Abstract: A method (and system) of analyzing protein folding trajectory includes a combinatorial pattern discovery process for analyzing multidimensional data from a simulation of the protein folding trajectory. The method of analyzing protein folding trajectory allows a user to understand the global state changes and folding mechanism of a protein during its folding process. The method may further include generating a collection of data points by simulation experiments, analyzing the collection of data points to extract patterned clusters, filtering the patterned clusters to remove insignificant patterned clusters to obtain a collection of filtered patterned clusters and analyzing the collection of filtered pattern clusters.

Abstract: Techniques for protein structure analysis are provided. In one aspect, a method of analyzing a multi-domain protein structure comprises the following steps. For at least one domain, a hydrophobic dipole, e.g., defined as a first-order hydrophobic moment of the domain, is calculated. A score representing the orientation of the hydrophobic dipole of the at least one domain relative to a hydrophobic dipole of one or more other domains of the multi-domain protein structure is then calculated.

Abstract: Techniques for protein structure analysis are provided. In one aspect, a method of characterizing at least a portion of a protein structure comprising amino acid residues comprises the following steps. A set of values characterizing the protein structure are determined, wherein each value represents a distance from a center of the protein structure to a center of a given one or more of the amino acid residues. One or more other sets of values characterizing the hydrophobicity of the protein structure are obtained. A Fourier transform is performed on each of the sets of values to obtain transformed values sets. The transformed value sets are compared to correlate the hydrophobicity with the protein structure.

Abstract: Techniques for analyzing one or more protein structures. In one aspect of the invention, the technique comprises the following steps. A normalized second-order hydrophobic moment is determined for a protein structure. The normalized second-order hydrophobic moment is then used for analysis of the protein structure. A scoring function in accordance with the normalized second-order hydrophobic moment for the protein structure may be determined. A score for the protein structure may then be generated using the scoring function. The scoring function may represent an integral of the normalized second-order hydrophobic moment. The scores may be generated for a plurality of protein structures. The scores generated for the plurality of protein structures may then be compared.

Abstract: A system and method for molecular dynamic simulation includes a database for storing data pertaining to at least one biomolecular system, a memory device for storing instructions for performing at least one algorithm having an electrostatic interaction calculating function and a multiple time step function, and subdividing forces on a basis of distance over which the forces act, and a processor for processing the data by executing the instructions in order to propagate the biomolecular system from a first set of coordinates to a second set of coordinates. The system and method significantly speed up the molecular dynamics simulation of biomolecular systems in which there are long-range and short-range electrostatic interactions and in which there are fast and slow motions, and make practicable the simulation of large protein solutions and thus, can be used to simulate protein folding and the binding of substrates to protein molecules.

Abstract: The invention provides a method for significantly speeding up the molecular dynamics simulation of large heterogeneous molecular assemblies in which there are a very large number of charged groups and in which there are strong and weak bonds. This method makes practicable the simulation of large protein solutions and thus can be used to simulate protein folding and the binding of substrates to protein molecules among other applications.