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On updating torsion angles of molecular conformations

Posted on by Neshakar Posted in Correspondence 1 Comments ⇩

The order of the updates is important and some bookkeeping of the atom positions is necessary. The atom positions are computed by chaining series of such matrices. A single local frame is attached to each atom group. Numeric errors can accumulate as rotations around the bonds are repeated. This paper reviews the widely used simple rotations scheme, simple local frames method, and introduces a new atom group local frames method for maintaining the molecular conformation changes due to the changes of torsional angles. Bookkeeping is not necessary and numeric errors do not accumulate upon rotations. This paper introduces a new atom group local frames method to efficiently maintain molecular conformations. Multiple local frames are needed at a bond if it has more than one child. The simple rotations scheme applies a sequence of rotations to update all atom positions. Thus, the conformational maintenance cost is greatly reduced, especially when many conformations are generated and updated such as in a minimization process. This method also provides lazy evaluations for atom positions. Abstract Efficiently maintaining molecular conformations is important for molecular modeling and protein engineering. Although, for each conformational change, the Cartesian coordinates of atoms can be updated in linear time which is optimal asymptotically , the constant factor becomes significant if a large number of updates are needed.

On updating torsion angles of molecular conformations


The order of the updates is important and some bookkeeping of the atom positions is necessary. The atom positions are computed by chaining series of such matrices. Bookkeeping is not necessary and numeric errors do not accumulate upon rotations. This method also provides lazy evaluations for atom positions. However, for many applications, such as molecular docking, the Cartesian coordinates of atoms are needed for computation. Multiple local frames are needed at a bond if it has more than one child. The simple rotations scheme applies a sequence of rotations to update all atom positions. Abstract Efficiently maintaining molecular conformations is important for molecular modeling and protein engineering. Thus, the conformational maintenance cost is greatly reduced, especially when many conformations are generated and updated such as in a minimization process. Zhang and Kavraki J. This paper introduces a new atom group local frames method to efficiently maintain molecular conformations. The three main representations for conformations of molecules are Cartesian coordinates, a distance geometry descriptor which consists of a distance matrix and the signs of the volumes of quadruples of atoms , and internal coordinates. Both quantitative and experimental comparisons show that the improved simple rotations, in which rotations are expressed in unit quaternions, are as efficient as the atom-group local frames and, thus, have the advantage of avoiding the need of precomputations of a set of local frames and transformations between them. In this paper, by expressing the torsion-angle change as a composition of translations and rotations, we observe that the simple rotations can be implemented in an efficient way by taking advantage of consecutive operations. A single local frame is attached to each atom group. The simple local frames method builds local frames at the bonds, and relational matrices between parents and children frames are constructed. No bookkeeping is necessary and numeric errors do not accumulate upon rotations. Numeric errors can accumulate as rotations around the bonds are repeated. On the basis of their implementations, they showed that the atom-group local frames are more efficient than the other two. Although, for each conformational change, the Cartesian coordinates of atoms can be updated in linear time which is optimal asymptotically , the constant factor becomes significant if a large number of updates are needed. This paper reviews the widely used simple rotations scheme, simple local frames method, and introduces a new atom group local frames method for maintaining the molecular conformation changes due to the changes of torsional angles. In biochemistry, conformational changes of a molecule are usually described in terms of internal coordinates.

On updating torsion angles of molecular conformations


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