Solvated protein–DNA docking using HADDOCK
نویسندگان
چکیده
منابع مشابه
Information-driven protein–DNA docking using HADDOCK: it is a matter of flexibility
Intrinsic flexibility of DNA has hampered the development of efficient protein-DNA docking methods. In this study we extend HADDOCK (High Ambiguity Driven DOCKing) [C. Dominguez, R. Boelens and A. M. J. J. Bonvin (2003) J. Am. Chem. Soc. 125, 1731-1737] to explicitly deal with DNA flexibility. HADDOCK uses non-structural experimental data to drive the docking during a rigid-body energy minimiza...
متن کاملSolvated docking: introducing water into the modelling of biomolecular complexes
MOTIVATION Interfacial water, which plays an important role in mediating biomolecular interactions, has been neglected in the modelling of biomolecular complexes. METHODS We present a solvated docking approach that explicitly accounts for the presence of water in protein-protein complexes. Our solvated docking protocol is based on the concept of the first encounter complex in which a water la...
متن کاملdMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking
Molecular-docking programs coupled with suitable scoring functions are now established and very useful tools enabling computational chemists to rapidly screen large chemical databases and thereby to identify promising candidate compounds for further experimental processing. In a broader scenario, predicting binding affinity is one of the most critical and challenging components of computer-aide...
متن کاملHADDOCK: a protein-protein docking approach based on biochemical or biophysical information.
The structure determination of protein-protein complexes is a rather tedious and lengthy process, by both NMR and X-ray crystallography. Several methods based on docking to study protein complexes have also been well developed over the past few years. Most of these approaches are not driven by experimental data but are based on a combination of energetics and shape complementarity. Here, we pre...
متن کاملCPORT: A Consensus Interface Predictor and Its Performance in Prediction-Driven Docking with HADDOCK
BACKGROUND Macromolecular complexes are the molecular machines of the cell. Knowledge at the atomic level is essential to understand and influence their function. However, their number is huge and a significant fraction is extremely difficult to study using classical structural methods such as NMR and X-ray crystallography. Therefore, the importance of large-scale computational approaches in st...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Journal of Biomolecular NMR
سال: 2013
ISSN: 0925-2738,1573-5001
DOI: 10.1007/s10858-013-9734-x