The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/.

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UCSF Chimera--a visualization system for exploratory research and analysis.

An N⋅log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented. The method is based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolutions using fast Fourier transforms. Timings and accuracies are presented for three large crystalline ionic systems.

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

J. Appl. Cryst.の発刊に際して

The alpha- and beta-subunits of membrane-bound ATP synthase complex bind ATP and ADP: beta contributes to catalytic sites, and alpha may be involved in regulation of ATP synthase activity. The sequences of beta-subunits are highly conserved in Escherichia coli and bovine mitochondria. Also alpha and beta are weakly homologous to each other throughout most of their amino acid sequences, suggesting that they have common functions in catalysis. Related sequences in both alpha and beta and in other enzymes that bind ATP or ADP in catalysis, notably myosin, phosphofructokinase, and adenylate kinase, help to identify regions contributing to an adenine nucleotide binding fold in both ATP synthase subunits.

Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold.

Recent advances in proteomics technologies such as two-hybrid, phage display and mass spectrometry have enabled us to create a detailed map of biomolecular interaction networks. Initial mapping efforts have already produced a wealth of data. As the size of the interaction set increases, databases and computational methods will be required to store, visualize and analyze the information in order to effectively aid in knowledge discovery. This paper describes a novel graph theoretic clustering algorithm, "Molecular Complex Detection" (MCODE), that detects densely connected regions in large protein-protein interaction networks that may represent molecular complexes. The method is based on vertex weighting by local neighborhood density and outward traversal from a locally dense seed protein to isolate the dense regions according to given parameters. The algorithm has the advantage over other graph clustering methods of having a directed mode that allows fine-tuning of clusters of interest without considering the rest of the network and allows examination of cluster interconnectivity, which is relevant for protein networks. Protein interaction and complex information from the yeast Saccharomyces cerevisiae was used for evaluation. Dense regions of protein interaction networks can be found, based solely on connectivity data, many of which correspond to known protein complexes. The algorithm is not affected by a known high rate of false positives in data from high-throughput interaction techniques. The program is available from ftp://ftp.mshri.on.ca/pub/BIND/Tools/MCODE
 .

/pdf/an-automated-method-for-finding-molecular-complexes-in-large-1xr24lgr4a.pdf

An automated method for finding molecular complexes in large protein interaction networks.

Orotidine-5'-monophosphate decarboxylase (ODCase) is one of most proficient enzymes, and this enzyme catalyzes the decarboxylation of orotidine-5'- monophosphate (OMP) to uridine-5'-monophosphate (UMP). A number of C6-substituted uridine derivatives are designed to investigate the mechanism of decarboxylation by this enzyme. In this process, novel reactions and mechanisms were uncovered for this decarboxylase. This led to the discovery of novel ODCase inhibitors and their biological activities. Medicinal chemistry of these novel inhibitors of ODCase in the context of its catalytic mechanism, and therapeutics development will be discussed.

Inhibition of orotidine-5'-monophosphate decarboxylase--discoveries and lessons.

The tetrameric flavoenzyme 2,4-pentadienoyl-CoA reductase has been crystallized from solutions containing polyethylene glycol as precipitant. The crystals grow in the monoclinic space group C2 with unit-cell dimensions a = 160.2, b = 120.2, c = 95.3 A, beta = 99.0 degrees. The packing parameter V(M) is 2.3 A(3) Da(-1) (Matthews parameter) for four monomers per asymmetric unit. Complete data sets to about 2.9 A resolution have been collected.

Emil F. Pai

Papers

Inhibition of orotidine-5'-monophosphate decarboxylase--discoveries and lessons.

Crystallization and preliminary X-ray diffraction study of the flavoenzyme 2,4-pentadienoyl-CoA reductase from Clostridium aminovalericum.

Crystal structure of ADP-ribosyltransferase Vis in complex with agmatine

There are always surprises.

Crystal structure of rat D428A mutant, urate bound form