We present an efficient algorithm for maintaining the boundary and surface area of protein molecules as they undergo conformational changes. We also describe a robust implementati...
Background: Estimators of free energies are routinely used to judge the quality of protein structural models. As these estimators still present inaccuracies, they are frequently e...
Federico Fogolari, Silvio C. E. Tosatto, Giorgio C...
The task of finding saddle points on potential energy surfaces plays a crucial role in understanding the dynamics of a micro-molecule as well as in studying the folding pathways ...
Background: In structural genomics, an important goal is the detection and classification of protein–protein interactions, given the structures of the interacting partners. We h...
Guillaume Launay, Raul Mendez, Shoshana J. Wodak, ...
In order to compute polarization energy of biomolecules, we describe a boundary element approach to solving the linearized Poisson–Boltzmann equation. Our approach combines sever...
Chandrajit L. Bajaj, Shun-Chuan Albert Chen, Alexa...