EXCEL

Microsoft Excel is a non-free commercial spreadsheet application written and distributed by Microsoft for Microsoft Windows and Mac OS X. It features calculation, graphing tools, pivot tables and a macro programming language called Visual Basic for Applications. It has been a very widely applied spreadsheet for these platforms, especially since version 5 in 1993. Excel forms part of Microsoft Office. The current versions are 2010 for Windows and 2011 for Mac.

 Microsoft Excel has the basic features of all spreadsheets, using a grid of cells arranged in numbered rows and letter-named columns to organize data manipulations like arithmetic operations. It has a battery of supplied functions to answer statistical, engineering and financial needs. In addition, it can display data as line graphs, histograms and charts, and with a very limited three-dimensional graphical display. It allows sectioning of data to view its dependencies on various factors from different perspectives (using pivot tables and the scenario manager). And it has a programming aspect, Visual Basic for Applications, allowing the user to employ a wide variety of numerical methods, for example, for solving differential equations of mathematical physics, and then reporting the results back to the spreadsheet. Finally, it has a variety of interactive features allowing user interfaces that can completely hide the spreadsheet from the user, so the spreadsheet presents itself as a so-called application, or decision support system (DSS), via a custom-designed user interface, for example, a stock analyzer, or in general, as a design tool that asks the user questions and provides answers and reports.In a more elaborate realization, an Excel application can automatically poll external databases and measuring instruments using an update schedule, analyze the results, make a Word report or Power Point slide show, and e-mail these presentations on a regular basis to a list of participants. Microsoft allows for a number of optional command-line switches to control the manner in which Excel starts.

SMILES notation - not " =) "

The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules.

The original SMILES specification was developed by Arthur Weininger and David Weininger in the late 1980s. It has since been modified and extended by others, most notably by Daylight Chemical Information Systems Inc. In 2007, an open standard called "OpenSMILES" was developed by the Blue Obelisk open-source chemistry community. Other 'linear' notations include the Wiswesser Line NotationROSDAL and SLN (Tripos Inc). (WLN),

In July 2006, the IUPAC introduced the InChI as a standard for formula representation. SMILES is generally considered to have the advantage of being slightly more human-readable than InChI; it also has a wide base of software support with extensive theoretical backing.

Protein Data Bank

The PDB is the Protein Data Bank, a single worlwide repository for 3D structural data of biological molecules. A PDB is a file, typically with a "pdb" file extension, contains 3D structural data of a particular biological molecule. In short, a PDB file is broken into two sections:

• a header that contains much background information on the molecule in question such as authors and experimental conditions.
• 3D coordinate data that contain the vital experimental data in the form of 3D cartesian coordinates, B-factors, atom information, and more.

Protein Data Bank files, containing some form of macromolecular coordinate set, are visualized via graphic computing. A myriad of advanced molecular visualization programs are used in academic and industrial setting, and some of these are specific to the field of research or the techniques used to collect the coordinate data. For example, X-ray crystallographers use O, XtalView, MAIN, or other programs for crystallographic modeling. These allow the researcher to model the coordinate set into the electron density from the collected X-ray data.

FTSH Peptidase

Structural studies on Helicobacter pyloriATP-dependent protease, FtsH. 

Author : Kim,S.H.,Kang,G.B.,   Song,H.-E.,Park, S.J.,Bea,M.-H., Eom, S.H.

Journal: (2008) J.SYNCHROTRON RADIAT.15: 208-210

PubMed: 18421140
PubMedCentral: PMC2394826
DOI: 10.1107/S090904950706846X
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The ATP-dependent protease, FtsH, degrades misassembled membrane proteins for quality control like SecY, subunit a of FoF1-ATPase, and YccA, and digests short-lived soluble proteins in order to control their cellular regulation, including sigma32, LpxC and lambdacII. The FtsH protein has an N-terminal transmembrane segment and a large cytosolic region that consists of two domains, an ATPase and a protease domain. To provide a structural basis for the nucleotide-dependent domain motions and a better understanding of substrate translocation, the crystal structures of the Helicobacter pylori (Hp) FtsH ATPase domain in the nucleotide-free state and complexed with ADP, were determined. Two different structures of HpFtsH ATPase were observed, with the nucleotide-free state in an asymmetric unit, and these structures reveal the new forms and show other conformational differences between the nucleotide-free and ADP-bound state compared with previous structures. In particular, one HpFtsH Apo structure has a considerable rotation difference compared with the HpFtsH ADP complex, and this large conformational change reveals that FtsH may have the mechanical force needed for substrate translocation.

