WebJan 31, 2024 · The input to FoXSDock was the HADDOCK active residues as the binding site and the SAXS profile of the CRY1:CLOCK:BMAL1 bHLH PAS-AB complex. The entire sequences of CRY1 and CLOCK:BMAL1 bHLH PAS-AB subject to crystallography and SAXS, including vector artifacts after TEV cleavage, were used in the modeling ( 21 ).
HADDOCK Web Server - Help - Universiteit Utrecht
WebFeb 14, 2024 · Among these residues, we considered the ones with a higher solvent accessibility to serve as the main interface residues. Therefore, those have a relative solvent accessibility (RSA) higher than 30% are defined as the "active residues" while those lower than 30% are the "passive residues" for the parameterization of HADDOCK. WebMar 24, 2016 · The so-called ‘passive residues’ (surface neighbors of active residues) were automatically determined by HADDOCK. Active and passive residues are converted into highly ambiguous distance restraints between the defined interfaces (no pairwise residue–residue contact information from the template is used in the AIR-guided … class 10 real number mcq
How to Perform DNA-Protein docking using HADDOCK web
WebMar 16, 2024 · I did docking with the guru interface and the active residues were proposed with i-tasser, but rmsd was 11.7. the result is uploaded. This RMSD value indicates the average distance between the best 4 models of this cluster (#2) and the best scoring model generated by HADDOCK.So this is only an information about how much the best 4 … WebJun 2, 2024 · When only short cyclic peptides (≤10 residues) are considered, the performance of HADDOCK further increases, reaching 88.2% in bound receptor docking and 68.75% for fully unbound docking. A success rate of 100% is reached for both holo and apo receptor conditions when considering acceptable or higher-quality models for the … WebJan 27, 2024 · Passive AIRs (solvent accessible surface neighbors of active residues) were automatically defined by HADDOCK based on these active AIRs. Two extra passive AIRs were included on the ‘back side’ of the Mre11 capping domain to allow for the extended structure seen in ATP-free T. maritima MR (PDB: 3QG5; Lammens et al., 2011 ). download game naruto mugen pc free