Method and a system for automating the execution of AMoRe over a heterogenous network of computers

• US 7,203,683 B2
• Filed: 10/11/2002
• Issued: 04/10/2007
• Est. Priority Date: 10/11/2001
• Status: Expired due to Fees

• Current Assignee: Emerald BioStructures, Inc. (Beryllium LLC)
• Original Assignee: Emerald BioStructures, Inc. (Beryllium LLC)
• Inventors: Mixon, Mark B., Stewart, Lance, Prasad, Sridhar, Feese, Michael
• Primary Examiner(s): Coby; Frantz
• Application Number:
  US10/269,401
• Publication Number:
  US 20040215398A1
• Time in Patent Office: 1,642 Days
• Field of Search: 707/102, 707/3, 707/4, 707/100, 707/101, 707/103.R, 707/104.1, 707/10, 435/7.21, 457/7.1
• US Class Current: 1/1
• CPC Class Codes: G16B 15/00 ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
• CPC Class Codes: G16B 15/30 Drug targeting using structural data; Docking or binding prediction
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: Y10S 707/99945 Object-oriented database structure processing

Abstract

This invention encompasses an apparatus for creating a database containing the results of distributed molecular replacement searches, which comprise data input system for inputting the results of distributed molecular replacement searches and related information and a database generator coupled to said data input system for receiving the results of distributed molecular replacement searches and related information and creating a database for storing the results of distributed molecular replacement searches and related information. The invention includes method of managing the invention of distributed molecular replacement searches.

Claims

1. A method for managing an execution of distributed molecular replacement searches over a heterogeneous network of computers, said method including:

a. configuring a computer cluster such that there is one master computer and a plurality of remote slave computers;

b. notifying an available remote computer host in the computer cluster of a reflection data, search model or search model fragment, command queue, and run parameters required for execution of a distributed molecular replacement search;

c. executing the distributed molecular replacement search at a remote slave host;

d. filtering distributed molecular replacement output files for solution;

e. scoring solutions at the remote host for the presence of a distributed molecular replacement solution;

f. loading the solutions into a database;

g. listening for a response from the remote host indicating that the distributed molecular replacement search has been completed and that the host is available for another distributed molecular replacement search; and

h. repeating steps c through h until a search model queue is completed.

2. The method claimed in claim 1, further comprising:

a. initialization of a computer cluster.

3. The method claimed in claim 1, further comprising:

a. loading reflection data information from the database into master computer memory.

4. The method claimed in claim 1, further comprising:

a. generating and loading a search model queue information from the database into the master computer memory.

5. The method claimed in claim 1, further comprising:

a. expanding a search model queue to include a queue of search model fragments if requested.