 Thermolysin

 
Structural basis for the autoprocessing of zinc metalloproteases in the thermolysin family.

Author : Gao,X.,Wang,J., Yu,D.-Q.,Bian, F.,   Xie, B.-B.,Chen,X.-L.,   Zhou, B.-C.,Lai,L.-H.,   Wang, Z.-X.,Wu,J.-W.,   Zhang,Y.-Z.

Journal: (2010) Proc.Natl.Acad.Sci.USA 107: 17569-17574

PubMed: 20876133
PubMedCentral: PMC2955107
DOI: 10.1073/pnas.1005681107
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Thermolysin-like proteases (TLPs), a large group of zinc metalloproteases, are synthesized as inactive precursors. TLPs with a long propeptide (?200 residues) undergo maturation following autoprocessing through an elusive molecular mechanism. We report the first two crystal structures for the autoprocessed complexes of a typical TLP, MCP-02. In the autoprocessed complex, Ala205 shifts upward by 33 ? from the previously covalently linked residue, His204, indicating that, following autocleavage of the peptide bond between His204 and Ala205, a large conformational change from the zymogen to the autoprocessed complex occurs. The eight N-terminal residues (residues Ala205-Gly212) of the catalytic domain form a new ?-strand, nestling into two other ?-strands. Simultaneously, the apparent T(m) of the autoprocessed complex increases 20?°C compared to that of the zymogen. The stepwise degradation of the propeptide begins with two sequential cuttings at Ser49-Val50 and Gly57-Leu58, which lead to the disassembly of the propeptide and the formation of mature MCP-02. Our findings give new insights into the molecular mechanism of TLP maturation.

Thermolysin-like proteases (TLPs), a large group of zinc metalloproteases, are synthesized as inactive precursors. TLPs with a long propeptide (?200 residues) undergo maturation following autoprocessing through an elusive molecular mechanism. We report the first two crystal structures for the autoprocessed... [ Read More & Search PubMed Abstracts ]

Leucyl Aminopeptidase

Crystal structure of the leucine aminopeptidase from Pseudomonas putida reveals the molecular basis for its enantioselectivity and broad substrate specificity.

Author : Kale,A., Pijning,T.,Sonke,T.,   Dijkstra,B.W.,   Thunnissen,A.M.

Journal: (2010) J.Mol.Biol. 398: 703-714

PubMed: 20359484
DOI: 10.1016/j.jmb.2010.03.042
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The zinc-dependent leucine aminopeptidase from Pseudomonas putida (ppLAP) is an important enzyme for the industrial production of enantiomerically pure amino acids. To provide a better understanding of its structure-function relationships, the enzyme was studied by X-ray crystallography. Crystal structures of native ppLAP at pH 9.5 and pH 5.2, and in complex with the inhibitor bestatin, show that the overall folding and hexameric organization of ppLAP are very similar to those of the closely related di-zinc leucine aminopeptidases (LAPs) from bovine lens and Escherichia coli. At pH 9.5, the active site contains two metal ions, one identified as Mn(2+) or Zn(2+) (site 1), and the other as Zn(2+) (site 2). By using a metal-dependent activity assay it was shown that site 1 in heterologously expressed ppLAP is occupied mainly by Mn(2+). Moreover, it was shown that Mn(2+) has a significant activation effect when bound to site 1 of ppLAP. At pH 5.2, the active site of ppLAP is highly disordered and the two metal ions are absent, most probably due to full protonation of one of the metal-interacting residues, Lys267, explaining why ppLAP is inactive at low pH. A structural comparison of the ppLAP-bestatin complex with inhibitor-bound complexes of bovine lens LAP, along with substrate modelling, gave clear and new insights into its substrate specificity and high level of enantioselectivity.

The zinc-dependent leucine aminopeptidase from Pseudomonas putida (ppLAP) is an important enzyme for the industrial production of enantiomerically pure amino acids. To provide a better understanding of its structure-function relationships, the enzyme was studied by X-ray crystallography. Crystal structures of... [ Read More & Search PubMed Abstracts ]