- Algorithms for finding the axis of a helix, J. Christopher, R. Swanson, and T. Baldwin.
The authors use this problem to detect structural patterns in protein
molecules.
- Alpha
shapes, defined by H. Edelsbrunner and others at U. Illinois,
provide a useful algorithmic tool for modeling shapes,
especially those formed by unions of spheres.
- Chemist's
http://www.csc.fi/lul/chem/graphics.html
Art Gallery. Molecular visualization pointers from L. Laaksonen,
Center for Scientific Computation, Finland.
- Computational Topology.
Survey paper by Dey, Edelsbrunner, and Guha, presented at the conference
"Computational Geometry -- Ten Years After". Includes descriptions of
applications in image processing, cartography, graphics, solid modeling,
mesh generation, and molecular modeling.
- DIMACS
Worksh. on Geometrical Methods for Conformational Modeling,
Aug. 1995. Program and talk abstracts.
- Discrete
algorithms in biology and chemistry (in German). Molecular modeling
and related projects at the German Nat. Res. Ctr. for Inf. Tech.,
Inst. for Algorithms and Scientific Computing.
- Fast
hierarchical methods for the n-body problem, CS 267, Berkeley, 1995.
- Geometric aspects of protein structure, Duke U.
- GRIP:
computer graphics for molecular studies, UNC.
- Molecular Geometry References, D. Abrahams-Gessel, Dartmouth.
- Nanotechnology, Ralph Merkle, Xerox PARC.
- Nanotechnology and molecular modeling on the WWW,
Sean Morgan.
- Network Science: computational chemistry.
- The NIH Molecular
Modeling home page. (Warning: lots of incredibly annoying cookies.)
- Parallel
n-body simulations using hierarchical octree representations of space.
- Protein
secondary structure assignment through Voronoi tesselation,
Dupuis, Sadoc, and Mornon.
- Prove protein volume evaluation software. This project at the
Free University of Brussels
uses Voronoi diagrams and weighted Voronoi diagrams to
analyze the portion of a molecule's volume taken up
by each atom in the molecule.
Mark Gerstein at Stanford has a directory with
very similar software and related papers.
- Rayasan
molecular modeling toolkit, Shastra project, U. Texas.
- Michel Sanner of Scripps studies algorithms for molecular modeling,
and published a paper on molecular surface accessability
at the 11th ACM Symp. Comp. Geom.
- Sausages,
proteins, and rho. In the talk announced here, J. MacGregor Smith
discusses Euclidean Steiner tree theory and describes potential
applications of Steiner trees to protein conformation and molecular
modeling.
- SMART: A
solvent-accessible triangulated surface generator for molecular graphics
and boundary element applications, R. J. Zauhar,
*J. Computer-Aided Molecular Design*9 (1995) 149-159. - Statistical
Geometry of Protein Structure. I. Vaisman performs statistical analysis
on Delaunay triangulations of protein atoms to find preferred clusters
of amino acids.
- The
Well-Separated Pair Decomposition and its Applications,
Paul Callahan's Johns Hopkins Ph.D. thesis
on hierarchical space decomposition
and its applications to n-body simulation.

Part of
Geometry in Action,
a collection of applications of computational geometry.

David Eppstein,
Theory Group,
ICS,
UC Irvine.

Semi-automatically filtered from a common source file.