Position-dependent protein mutant profile based on mean force field calculation
نویسندگان
چکیده
منابع مشابه
Position-dependent protein mutant profile based on mean force field calculation.
The application of the mean force field in protein mutant stability prediction is explored. Based on protein main chain characteristics, including polar fraction, accessibility and dihedral angles, the mean force field was constructed to evaluate the compatibility between an amino acid residue and its environment, from which a position-dependent protein mutant profile was constructed. At each p...
متن کاملIterative Force-Field Calculation and Molecular Dynamics of Cyclooctanone
Body's iterative force-field computer program has been used to calculate strain energies in cyclooctanone (I). 348 MHZ 1H NMR spectra of (I) have been investigated over the temperature range of 25° to -160°C. Two conformation processes affect the 1H NMR spectrum of (I). Iterative force-field calculations on the conformations and conformational interconversion paths of ...
متن کاملPotential of mean force and pKa profile calculation for a lipid membrane-exposed arginine side chain.
The issue of ionizable protein side chains interacting with lipid membranes has been the focus of much attention since the proposal of the paddle model of voltage-gated ion channels, which suggested multiple arginine (Arg) side chains may move through the hydrocarbon core of a lipid membrane. Recent cell biology experiments have also been interpreted to suggest that these side chains would face...
متن کاملOrientation-dependent potential of mean force for protein folding.
We present a solvent-implicit minimalistic model potential among the amino acid residues of proteins, obtained by using the known native structures [deposited in the Protein Data Bank (PDB)]. In this model, the amino acid side chains are represented by a single ellipsoidal site, defined by the group of atoms about the center of mass of the side chain. These ellipsoidal sites interact with other...
متن کاملPhysicochemical Position-Dependent Properties in the Protein Secondary Structures
Background: Establishing theories for designing arbitrary protein structures is complicated and depends on understanding the principles for protein folding, which is affected by applied features. Computer algorithms can reach high precision and stability in computationally designing enzymes and binders by applying informative features obtained from natural structures. Methods: In this study, a ...
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: "Protein Engineering, Design and Selection"
سال: 1996
ISSN: 1741-0126,1741-0134
DOI: 10.1093/protein/9.6.479