During the last few years new functionalities of RNA have been discovered, renewing the need for computational tools for their analysis. To this respect, multiple sequence alignmen...
Abstract: Version 9 of the Amber simulation programs includes a new semi-empirical hybrid QM/MM functionality. This includes support for implicit solvent (generalized Born) and for...
Background: The alignment of multiple protein sequences is a fundamental step in the analysis of biological data. It has traditionally been applied to analyzing protein families f...
Background: Similaritysearch in chemical structure databases is an important problem with many applications in chemical genomics, drug design, and efficient chemical probe screeni...
Xiaohong Wang, Jun Huan, Aaron M. Smalter, Gerald ...
A realistic simulation system, which couples geometry and physics, can provide a useful toolkit for virtual environments. Interactions among moving objects in the virtual worlds a...