PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains

@article{Aleksiev2009PiSQRDAW,
  title={PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains},
  author={Tyanko Aleksiev and Raffaello Potestio and F. Pontiggia and Stefano Cozzini and Cristian Micheletti},
  journal={Bioinformatics},
  year={2009},
  volume={25 20},
  pages={
          2743-4
        }
}
SUMMARY The PiSQRD web resource can be used to subdivide protein structures in quasi-rigid dynamical domains. The latter are groups of amino acids behaving as approximately rigid units in the course of protein equilibrium fluctuations. The PiSQRD server takes as input a biomolecular structure and the desired fraction of protein internal fluctuations that must be accounted for by the relative rigid-body motion of the dynamical domains. Next, the lowest energy modes of fluctuation of the protein… 

Figures from this paper

KOSMOS: a universal morph server for nucleic acids, proteins and their complexes

KOSMOS is the first online morph server to be able to address the structural dynamics of DNA/RNA, proteins and even their complexes, such as ribosomes by combining a variety of ENMs from full-atom to coarse-grained, backbone and hybrid models with one connection rule.

Corresponding Functional Dynamics across the Hsp90 Chaperone Family: Insights from a Multiscale Analysis of MD Simulations

Analysis of atomistic simulations of Hsp90 family representatives for which crystal structures of the full length protein are available reveals that the ligand-dependent structural modulations mostly consist of relative rigid-like movements of a limited number of quasi-rigid domains, shared by the three proteins.

Key intermolecular interactions in the E. coli 70S ribosome revealed by coarse-grained analysis.

In this work, intermolecular interactions in the Escherichia coli 70S ribosome are investigated by coarse-grained (CG) analysis and show a clear connection between the intermolescular interactions and the structural and functional properties of the ribosomes because of the reduced complexity in domain-based CG models.

MOBI: a web server to define and visualize structural mobility in NMR protein ensembles

MOBI uses structural superposition and local conformational differences to derive a robust binary mobility definition that is in excellent agreement with the manually curated definition used in the CASP8 experiment for intrinsic disorder in NMR structure.

Comparing interfacial dynamics in protein-protein complexes: an elastic network approach

The results suggest that these structurally- and biologically-different types of interfaces are stabilized by different balancing mechanisms between enthalpy and conformational entropy.

Determining Geometrically Stable Domains in Molecular Conformation Sets.

This work proposes a geometric approach for finding dynamic domains, where traces of atomic movements are compared in a pairwise manner, and search for their best superposition, and demonstrates its efficiency in analyzing ensembles of structures generated by NMR experiments and conformation sets from biomolecular simulations, such as molecular dynamics.

Exploring the Unfolding Pathway of Maltose Binding Proteins: An Integrated Computational Approach.

This work analyzes the topological origin and the dynamical role of the unfoldons using an integrated approach which combines a graph-theoretical analysis of the interaction network of the MBP native-state with steered molecular dynamics simulations.

Conformational fluctuations of UreG, an intrinsically disordered enzyme.

The recently developed replica exchange with solute tempering (REST2) computational methodology is used to explore the conformational space of UreG from Helicobacter pylori (HpUreG) and to identify its structural fluctuations.

References

SHOWING 1-10 OF 11 REFERENCES

ProMode: a database of normal mode analyses on protein molecules with a full-atom model

ProMode, a database collecting NMA results on protein molecules, was constructed and it is hoped that realistic animations of the protein dynamics can be observed easily without expensive software and hardware, and that the dynamic properties for various proteins can be compared with each other.

Optimal description of a protein structure in terms of multiple groups undergoing TLS motion.

A procedure, TLSMD, has been developed that analyzes the distribution of ADPs in a previously refined protein crystal structure in order to generate optimal multi-group TLS descriptions of the constituent protein chains, applicable to crystal structures at any resolution.

Accurate and efficient description of protein vibrational dynamics: Comparing molecular dynamics and Gaussian models

The model presented here emerges as a powerful tool to provide preliminary, fast yet accurate characterizations of protein near‐native motion as well as the same exact and computationally efficient treatment as previous simpler models.

The Protein Data Bank

The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.

Model‐free methods of analyzing domain motions in proteins from simulation: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme

A method based on the curl of the atomic displacements is described, which yields a sharp discrimination of domains, and which defines a unique interdomain screw‐axis, which is one more than provided by a pure mechanical hinge.

Large-amplitude nonlinear motions in proteins.

  • García
  • Physics, Chemistry
    Physical review letters
  • 1992
A molecular-dynamics calculation on a hydrated protein, crambin, demonstrates that (i) neighboring dihedral angles are correlated to local transitions in the protein backbone, and that (ii) the

The molecular modeling toolkit: A new approach to molecular simulations

  • K. Hinsen
  • Computer Science
    J. Comput. Chem.
  • 2000
The Molecular Modeling Toolkit is a library that implements common molecular simulation techniques, with an emphasis on biomolecular simulations, using modern software engineering techniques to overcome limitations associated with the large monolithic simulation programs that are commonly used for biomolecules.

On the rigid-body motion of molecules in crystals

The molecular modeling toolkit

  • J. Comput. Chem
  • 2000