Abstract: The disclosure relates to a method of estimating the polar component of the solvation energy for a molecule embedded in different media. In one embodiment, the molecule is partially embedded in a membrane. For an atom of the molecule, the polar component of the atom's solvation energy is represented as a combination of at least a self-energy term and a screening-effect term. The self-energy term represents the contribution to the atom's polar component made by the membrane and the molecule's other atoms located inside the membrane. The screening-effect term represents the typically negative contribution to the atom's polar component made by the molecule's other atoms located outside the membrane. An analytical function is used to calculate the self-energy term.

Abstract: Systems and methods for storing protein structure information are provided. The system comprises a non-public database storing protein structure information, wherein the non-public database is coupled to a public database of non-proprietary protein structure information and to non-public sources of proprietary protein structure information. The non-public database may also be coupled to a database having protein structure information for substantially all the proteins of at least one organism genome. The method may comprise loading protein structure data from at least one public database and loading protein structure data from one or more proprietary sources of protein structure information. The public database may comprise the Protein Data Bank (PDB). Certain types of additional information are also advantageously loaded into the database. These may include classification data corresponding to at least one protein ontology.

Abstract: The present disclosure includes a method for locating functionally relevant atoms in protein structures, and a representation of spatial arrangements of these atoms allowing for flexible description of active sites in proteins. The search method can be based on comparison of local structure features of proteins that share a common biochemical function. Generally, the method does not depend on overall similarity of structures and sequences of compared proteins, or on previous knowledge about functionally relevant residues. The compared protein structures can be condensed to a graph representation, with atoms as nodes and distances as edge labels. Protein graphs can then be compared to extract all possible Common Structural Cliques. These cliques can be merged to create structural templates: graphs that describe structural analogies between compared proteins. Structures of serine endopeptidases were compared in pairs using the presented algorithm with different geometrical parameters.

Abstract: The disclosure relates to a method of estimating the polar component of the solvation energy for a molecule embedded in different media. In one embodiment, the molecule is partially embedded in a membrane. For an atom of the molecule, the polar component of the atom's solvation energy is represented as a combination of at least a self-energy term and a screening-effect term. The self-energy term represents the contribution to the atom's polar component made by the membrane and the molecule's other atoms located inside the membrane. The screening-effect term represents the typically negative contribution to the atom's polar component made by the molecule's other atoms located outside the membrane. An analytical function is used to calculate the self-energy term. In a preferred embodiment, the analytical function is a function of the distance from the atom to the membrane, the van der Waals radius of the atom, and the thickness of the membrane.

Abstract: A system and methods for rapidly and accurately assessing ligand binding characteristics for diverse classes of protein molecules. Modeling methods are used to represent the protein molecules and simulate their interaction with ligand molecules. Protein/ligand interactions are characterized by a fingerprint analysis that permits grouping of the proteins based on predicted structural features and ligand reactivity rather than sequence similarities or homology alone.

Abstract: Magnetic resonance data is generated as a set of digital signals in the time domain. Each signal represents a multiplicity of parameters (for example two or three dimensions in the frequency domain). Transformation of such multiparameter (multidimensional) time domain signals into the frequency domain to provide multidimensional spectra (in frequency or in space for resonance imaging) utilizes discrete Fourier transformation in a spectral region of interest by calculating matrix products of data points corresponding to successively spaced values of the time domain signal in sequence with data signals corresponding to successive frequency points to obtain the output spectra. To increase the efficiency of the calculations "zero padding" may be accomplished directly in the frequency domain reconstructing more or less data points there than the corresponding number of the acquired time domain points, to increase or decrease digital resolution. Small information rich regions of the spectra (e.g.