---
res:
bibo_abstract:
- Geometry is crucial in our efforts to comprehend the structures and dynamics of
biomolecules. For example, volume, surface area, and integrated mean and Gaussian
curvature of the union of balls representing a molecule are used to quantify its
interactions with the water surrounding it in the morphometric implicit solvent
models. The Alpha Shape theory provides an accurate and reliable method for computing
these geometric measures. In this paper, we derive homogeneous formulas for the
expressions of these measures and their derivatives with respect to the atomic
coordinates, and we provide algorithms that implement them into a new software
package, AlphaMol. The only variables in these formulas are the interatomic distances,
making them insensitive to translations and rotations. AlphaMol includes a sequential
algorithm and a parallel algorithm. In the parallel version, we partition the
atoms of the molecule of interest into 3D rectangular blocks, using a kd-tree
algorithm. We then apply the sequential algorithm of AlphaMol to each block, augmented
by a buffer zone to account for atoms whose ball representations may partially
cover the block. The current parallel version of AlphaMol leads to a 20-fold speed-up
compared to an independent serial implementation when using 32 processors. For
instance, it takes 31 s to compute the geometric measures and derivatives of each
atom in a viral capsid with more than 26 million atoms on 32 Intel processors
running at 2.7 GHz. The presence of the buffer zones, however, leads to redundant
computations, which ultimately limit the impact of using multiple processors.
AlphaMol is available as an OpenSource software.@eng
bibo_authorlist:
- foaf_Person:
foaf_givenName: Patrice
foaf_name: Koehl, Patrice
foaf_surname: Koehl
- foaf_Person:
foaf_givenName: Arseniy
foaf_name: Akopyan, Arseniy
foaf_surname: Akopyan
foaf_workInfoHomepage: http://www.librecat.org/personId=430D2C90-F248-11E8-B48F-1D18A9856A87
orcid: 0000-0002-2548-617X
- foaf_Person:
foaf_givenName: Herbert
foaf_name: Edelsbrunner, Herbert
foaf_surname: Edelsbrunner
foaf_workInfoHomepage: http://www.librecat.org/personId=3FB178DA-F248-11E8-B48F-1D18A9856A87
orcid: 0000-0002-9823-6833
bibo_doi: 10.1021/acs.jcim.2c01346
bibo_issue: '3'
bibo_volume: 63
dct_date: 2023^xs_gYear
dct_identifier:
- UT:000920370700001
dct_isPartOf:
- http://id.crossref.org/issn/1549-9596
- http://id.crossref.org/issn/1549-960X
dct_language: eng
dct_publisher: American Chemical Society@
dct_title: Computing the volume, surface area, mean, and Gaussian curvatures of
molecules and their derivatives@
fabio_hasPubmedId: '36638318'
...