Sandor Szalma

US Patent:

7107156, Sep 12, 2006

Filed:

Jul 23, 2002

Appl. No.:

10/205594

Inventors:

Velin Zlatkov Spassov - San Diego CA, US
Liqun Yan - San Diego CA, US
Sandor Szalma - San Diego CA, US

Assignee:

Accelrys Software Inc. - San Diego CA

International Classification:

G06F 19/00
G01N 33/48
G01N 31/00
G06G 7/48

US Classification:

702 27, 702 19, 702 22, 703 11

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.

US Patent:

20020072887, Jun 13, 2002

Filed:

Aug 20, 2001

Appl. No.:

09/933580

Inventors:

Sandor Szalma - San Diego CA, US
Mariusz Milik - San Diego CA, US
Krzysztof Olszewski - San Diego CA, US
Lisa Yan - San Diego CA, US
Azat Badretdinov - San Diego CA, US
Scott Kahn - Poway CA, US

International Classification:

G06G007/48

US Classification:

703/011000

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.

US Patent:

20040015301, Jan 22, 2004

Filed:

Apr 15, 2003

Appl. No.:

10/417891

Inventors:

Mariusz Milik - San Diego CA, US
Sandor Szalma - San Diego CA, US
Krzysztof Olszewski - San Diego CA, US

International Classification:

G06F019/00

US Classification:

702/027000

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. Additionally, a structural template was extracted from the structures of aminotransferases, two different proteins that catalyze the same type of chemical reaction. Presented results show that the method works efficiently even in the case of large protein systems, and allows for extraction of common structural features from proteins catalyzing a particular chemical reaction, but that evolved from different ancestors by convergent evolution.

US Patent:

20050182746, Aug 18, 2005

Filed:

Nov 24, 2004

Appl. No.:

10/997687

Inventors:

Steven Potts - San Diego CA, US
Sandor Szalma - San Diego CA, US
Yin Yu - San Diego CA, US
Scott Kahn - Poway CA, US
David Edwards - San Diego CA, US

International Classification:

G06F007/00

US Classification:

707001000

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. Mass spectroscopy data, NMR data and x-ray crystallography data may also be loaded into the database.