Abstract: A new approach to identifying binding conformations of chemical fragments and biological molecules is presented, in which fragment poses are explored in a systematic fashion. In an embodiment, for each pose, a fast computation is performed of the fragment interaction with the biological molecule using interpolation on a grid. Once the energies of fragment poses are computed, thermodynamical quantities such as binding affinity, binding enthalpy, and binding entropy are computed by direct sum over fragment poses. Using the present invention, it is possible to navigate fragment configuration space to identify separate binding modes. The present invention can be used to scan an entire biological molecule to identify possible binding pockets, or it can be used for localized explorations limited to interesting areas of known binding pockets.

Abstract: A method and system are provided for subdividing an arbitrarily shaped object into a collection of geometric elements ("cells") having predefined, simple topologies which facilitate further subdivision into tetrahedra, and which are well suited for further applications, such as finite element calculations. Initially, a representation of the object includes one or more regions, at least one of the regions not meeting the definition of "cell", each region having vertices, edges, and faces. An edge is selected according to a priority scheme, and slices which run through the edge and which also either run through other edges or vertices of the representation, are coplanar with other faces of the representation, or have other predetermined attributes, are considered for use in subdividing the representation. A score, which was initially calculated for the representation, is recalculated for hypothetical subdivisions of the representation incorporating each respective one of such slices.

Abstract: A method is provided for producing a mesh representation of an arbitrarily shaped object, for applications such as finite element analysis. The method includes the identifying elements of a mesh, such as a tetrahedral mesh, which are suitable, based on predetermined criteria, for merging into one of a predetermined set of target elements. For instance, if the predetermined set of target elements includes pentahedra and hexahedra, and the method operates on a tetrahedral mesh, then tetrahedra of the mesh are identified based on known ways of decomposing the target elements into tetrahedra. The groups of tetrahedra are identified based on whether they share faces in common, and whether they have faces which share a common edge and which are either coplanar or have an angle between the faces which satisfies a predetermined condition. The latter faces are referred to as quadrilateral pairs. A graph representation of the mesh is used, preferably including nodes representing regions of the mesh (i.e.

Abstract: A method for producing a set of points for a mesh of finite elements for a body to be analyzed, the body exhibiting boundaries and faces. The method comprises the steps of: producing an initial mesh of elements for the body, each element having a plurality of vertices and edges; for each vertex in a first subset of the vertices, finding points of intersection (POI) between a sphere of radius R, centered at a vertex being considered, and the boundaries and edges; determining if a found POI is either on or within the boundaries of the body and exhibits more than a minimum clearance distance from the boundaries, and vertices, any such POI being classified as a selected POI; inserting a selected POI in the initial mesh; and repeating the aforementioned steps for all POI's in the first subset and then proceeding to succeeding subsets of vertices until all POI's in all subsets have been considered.

Abstract: A method is described for producing a mesh of finite elements that are entirely within a body to be analyzed, the body exhibiting edges and surfaces. The method comprises the steps of: producing an initial mesh of elements for the body, each element having a plurality of vertices and edges; finding any body edge segment which is not coincident with a finite element edge and adding a vertex on that segment, the added vertex positioned to minimize the number new vertex points needed on the body edge segment. Additional finite elements are then created by connecting the new vertex to adjacent close vertices. A finite element is now identified which has both an edge coincident with an edge segment of the body and another edge segment that passes through a face of the body.

Abstract: A method for fine decomposition in finite element mesh generation, in which a polygonal boundary of a domain is input into the system by an analyst and the domain is automatically divided into rough elements generally corresponding to Voronoi regions, that is, regions which are closer to respective ones of the polygonal line segments or reflex vertices therebetween. Any arc portion of these regions is converted to a straight line. Additional lines are formed between interior vertices of the rough regions so that all rough regions are either triangles or trapezoids. Adjacent rough regions are then paired across internal boundaries and are classified into four types. The rough regions are then subdivided into fine regions of triangular shape according to rules associated with each of the four types. The degree of fine subdivision can be controlled according to known equations providing the total number of fine elements.