Structural Bioinformatics

In 1971 the Protein Data Bank - PDB [146] (see Section 5.8 for a complete story and description) - was established at Brookhaven National Laboratories - BNL -as an archive for biological macromolccular cr7stal structures. This database moved in 1998 to the Research Collaboratory for Structural Bioinformatics -RCSB. A key component in the creation of such a public archive of information was the development of a method for effreient and uniform capture and curation of the data [147], The result of the effort was the PDB file format [53], which evolved over time through several different and non-uniform versions. Nevertheless, the PDB file format has become the standard representation for exchanging inacromolecular information derived from X-ray diffraction and NMR studies, primarily for proteins and nucleic acids. In 1998 the database was moved to the Research Collaboratory for Structural Bioinformatics - RCSB. 

D images, and a variety of links to other resources bibliographic citations), the data entries are annotated by RCSB (Research CoUaboratory for Structural Bioinformatics) with additional information. 

PDB Research Col-laboratory for Structural Bioinformat-ics (RCSB) macromole-cular structure data on proteins, nucleic acids, protein-nucleic acid complexes, and viruses nu- meric. biblio. -20000 records experi- ments Research Col-laboratory for Structural Bioinformatics online, CD-ROM periodi- cally WU7W.TCsh.0Tg/ pdh/... 

Three key areas are the organisation of knowledge in databases, sequence analysis, and structural bioinformatics. 

Biocomputing Molecular simulation Molecular dynamics Structural bioinformatics... 

In general the relevance of predictions of structure-function relationships based on molecular modeling and structural bioinformatics are threefold. First they can be used to answer the question of which partners (proteins) could interact. Second, predictions generate new hypotheses about binding site, about molecular mechanisms of activation and interaction between two partners, and can lead to new ideas for pharmacological intervention. The third aim is to use the predictions for structure-based drug design. 

The protein structure prediction problem refers to the combinatorial problem to calculate the 3D structure of a protein from its sequence alone. It is one of the biggest challenges in structural bioinformatics. 

Stress Proteins Structural Bioinformatics Structural Genomics Strychnine STX... 

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB-PDB at http //www.rcsb.org/pdb/) is the online source for X-ray and NMR structural data. Many software programs mentioned in Section 3.12 include the facility to visualize imported data however, two free software programs operate well in this regard. These are RasMol and Chime, described below. 

In the present report we are reviewing some aspects of structural bioinformatics, some of its essential components, and their proper and efficient utilization on drag discovery process to foster the speed. 

RCSB Protein Data Bank, from the Research Collaboratory for Structural Bioinformatics,... 

Laurie ATR, Jackson RM (2005) Structural bioinformatics Q-SiteFinder an energy-based method for the prediction of protein—ligand binding sites. Bioinformatics 21 1908-1916... 

Data formats in the Brookhaven Protein Databank have become an intensively discussed topic in the last few years. The original PDB file format [17] was created in the late 1970s and maintained by the Research Collaboratory for Structural Bioinformatics [13]. In order to improve the organization of bibliographic... 

XML technologies [22, 23] have become a general standard for storing and converting all kinds of data and technically more robust solutions than mmCif based on XML, such as PROXIML [24], were proposed but still not accepted by the Research Collaboratory for Structural Bioinformatics. 

Bioinformatics is of enormous benefit in proteomic and pharmacoproteomic research. Structural bioinformatics and functional bioinformatics are powerful... 

The Protein Data Bank (PDB) is the collection of publicly available structures of proteins, nucleic acids, and other biological macromolecules initiated by Brook-haven National Laboratory and now maintained by the Research Collaboratory for Structural Bioinformatics (RCSB) at http //www.rcsb.org/pdb/ (Berman et al., 2000). The PDB coordinates of biomacromolecules can be classified into the following ... 

Sujatha S, Balaji S, Srinivasan N (2001) PALI a database of alignments and phylogeny of homologous protein structures. Bioinformatics 17 375-376... 

Bourne P, Weissig H, eds (2003) Structural Bioinformatics, Other Structure-Based Databases, NY John Wiley Sons, Inc, 427... 

RDC data should be collected, as well as by means of computational analysis. The problem is even less tractable for IDPs where the size of the ensemble covering all relevant motions and reproducing the measured NMR parameters is a key issue. Furthermore, the diversity of such structural ensembles poses difficulties in their analysis by structural bioinformatics tools.127... 

P. Bourne,andH. Weissig (eds.), (2003). In Structural Bioinformatics. John Wiley Sons, Hoboken,... 

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