Rigid-body correction

Figure 10 Mean values of bond lengths and bond angles of pyrazole structures (a) Ehrlich (X-ray) (b) Berthou et at. (X-ray) (c) Rasmussen et at. (neutron, corrected for rigid body motion) (d) Rasmussen et at. (X-ray, 295 K) ...

Vibration corrected bond lengths based on the riding model for C(2)—N(1), rigid body libration for other C—N bonds, libration plus riding motion for N—H bonds. 

Usually, the top peaks of the translation search are then submitted to a low resolution quick rigid-body refinement, for which quick algorithms have been devised (Huber and Schneider, 1985 Navaza and Saludjian, 1997).The resolution is usually taken to be 12-4 Angstroms or so if one wants to use the low resolution terms, one should use a solvent effect correction technique (Fokine and Urzhumtsev, 2002). 

The need for automated protocols is apparent from the strategy adopted by AMoRe to circumvent the problem that the score of the rotation function (RF) is far from being perfect and does not always rank the solutions correctly (Navaza, 2001). Indeed, it is often observed that the true solution is not the top solution, with many false positives. Hence, AMoRe runs a translation function (TF) for each of, typically, the top 50 or 100 solutions of the rotation function. This is actually quite rapid as TF is based on FFT then, the first 10 solutions of each of these TF runs is in turn refined using a very effective implementation of rigid-body refinement (Navaza, 2001). 

Figure 7 The 20 highest ranking putative complexes from the best 100 FTDOCK candidates obtained after fine-grained rigid-body docking of the unbound barnase and barstar structures. Barnase is shown in the middle by dashed lines, surrounded by putative clusters of barstar orientations. The dense cluster to the right contains the correct docking orientation (shown in bold).

The librational motion can cause one atom to move in an arc relative to another. This is particularly so for hydrogen atoms and affects both the X-H and H- A bond lengths. Corrections are made by assuming that the motion is harmonic and that the molecules librate as a rigid body about their center of mass... 

In naphthalene and other polycyclic aromatic hydrocarbons apparent bond lengths become shorter, especially when they are more distant from the molecular center. When corrected for effects of rigid-body libration, this trend disappears. Studies of naphthalene, anthracene, and 4-hydroxybiphenyl illustrate this. In naphthalene... 

The first term is evidently the vibrational energy of the molecule, considered as a harmonic oscillator. The second term is the energy of rotation, assuming that the molecule is a rigid body,1 while the third term is the correction which takes account of the stretching of the actual, non-rigid molecule due to the rotation. The terms of higher order are unreliable because of the inaccuracy of the assumed potential function. 

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