Bio-Prodict is focused on delivering solutions for guiding scientific research in the field of protein engineering, molecular design and DNA diagnostics. We apply novel approaches to data mining, storage and analysis of protein data and combine these with state-of-the art analysis methods and visualization tools to create custom-built information systems for protein superfamilies. Over the years, these systems have proved to be powerful instruments for understanding many of the complex aspects involved in protein function and mutation effect prediction. Years of experience in software design, structural biology and the analysis of protein super-family data make Bio-Prodict your choice for protein-related data analysis and software design.
For any one protein family there is already an overwhelming amount of data available. Managing and integrating all this data can be a daunting task; studies that involve carrying over information from one protein to the other seem simple at a first glance, however, the amount of data that needs to be collected from heterogeneous sources, converted to syntactic and semantic homogeneity, validated, curated, stored and indexed, is enormous. To manage the increasing amounts of protein-related data Bio-Prodict has developed 3DM: systems that can automatically collect, store and connect many different super-family data types from various sources. Examples of data types that are used by 3DM are sequences, structural information, protein-ligand and protein-protein contact information, mutational data (which is automatically retrieved from literature), and information extracted from multiple sequence alignments (correlated mutations, amino acid conservation patterns, subfamily specific residues, etc). All these different data types are stored in specialized protein super-family system that are centered around a structure based multiple sequence alignment.
3DM applies a unified numbering scheme to the alignment, the sequences, and the structures. This numbering scheme makes it easy to visualize and integrate all different data types in the alignment, in the structures and in relation to each other, enabling easy detection of correlations between the different data types. Using a common numbering scheme for all proteins in the system allows for the easy transfer of information between proteins. 3DM super-family systems have a highly flexible setup making it easy to implement in-house data (such as mutational information).
3DM is tightly integrated with the state of the art molecular graphics and modeling software YASARA , which makes it easy to project the different data types on a protein structures and visualize trends extracted from the 3DM systems in a structural context. The use of YASARA, winner of the CASP8 refinement section, to build 3DM-based homology models ensures that you get the highest quality models possible.
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