SEM (Symmetry Equivalent Molecules): a web-based GUI to generate and visualize the macromolecules

Hussain, A.; Kumar, Ch. Kiran; Rajesh, C. K.; Sheik, S. S.; Sekar, K.

doi:10.1093/nar/gkg587

Cited by 3 publications

(2 citation statements)

References 7 publications

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“…Several internet computing engines and software programs were used to carry out analysis of the crystal structures. Trimers and the unit cell were generated from the coordinates and space-group information of the monomer in the asymmetric unit using the online package SEM (Symmetry Hussain et al, 2003). PSAP (Protein Structural Analysis Package; Balamurugan et al, 2007) was used to find the various interactions in the structure, including the ion pairs and water-mediated ion pairs.…”

Section: In Silico Analysismentioning

confidence: 99%

Observation of a calcium-binding site in the γ-class carbonic anhydrase fromPyrococcus horikoshii

Jeyakanthan

Rangarajan

Mridula

et al. 2008

Acta Crystallogr D Biol Crystallogr

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Carbonic anhydrases are zinc-containing metalloenzymes that catalyze the interconversion of carbon dioxide and bicarbonate. Three crystal structures of gamma-class carbonic anhydrase (one of which is bound to a bicarbonate molecule) from the aerobic OT3 strain of the hyperthermophilic archeon Pyrococcus horikoshii have been solved by molecular replacement in space group F4(1)32. The asymmetric unit contains a monomer of 173 amino acids and a catalytic Zn2+ ion. The protein fold is a regular prism formed by a left-handed beta-helix, similar to previously reported structures. The active-site Zn2+ ion located at the interface between the two monomers is bound to three histidyl residues and a water molecule in a tetrahedral fashion. In addition to the 20 beta-strands comprising the beta-helix, there is also a long C-terminal alpha-helix. For the first time, Ca2+ ions have been observed in addition to the catalytic Zn2+ ion. It is hypothesized that Tyr159 (which corresponds to the catalytically important Asn202 in previously reported structures) utilizes C-H...pi interactions to fulfill its functions. This study may shed light on the catalytic mechanism of the enzyme and throw open new questions on the mechanism of product removal in carbonic anhydrases.

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Section: In Silico Analysismentioning

confidence: 99%

Observation of a calcium-binding site in the γ-class carbonic anhydrase fromPyrococcus horikoshii

Jeyakanthan

Rangarajan

Mridula

et al. 2008

Acta Crystallogr D Biol Crystallogr

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“…Furthermore, users can superpose subunits (in the case of multi-subunit protein structures) using the option 'Superpose subunits in a given structure' (Sumathi et al, 2006). Users can also generate and visualize all the symmetry equivalent molecules (Hussain et al, 2003) using the option 'Symmetry equivalent molecules'. It is worth mentioning that, by properly maneuvering various options provided in the computing engine, users can obtain better perspectives of the interaction of the molecule(s) in the asymmetric unit with their symmetry related molecules.…”

Section: Utilitiesmentioning

confidence: 99%

PSAP: protein structure analysis package

et al. 2007

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A computing engine, theProtein Structure Analysis Package(PSAP), has been developed to calculate and display various hidden structural and functional features of three-dimensional protein structures. The proposed computing engine has several utilities to enable structural biologists to analyze three-dimensional protein molecules and provides an easy-to-use Web interface to compute and visualize the necessary features dynamically on the client machine. Users need to provide the Protein Data Bank (PDB) identification code or upload three-dimensional atomic coordinates from the client machine. For visualization, the free molecular graphics programsRasMolandJmolare deployed in the computing engine. Furthermore, the computing engine is interfaced with an up-to-date local copy of the PDB. The atomic coordinates are updated every week and hence users can access all the structures available in the PDB. The computing engine is free and is accessible online at http://iris.physics.iisc.ernet.in/psap/.

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Software Extensions to UCSF Chimera for Interactive Visualization of Large Molecular Assemblies

Goddard

Huang

Ferrin³

2005

Structure

224

188

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Many structures of large molecular assemblies such as virus capsids and ribosomes have been experimentally determined to atomic resolution. We consider four software problems that arise in interactive visualization and analysis of large assemblies: how to represent multimers efficiently, how to make cartoon representations, how to calculate contacts efficiently, and how to select subassemblies. We describe techniques and algorithms we have developed and give examples of their use. Existing molecular visualization programs work well for single protein and nucleic acid molecules and for small complexes. The methods presented here are proposed as features to add to existing programs or include in next-generation visualization software to allow easy exploration of assemblies containing tens to thousands of macromolecules. Our approach is pragmatic, emphasizing simplicity of code, reliability, and speed. The methods described have been distributed as the Multiscale extension of the UCSF Chimera (www.cgl.ucsf.edu/chimera) molecular graphics program.

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SEM (Symmetry Equivalent Molecules): a web-based GUI to generate and visualize the macromolecules

Cited by 3 publications

References 7 publications

Observation of a calcium-binding site in the γ-class carbonic anhydrase fromPyrococcus horikoshii

Observation of a calcium-binding site in the γ-class carbonic anhydrase fromPyrococcus horikoshii

PSAP: protein structure analysis package

Software Extensions to UCSF Chimera for Interactive Visualization of Large Molecular Assemblies

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