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The objective of this work is to obtain a water model for simulations of biological macromolecules in solution. A pragmatic approach is taken in which we use the same type of force field for the water as used for the solute and derive the water potential as an integral part of the ENCAD macromolecular potential. 1,2 Here we describe a flexible(More)
L We present the complete set of energy parameters used in the ENCAD (Energy Calculation and Dynamics) simulation program [J. Mol. Biol. 168 (1983) 5951. Full details are given of the form of the potential, which has been designed for efficient simulation of trajectories of macromolecules in solution. Emphasis is placed on energy conservation and the(More)
The Protein Data Bank in Europe (PDBe; pdbe.org) is actively involved in managing the international archive of biomacromolecular structure data as one of the partners in the Worldwide Protein Data Bank (wwPDB; wwpdb.org). PDBe also develops new tools to make structural data more widely and more easily available to the biomedical community. PDBe has(More)
The stability, dynamic, and structural properties of ubiquitin and two multiple hydrophobic core mutants were studied. One of the mutants (U4) has seven substitutions in the hydrophobic core (M1L, I3L, V5I, I13F, L15V, V17M, and V26L). On average, its side chains are larger than the wild-type, and it can thus be thought of as having an overpacked core. The(More)
The Protein Data Bank in Europe (http://pdbe.org) accepts and annotates depositions of macromolecular structure data in the PDB and EMDB archives and enriches, integrates and disseminates structural information in a variety of ways. The PDBe website has been redesigned based on an analysis of user requirements, and now offers intuitive access to improved(More)
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