Computational Algorithm for Chemical Space Navigation
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current computational methods are inadequate for efficiently navigating the vastness of chemical space to effectively retrieve chemical formula information, particularly in drug discovery and lead generation, due to limitations in existing algorithms and databases.
Innovation Solution
A computational and combinatorial algorithmic method is developed to search for chemical formulas that react with or catalyze a given formula, using a client/server system and molecular graph representations to efficiently explore chemical space, including the ability to input chemical formulas and byproduct formulas to obtain lists of related compounds, dipeptides, and proteins.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If traditional computational methods are used to search chemical space, then the approach is simple and easy to implement, but the efficiency and effectiveness of retrieving chemical formula information is insufficient
Solution Approach 1:
The patent segments the chemical space search problem into multiple components: molecular graph representation, reaction template matching, and combinatorial algorithm execution. This segmentation allows the complex task of searching through vast chemical spaces to be broken down into manageable computational steps, improving efficiency while maintaining systematic coverage.
Solution Approach 2:
The patent introduces molecular graphs and reaction templates as intermediary representations between the input chemical formulas and the target compounds. These intermediaries enable efficient pattern matching and reduce the computational complexity of directly searching through entire chemical spaces, allowing systematic exploration without exhaustive brute-force methods.
2Adaptability or versatility
If existing algorithms and databases are used, then the system is relatively simple, but it cannot effectively navigate the vastness of chemical space for lead generation
Solution Approach 1:
The patent transforms the search problem from a one-dimensional brute-force enumeration of chemical compounds into a multi-dimensional search using molecular graph representations. By representing molecules as graphs with nodes and edges, and using reaction templates as search criteria, the system can efficiently navigate the vast chemical space across multiple dimensions of molecular structure and reactivity, enabling effective lead generation.
3Reliability
If systematic exploration of chemical space is performed, then comprehensive coverage is achieved, but the complexity of finding target molecules increases
Solution Approach 1:
The patent implements feedback mechanisms through the combinatorial algorithm that iteratively refines search results based on reaction templates and molecular graph patterns. The system receives feedback from the reaction outcomes and adjusts subsequent searches to focus on promising leads, maintaining comprehensive coverage while reducing the complexity of identifying target molecules through intelligent search refinement.
Data Source
AI summary
A method is provided to create lead compound(s) by discovering a general chemical structure, moieties, formula(s) to explore suitable compositions by computer simulation and/or robotic biological or biochemical experiments at least partially based upon employing said lead compound(s) discover method, which includes steps for inputting at least one chemical formula and at least one byproduct formula, steps for creating a list of dipeptides that might dissociate the byproduct from the input formula by way of catalysis, steps for using these dipeptides to fingerprint a protein from its peptide sequence, and searching a protein database or use experimental methods to search for such proteins. A composition creating means is provide by way of computer simulation and/or robotic biological or biochemical experiments at least partially based upon employing, as lead compound(s), the final chemical structure, moieties, formula(s) generated and communicated the above method.