Marching cubes: A high resolution 3D surface construction algorithm
SIGGRAPH '87 Proceedings of the 14th annual conference on Computer graphics and interactive techniques
Least-Squares Estimation of Transformation Parameters Between Two Point Patterns
IEEE Transactions on Pattern Analysis and Machine Intelligence
Rotation invariant spherical harmonic representation of 3D shape descriptors
Proceedings of the 2003 Eurographics/ACM SIGGRAPH symposium on Geometry processing
BIBM '11 Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine
Recognition of binding patterns common to a set of protein structures
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Hi-index | 0.00 |
Electrostatic focusing is a general phenomenon that occurs in cavities and grooves on the molecular surface of biomolecules. Narrow surface features can partially shield charged atoms from the high-dielectric solvent, enhancing electrostatic potentials inside the cavity and projecting electric field lines outward into the solvent. This effect has been observed in many instances and is widely considered in the human examination of molecular structure, but it is rarely integrated into the digital representations used in protein structure comparison software. To create a computational representation of electrostatic focusing, that is compatible with structure comparison algorithms, this paper presents an approach that generates three-dimensional solids that approximate regions where focusing occurs. We verify the accuracy of this representation against instances of focusing in proteins and DNA. Noting that this representation also identifies thin focusing regions on the molecular surface that are unlikely to affect binding, we describe a second algorithm that conservatively isolates larger focusing regions. The resulting 3D solids can be compared with Boolean set operations, permitting a new range of analyses on the regions where electrostatic focusing occurs. They also represent a novel integration of molecular shape and electrostatic focusing into the same structure comparison framework.