@article {586,
	title = {SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks.},
	journal = {Nucleic Acids Res},
	volume = {37},
	year = {2009},
	month = {2009 Jul},
	pages = {W109-14},
	abstract = {<p>Understanding the structure and the dynamics of the complex intercellular network of interactions that contributes to the structure and function of a living cell is one of the main challenges of today{\textquoteright}s biology. SNOW inputs a collection of protein (or gene) identifiers and, by using the interactome as scaffold, draws the connections among them, calculates several relevant network parameters and, as a novelty among the rest of tools of its class, it estimates their statistical significance. The parameters calculated for each node are: connectivity, betweenness and clustering coefficient. It also calculates the number of components, number of bicomponents and articulation points. An interactive network viewer is also available to explore the resulting network. SNOW is available at http://snow.bioinfo.cipf.es.</p>},
	keywords = {Computer Graphics, Data Interpretation, Statistical, Databases, Protein, Humans, Internet, Protein Interaction Mapping, Software},
	issn = {1362-4962},
	doi = {10.1093/nar/gkp402},
	author = {Minguez, Pablo and G{\"o}tz, Stefan and Montaner, David and Al-Shahrour, F{\'a}tima and Dopazo, Joaquin}
}
@article {603,
	title = {DBAli tools: mining the protein structure space.},
	journal = {Nucleic Acids Res},
	volume = {35},
	year = {2007},
	month = {2007 Jul},
	pages = {W393-7},
	abstract = {<p>The DBAli tools use a comprehensive set of structural alignments in the DBAli database to leverage the structural information deposited in the Protein Data Bank (PDB). These tools include (i) the DBAlit program that allows users to input the 3D coordinates of a protein structure for comparison by MAMMOTH against all chains in the PDB; (ii) the AnnoLite and AnnoLyze programs that annotate a target structure based on its stored relationships to other structures; (iii) the ModClus program that clusters structures by sequence and structure similarities; (iv) the ModDom program that identifies domains as recurrent structural fragments and (v) an implementation of the COMPARER method in the SALIGN command in MODELLER that creates a multiple structure alignment for a set of related protein structures. Thus, the DBAli tools, which are freely accessible via the World Wide Web at http://salilab.org/DBAli/, allow users to mine the protein structure space by establishing relationships between protein structures and their functions.</p>},
	keywords = {Algorithms, Amino Acid Sequence, Computational Biology, Data Interpretation, Statistical, Databases, Protein, Internet, Molecular Sequence Data, Protein Conformation, Proteins, Pseudomonas aeruginosa, Sequence Alignment, Sequence Analysis, Protein, Sequence Homology, Amino Acid, Software, Structure-Activity Relationship},
	issn = {1362-4962},
	doi = {10.1093/nar/gkm236},
	author = {Marti-Renom, Marc A and Pieper, Ursula and Madhusudhan, M S and Rossi, Andrea and Eswar, Narayanan and Davis, Fred P and Al-Shahrour, F{\'a}tima and Dopazo, Joaquin and Sali, Andrej}
}
