Homology modeling plays a central role in determining protein structure in the structural
genomics project. The importance of homology modeling has been steadily increasing …

Comparative modelling of protein 3D structure can now be applied with reasonable
accuracy to ten times more protein sequences than the number of experimentally …

Modeling a protein structure based on a homologous structure is a standard method in
structural biology today. In this process an alignment of a target protein sequence onto the …

We present our database-screening tool SLIDE, which is capable of screening large data
sets of organic compounds for potential ligands to a given binding site of a target protein. Its …

We introduce a computational method to optimize the in vitro evolution of proteins.
Simulating evolution with a simple model that statistically describes the fitness landscape …

The last stage of protein folding, the “endgame,” involves the ordering of amino acid side-
chains into a well defined and closely packed configuration. We review a number of topics …

A 'protein design cycle', involving cycling between theory and experiment, has led to recent
advances in rational protein design. A reductionist approach, in which protein positions are …

Finding the minimum energy amino acid side-chain conformation is a fundamental problem
in both homology modeling and protein design. To address this issue, numerous …

Virtual screening can reduce costs and increase hit rates for lead discovery by eliminating
the need for robotics, reagent acquisition or production, and compound storage facilities …

Protein–protein binding is one of the critical events in biology, and knowledge of proteic
complexes three‐dimensional structures is of fundamental importance for the biochemical …