Treating flexibility in molecular docking is a major challenge in cell biology research. Here
we describe the background and the principles of existing flexible protein–protein docking …

A general framework for constructing and using probabilistic models of complex systems that
would enable a computer to use available information for making decisions. Most tasks …

The formalism of probabilistic graphical models provides a unifying framework for capturing
complex dependencies among random variables, and building large-scale multivariate …

Protein side-chain packing (PSCP), the task of determining amino acid side-chain
conformations given only backbone atom positions, has important applications to protein …

Proteins play a critical role in carrying out biological functions, and their 3D structures are
essential in determining their functions. Accurately predicting the conformation of protein …

Szeliski et al. published an influential study in 2006 on energy minimization methods for
Markov random fields. This study provided valuable insights in choosing the best …

The paper addresses the problem of generating multiple hypotheses for prediction tasks that
involve interaction with users or successive components in a cascade. Given a set of …

Proteomics techniques have been used to generate comprehensive lists of protein
interactions in a number of species. However, relatively little is known about how these …

Seven years ago, Szeliski et al. published an influential study on energy minimization
methods for Markov random fields (MRF). This study provided valuable insights in choosing …

Prediction of side chain conformations of amino acids in proteins (also termed “packing”) is
an important and challenging part of protein structure prediction with many interesting …