BITS Meetings' Virtual Library:
Abstracts from Italian Bioinformatics Meetings from 1999 to 2013


766 abstracts overall from 11 distinct proceedings





Display Abstracts | Brief :: Order by Meeting | First Author Name
1. Ausiello G, Zanzoni A, Peluso D, Via A, Helmer-Citterich M
High-throughput exploration of functional residues in protein structures
Meeting: BITS 2005 - Year: 2005
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Topic: Structural Bioinformatics

Abstract: The detection of local similarities between protein structures may give insights for the identification of a common function. Different tools exist which try to elucidate the mechanisms connecting the similarity of local subsets of residues with the biological activity of whole proteins: i) databases of functionally annotated structures and ii) structural comparison algorithms. Both types of tools suffer from two major problems. The first is the low degree of integration among databases containing functional information. The second is the low or absent integration between existing methods for structural comparison and functional annotation resources.

2. Bortolami O, Tosatto SCE
DISSVM: a novel predictor of intrinsically disordered regions in protein
Meeting: BITS 2005 - Year: 2005
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Topic: Structural Bioinformatics

Abstract: The prediction of intrinsically disordered regions in proteins from sequence is increasingly becoming of interest, as the presence of many such regions in the complete genome sequences are discovered. Recent reports also indicate disordered regions to be conserved in evolution and to have a distinct preference for certain functional classes.

3. Punta M, Rost B
PROFcon: prediction of internal protein contacts
Meeting: BITS 2005 - Year: 2005
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Topic: Structural Bioinformatics

Abstract: Novel and more efficient structural prediction methods are needed in order to reduce the everincreasing gap between the number of known protein sequences and structures. Better predictions of non-local contacts between residues could help improve fold recognition and de novo modeling. In the present study, we introduce PROFcon, a novel contact prediction method based on a neural network that combines information from various sources. PROFcon predictions are then used to estimate experimental folding rates of two-state proteins (i.e. proteins that fold without intermediate states).

4. Schneider TR
Using coordinate uncertainties in structure comparison
Meeting: BITS 2005 - Year: 2005
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Topic: Structural Bioinformatics

Abstract: Coordinate uncertainties in crystal structures of biological macromolecules can vary from 0.01 Angstroem for a well determined atom in a high-resolution structure to 1 Angstroem for a mobile atom in a structure determined at low resolution. Given this wide range, it is essential to take into account the coordinate uncertainties in the comparison of structural models in order to discriminate significant differences from noise. Furthermore, given the rapid growth of available structure data, new methods for the analysis of large numbers of structural models need to be implemented.

5. Kleywegt GJ
Structural Bioinformatics - Understanding Protein Structure and Function
Meeting: BITS 2004 - Year: 2004
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Topic: Structural bioinformatics

Abstract: Structural Bioinformatics deals with the interface between sequence and structure (e.g., structure prediction, structure-based sequence alignment), that between structure and function (e.g., predicting function on the basis of observed structural similarities), and with the analysis of structural information per se (e.g., fold comparison and database construction). In this talk I will discuss four of our recent and on-going Structural Bioinformatics projects. - We have assessed and compared the performance of eleven web-based servers for fold-comparison that can be used to find out if a newly determined protein structure displays any similarity to known structures. - We have previously described SPASM and the SPASM server that can be used to answer the question: "does this structural motif (e.g., active site, ligand-binding site, or a strange loop) occur in any other protein structures?". One of the earliest tests of the method was to answer the question: "do left-handed helices occur in natural protein structures?". We found a very significant hit and have therefore undertaken a more detailed investigation. The preliminary results of this study will be presented. - In order to make working with sequences easier for structural biologists (and, hopefully, to make working with structures less daunting to people from the "sequence world"), we have developed a workbench called Indonesia . This program, written in Java, can be used to superimpose structures and derive sequence alignments from that, align sequences from scratch or to a profile derived from a (possibly structure-based) sequence alignment, derive HMMs from such alignments, identify short sequence patterns in them, etc. Sequence alignments can also be imported from a range of other programs, and they can edited, coloured, decorated and printed with the program. - The Uppsala Electron Density Server, EDS, provides access to electron-density maps for more than 10,000 crystal structures in the PDB. In addition to the maps, several validation statistics are provided for every entry. It is hoped that this server will help to increase the appreciation of non-crystallographers for the varying quality (accuracy and precision) of the macromolecular crystal structures available from the PDB.



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