Aligning chemical structure diagrams with local search

Aligning chemical structure diagrams with local search

Chemists working in biomolecular application projects are usually looking at many related molecules (e.g. results of a virtual screening run, lead series development or library design). For a convenient visual analysis of this data it is essential that differences between molecules are easily detectable. This can be quite difficult if structural similarities are not taken into account while cre...

From Structure Diagrams to Visual Chemical Patterns

The intuitive way of chemists to communicate molecules is via two-dimensional structure diagrams. The straightforward visual representations are mostly preferred to the often complicated systematic chemical names. For chemical patterns, however, no comparable visualization standards have evolved so far. Chemical patterns denoting descriptions of chemical features are needed whenever a set of mo...

Search and Inference with Diagrams

We developed a process for presenting diagrammatic information on the World Wide Web such that the information is searchable and accessible to inference engines. We implemented this process for chart diagrams. Generally, information that is presented diagrammatically is stored in an image file. Typical search engines have access only to image tags and surrounding text. Hence, the information pr...

Fast local search methods for solving limited memory influence diagrams

Aligning Protein Sequences with Predicted Secondary Structure

Accurately aligning distant protein sequences is notoriously difficult. Since the amino acid sequence alone often does not provide enough information to obtain accurate alignments under the standard alignment scoring functions, a recent approach to improving alignment accuracy is to use additional information such as secondary structure. We make several advances in alignment of protein sequence...