Improved chemical shift prediction by Rosetta conformational sampling
نویسندگان
چکیده
منابع مشابه
SHIFTX2: significantly improved protein chemical shift prediction
A new computer program, called SHIFTX2, is described which is capable of rapidly and accurately calculating diamagnetic (1)H, (13)C and (15)N chemical shifts from protein coordinate data. Compared to its predecessor (SHIFTX) and to other existing protein chemical shift prediction programs, SHIFTX2 is substantially more accurate (up to 26% better by correlation coefficient with an RMS error that...
متن کاملImprovements to Robotics-Inspired Conformational Sampling in Rosetta
To accurately predict protein conformations in atomic detail, a computational method must be capable of sampling models sufficiently close to the native structure. All-atom sampling is difficult because of the vast number of possible conformations and extremely rugged energy landscapes. Here, we test three sampling strategies to address these difficulties: conformational diversification, intens...
متن کاملEnhanced Conformational Space Sampling Improves the Prediction of Chemical Shifts in Proteins
A biased-potential molecular dynamics simulation method, accelerated molecular dynamics (AMD), was combined with the chemical shift prediction algorithm SHIFTX to calculate (1)H(N), (15)N, (13)Calpha, (13)Cbeta, and (13)C' chemical shifts of the ankyrin repeat protein IkappaBalpha (residues 67-206), the primary inhibitor of nuclear factor kappa-B (NF-kappaB). Free-energy-weighted molecular ense...
متن کاملConformational Sampling by Self-Organization
A new stochastic algorithm for conformational sampling is described. The algorithm generates molecular conformations that are consistent with a set of geometric constraints, which include interatomic distance bounds and chiral volumes derived from the molecular connectivity table. The algorithm repeatedly selects individual geometric constraints at random and updates the respective atomic coord...
متن کاملProQM-resample: improved model quality assessment for membrane proteins by limited conformational sampling
SUMMARY Model Quality Assessment Programs (MQAPs) are used to predict the quality of modeled protein structures. These usually use two approaches: methods using consensus of many alternative models and methods requiring only a single model to do its prediction. The consensus methods are useful to improve overall accuracy; however, they frequently fail to pick out the best possible model and can...
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: 2012
ISSN: 0925-2738,1573-5001
DOI: 10.1007/s10858-012-9677-7