled DNA brought together by (self-)attractive interactions. The conformations predicted by th...

Protein-structure elucidation is currently slow and expensive by physical means and current prediction algorithms either lack accuracy or scope. A data-driven dynamic-programming algorithm for predicting protein structures is presented. Observed conformations of short amino-acid chains in the Protein Data Bank are reduced to canonical conformations using singular value decomposition to remove c...

Hemoglobin is a tetrameric oxygen transport protein in animal bodies. However, there is a paucity of information regarding differences between alpha and beta subunits of hemoglobin in terms of oxygen affinity. The sequential model of Koshland, Nemthy and Filmer (KNF model) has attributed similar affinities to both alpha and beta subunits. The main purpose of the present study is to construct a ...