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MolLoc: a web tool for the local structural alignment of molecular surfaces
Stefano Angaran1, Mary Ellen Bock, Claudio Garutti
1Department of Information Engineering, University of Padova, Via Gradenigo 6a, Padova, Italy.
Nucleic Acids Research
|May 26, 2009
Summary
MolLoc is a web server for comparing molecular surfaces, identifying local similarities between structures. It aids in discovering shared surface features even in molecules with different sequences and folds.
Area of Science:
- Structural bioinformatics
- Computational chemistry
- Molecular modeling
Background:
- Comparing molecular structures is crucial for understanding function and drug discovery.
- Existing methods may not effectively capture local surface similarities between diverse molecules.
Purpose of the Study:
- Introduce MolLoc, a novel web server for molecular local surface comparison.
- Enable the identification of shared surface characteristics between protein structures.
Main Methods:
- Utilizes PDB files for structural input.
- Performs local surface comparisons focusing on binding sites, cavities, or selected residues.
- Generates structural alignments maximizing surface superposition.
- Identifies atom pairs with similar physicochemical properties in close spatial proximity.
Main Results:
- Provides structural alignments based on surface superposition.
- Identifies conserved physicochemical properties on molecular surfaces.
- Derives new orientations to best superimpose identified atom subsets.
- Facilitates the detection of local surface similarity in proteins with varying sequences and folds.
Conclusions:
- MolLoc offers a powerful tool for local surface comparison.
- The approach is effective for identifying subtle structural similarities.
- Useful for hypothesis generation in drug design and understanding protein function.
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