A New Method for Fast and Accurate Derivation of Molecular Conformations

Zhang, Ming; Kavraki, Lydia E.

doi:10.1021/ci010327z

Cited by 63 publications

(47 citation statements)

References 11 publications

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“…Thus, several atoms in each peptide unit have constant coordinates in these frames. As proposed in a recent work [32], frames only need to be attached to rigid units (called atomgroups by the authors). Then, the relative location of atoms in an atomgroup only requires positional coordinates, yielding to a more efficient method for updating conformations.…”

Section: Kinematics Inspired Modelmentioning

confidence: 99%

Geometric algorithms for the conformational analysis of long protein loops

et al. 2004

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The efficient filtering of unfeasible conformations would considerably benefit the exploration of the conformational space when searching for minimum energy structures or during molecular simulation. The most important conditions for filtering are the maintenance of molecular chain integrity and the avoidance of steric clashes. These conditions can be seen as geometric constraints on a molecular model. In this paper, we discuss how techniques issued from recent research in Robotics can be applied to this filtering. Two complementary techniques are presented: one for conformational sampling and another for computing conformational changes satisfying such geometric constraints. The main interest of the proposed techniques is their application to the structural analysis of long protein loops. First experimental results demonstrate the efficacy of the approach for studying the mobility of loop 7 in amylosucrase from Neisseria polysaccharea.The supposed motions of this 17-residue loop would play a very important role in the activity of this enzyme.

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Section: Kinematics Inspired Modelmentioning

confidence: 99%

Geometric algorithms for the conformational analysis of long protein loops

et al. 2004

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“…[57]). Hence, one can represent the backbone of a protein in terms of φ, ψ, ω angles and the mobility of the side chains in terms of dihedral angles χ.…”

Section: Arap Energy and Dihedral Anglesmentioning

confidence: 99%

As-Rigid-As-Possible molecular interpolation paths

Nguyen

Jaillet

Redon

2017

J Comput Aided Mol Des

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This paper proposes a new method to generate interpolation paths between two given molecular conformations. It relies on the As-Rigid-AsPossible (ARAP) paradigm used in Computer Graphics to manipulate complex meshes while preserving their essential structural characteristics. The adaptation of ARAP approaches to the case of molecular systems is presented in this contribution. Experiments conducted on a large set of benchmarks show how such a strategy can efficiently compute relevant interpolation paths with large conformational rearrangements.

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“…The library provides a representation for atoms to undergo rotation about their covalent bonds. The development of the wkTorsion library was motivated by the Atom Group local frames method of (Zhang and Kavraki, 2002). That method was concerned with better ways to represent and analyze conformational change of molecules resulting from changes in torsion angles.…”

Section: Wktorsion Librarymentioning

confidence: 99%