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Results for DC.creator="R." AND DC.creator="A." AND DC.creator="Engh" in section 18.3.2 of volume F page 1 of 2 pages. |
Formulation of refinement restraints
International Tables for Crystallography (2012). Vol. F, Section 18.3.2, pp. 475-483 [ doi:10.1107/97809553602060000857 ]
Formulation of refinement restraints 18.3.2. Formulation of refinement restraints A priori information regarding protein structure can be used in two ... In this chapter, we focus on the use of restraints. A common form of restraint is an energy function parameterized to represent a conformational energy of a protein, driving the refinement toward ...
Special geometries: cofactors, ligands, metals etc.
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.8, pp. 482-483 [ doi:10.1107/97809553602060000857 ]
... general orientation of an inhibitor for molecular modelling studies with a still lower effective accuracy, it may be that no refinement ... requirements increase, so does the need for good parameterization and a way of estimating when the density is incompatible with known ... of ligands selected from racemic mixtures, or the occurrence of a chemical reaction, or even falsely characterized substances. For such ...
Effects of hydrogen atoms in parameterization
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.7, p. 482 [ doi:10.1107/97809553602060000857 ]
... artifactual coupling might theoretically be of some concern, but is a second-order effect and presumably introduces effects smaller than the ...
Non-bonded interactions
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.6, p. 482 [ doi:10.1107/97809553602060000857 ]
Non-bonded interactions 18.3.2.6. Non-bonded interactions Like the potential parameterization of torsion-angle statistics with the CSD, parameterization of non-bonded interactions, typically into terms representing packing (an empirical mix of London dispersion forces and solvent effects), electrostatics and hydrogen bonding, is probably more strongly influenced by protein environment than ...
Torsion angles
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.5, p. 482 [ doi:10.1107/97809553602060000857 ]
... bonds or angles. However, since the torsion-angle distribution is a function not only of potential interactions of the peripheral groups ...
Planarity restraints
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.4, pp. 481-482 [ doi:10.1107/97809553602060000857 ]
... of parameterization described above. Physically realistic deviations should be allowed. A survey of several planar atoms, such as CG of aromatic ... values from perfect planarity might also be expected, particularly as a function of the protein fold environment. For example, an average ... References Marquart, M., Walter, J., Deisenhofer, J., Bode, W. & Huber, R. (1983). The geometry of the reactive site and ...
Sulfur-containing residues: methionine, cysteine, disulfides
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.3.7, p. 481 [ doi:10.1107/97809553602060000857 ]
... length. The 49 fragments now in the CSD also show a sample deviation for the 1.774Å average bond length of 0.056 ... sigma] outlier rejection, the tabulated value of 1.779Å still has a large sample deviation of 0.041Å. In practice, the use ...
Basic residues: arginine, lysine
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.3.6, p. 481 [ doi:10.1107/97809553602060000857 ]
Basic residues: arginine, lysine 18.3.2.3.6. Basic residues: arginine, lysine The 98 arginine fragments in the database did not show alterations from the EH values, except generally tighter restraints at the guanidinium group. Lysine CD-CE bond lengths are somewhat shorter in the new statistics, while the two angles derived from the ...
Acidic residues: glutamate, aspartate
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.3.5, p. 481 [ doi:10.1107/97809553602060000857 ]
... with delocalized charges as well as carboxylate groups encoded with a single charged oxygen atom. This distribution presumably reflects the variations ... of delocalization was evident. One measure of parameter variation as a function of varying charge delocalization is the anticorrelation of C ...
Neutral polar residues: serine, threonine, glutamine, asparagine
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.3.4, p. 481 [ doi:10.1107/97809553602060000857 ]
... are taken from arginine. This choice of fragments arose from a desire to maximize the number of fragments for the amide ...
International Tables for Crystallography (2012). Vol. F, Section 18.3.2, pp. 475-483 [ doi:10.1107/97809553602060000857 ]
Formulation of refinement restraints 18.3.2. Formulation of refinement restraints A priori information regarding protein structure can be used in two ... In this chapter, we focus on the use of restraints. A common form of restraint is an energy function parameterized to represent a conformational energy of a protein, driving the refinement toward ...
Special geometries: cofactors, ligands, metals etc.
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.8, pp. 482-483 [ doi:10.1107/97809553602060000857 ]
... general orientation of an inhibitor for molecular modelling studies with a still lower effective accuracy, it may be that no refinement ... requirements increase, so does the need for good parameterization and a way of estimating when the density is incompatible with known ... of ligands selected from racemic mixtures, or the occurrence of a chemical reaction, or even falsely characterized substances. For such ...
Effects of hydrogen atoms in parameterization
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.7, p. 482 [ doi:10.1107/97809553602060000857 ]
... artifactual coupling might theoretically be of some concern, but is a second-order effect and presumably introduces effects smaller than the ...
Non-bonded interactions
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.6, p. 482 [ doi:10.1107/97809553602060000857 ]
Non-bonded interactions 18.3.2.6. Non-bonded interactions Like the potential parameterization of torsion-angle statistics with the CSD, parameterization of non-bonded interactions, typically into terms representing packing (an empirical mix of London dispersion forces and solvent effects), electrostatics and hydrogen bonding, is probably more strongly influenced by protein environment than ...
Torsion angles
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.5, p. 482 [ doi:10.1107/97809553602060000857 ]
... bonds or angles. However, since the torsion-angle distribution is a function not only of potential interactions of the peripheral groups ...
Planarity restraints
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.4, pp. 481-482 [ doi:10.1107/97809553602060000857 ]
... of parameterization described above. Physically realistic deviations should be allowed. A survey of several planar atoms, such as CG of aromatic ... values from perfect planarity might also be expected, particularly as a function of the protein fold environment. For example, an average ... References Marquart, M., Walter, J., Deisenhofer, J., Bode, W. & Huber, R. (1983). The geometry of the reactive site and ...
Sulfur-containing residues: methionine, cysteine, disulfides
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.3.7, p. 481 [ doi:10.1107/97809553602060000857 ]
... length. The 49 fragments now in the CSD also show a sample deviation for the 1.774Å average bond length of 0.056 ... sigma] outlier rejection, the tabulated value of 1.779Å still has a large sample deviation of 0.041Å. In practice, the use ...
Basic residues: arginine, lysine
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.3.6, p. 481 [ doi:10.1107/97809553602060000857 ]
Basic residues: arginine, lysine 18.3.2.3.6. Basic residues: arginine, lysine The 98 arginine fragments in the database did not show alterations from the EH values, except generally tighter restraints at the guanidinium group. Lysine CD-CE bond lengths are somewhat shorter in the new statistics, while the two angles derived from the ...
Acidic residues: glutamate, aspartate
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.3.5, p. 481 [ doi:10.1107/97809553602060000857 ]
... with delocalized charges as well as carboxylate groups encoded with a single charged oxygen atom. This distribution presumably reflects the variations ... of delocalization was evident. One measure of parameter variation as a function of varying charge delocalization is the anticorrelation of C ...
Neutral polar residues: serine, threonine, glutamine, asparagine
International Tables for Crystallography (2012). Vol. F, Section 18.3.2.3.4, p. 481 [ doi:10.1107/97809553602060000857 ]
... are taken from arginine. This choice of fragments arose from a desire to maximize the number of fragments for the amide ...
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