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A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
TMPad: an integrated structural database for helix-packing folds in transmembrane proteins
Allan Lo1, Cheng-Wei Cheng, Yi-Yuan Chiu
1Bioinformatics Laboratory, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan, Republic of China.
Nucleic Acids Research
|December 24, 2010
Summary
Transmembrane (TM) proteins are crucial for biological processes. The new TMPad database provides detailed structural information on TM protein helix-packing, aiding research into protein function and dynamics.
Area of Science:
- Structural Biology
- Biochemistry
- Bioinformatics
Background:
- Alpha-helical transmembrane (TM) proteins are vital for cellular functions.
- Understanding TM helix-helix interactions is key to protein folding, dynamics, and function.
- Experimental data and comprehensive databases for TM helix-packing are limited.
Purpose of the Study:
- To develop a comprehensive database of experimentally observed helix-helix interactions in TM proteins.
- To provide pre-calculated geometric descriptors and related structural information for TM helix-packing.
- To facilitate the study of relationships between helix-helix interactions and TM protein structure/function.
Main Methods:
- Development of the TransMembrane Protein Helix-Packing Database (TMPad).
- Integration of experimentally observed helix-helix interactions and structural data.
- Inclusion of geometric descriptors (contacts, distances, angles, shifts) and sequence/topology/ligand information.
Main Results:
- TMPad offers pre-calculated geometric descriptors at the helix-packing interface.
- The database includes sequence, topology, lipid accessibility, and ligand-binding data.
- Structural classification, schematic diagrams, and visualization tools are provided.
Conclusions:
- TMPad serves as a valuable online resource for investigating TM protein helix-packing.
- The database aids in deciphering the link between helix-helix interactions and TM protein structure/function.
- TMPad is publicly accessible for researchers worldwide.
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