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Amino acids control the protein folding process and maintain its functional fold. This study underlines the interest of the Laguerre tessellation to determine relevant amino acid volumes in proteins. Previous studies used a limited number of proteins and only buried residues. The present computations improve the method and results on three main points: (i)(More)
Protein structures are valuable tools to understand protein function. Nonetheless, proteins are often considered as rigid macromolecules while their structures exhibit specific flexibility, which is essential to complete their functions. Analyses of protein structures and dynamics are often performed with a simplified three-state description, i.e., the(More)
Protein structures are an ensemble of atoms determined experimentally mostly by X-ray crystallography or Nuclear Magnetic Resonance. Studying 3D protein structures is a key point for better understanding protein function at a molecular level. We propose a set of accurate tools, for analysing protein structures, based on the reliable method of(More)
Transmembrane proteins (TMPs) are major drug targets, but the knowledge of their precise topology structure remains highly limited compared with globular proteins. In spite of the difficulties in obtaining their structures, an important effort has been made these last years to increase their number from an experimental and computational point of view. In(More)
Hydroxamate analogs of fosfoxacin, the phosphate homolog of fosmidomycin, have been synthesized and their activity tested on Escherichia coli and Mycobacterium smegmatis DXRs. Except for compound 4b, the IC50 values of phosphate derivatives are approximately 10-fold higher than those of the corresponding phosphonates. Although their inhibitory activity on(More)
The calculation of the free energy of conformation is key to understanding the function of biomolecules and has attracted significant interest in recent years. Here, we present an improvement of the confinement method that was designed for use in the context of explicit solvent MD simulations. The development involves an additional step in which the(More)
The 3D structure of a protein is the main physical support of a protein's biological function; 3D protein folds are primarily maintained through interactions between amino acids. Inter-residue contacts are essential for the stability of protein folds. Therefore, many methodologies in the fields of structure analysis, structure prediction, and(More)
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