Molecular flexibility in computational protein design: an algorithmic perspective

Accommodating protein flexibility in computational drug design.

The need to account for the dynamic behavior of a receptor has long been recognized as a complicating factor in computational drug design. The use of a single, rigid protein structure—usually from a high-quality X-ray crystal structure— still is the standard in most applications (Zheng and Kyle, 1997; Walters et al., 1998). The choice to use a single protein structure is usually based on speed....

Computational molecular biology - an algorithmic approach

Computational molecular biology is a new discipline, bringing together computational, statistical, experimental, and technological methods, which is energizing and dramatically accelerating the discovery of new technologies and tools for molecular biology. The MIT Press Series on Computational Molecular Biology is intended to provide a unique and effective venue for the rapid publication of mon...

Design and computational flexibility

This article discusses three levels of computer use—literacy, fluency and flexibility. Literacy is about the use of particular tools to satisfy well-defined tasks while fluency is a deeper form of knowledge that allows people to adapt to the uncertainties of computing and keep up with new, technological trends. Computational flexibility suggests the further capacity to invent software when exis...

Algorithmic Contributions to Computational Molecular Biology

Liquid Democracy: An Algorithmic Perspective

We study liquid democracy, a collective decision making paradigm that allows voters to transitively delegate their votes, through an algorithmic lens. In our model, there are two alternatives, one correct and one incorrect, and we are interested in the probability that the majority opinion is correct. Our main question is whether there exist delegation mechanisms that are guaranteed to outperfo...