Protein-protein docking with a reduced protein model accounting for side-chain flexibility
نویسندگان
چکیده
منابع مشابه
ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility.
Protein-small molecule docking algorithms provide a means to model the structure of protein-small molecule complexes in structural detail and play an important role in drug development. In recent years the necessity of simulating protein side-chain flexibility for an accurate prediction of the protein-small molecule interfaces has become apparent, and an increasing number of docking algorithms ...
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Conventional rigid docking algorithms have been unsatisfactory in their computational results, largely due to the fact that protein structures are flexible in live environments. In response, we propose to introduce the side-chain flexibility in protein motif into the docking. First, the Morse theory is applied to curvature labeling and surface region growing, for segmentation of the protein sur...
متن کاملImproved side-chain modeling for protein-protein docking.
Success in high-resolution protein-protein docking requires accurate modeling of side-chain conformations at the interface. Most current methods either leave side chains fixed in the conformations observed in the unbound protein structures or allow the side chains to sample a set of discrete rotamer conformations. Here we describe a rapid and efficient method for sampling off-rotamer side-chain...
متن کاملProtein-protein docking with backbone flexibility.
Computational protein-protein docking methods currently can create models with atomic accuracy for protein complexes provided that the conformational changes upon association are restricted to the side chains. However, it remains very challenging to account for backbone conformational changes during docking, and most current methods inherently keep monomer backbones rigid for algorithmic simpli...
متن کاملProtein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations.
Protein-protein docking algorithms provide a means to elucidate structural details for presently unknown complexes. Here, we present and evaluate a new method to predict protein-protein complexes from the coordinates of the unbound monomer components. The method employs a low-resolution, rigid-body, Monte Carlo search followed by simultaneous optimization of backbone displacement and side-chain...
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ژورنال
عنوان ژورنال: Protein Science
سال: 2003
ISSN: 0961-8368,1469-896X
DOI: 10.1110/ps.0239303