LFM-Pro: a tool for detecting significant local structural sites in proteins

Sacan, Ahmet
Ozturk, Ozgur
Ferhatosmanoglu, Hakan
Wang, Yusu
Motivation: The rapidly growing protein structure repositories have opened up new opportunities for discovery and analysis of functional and evolutionary relationships among proteins. Detecting conserved structural sites that are unique to a protein family is of great value in identification of functionally important atoms and residues. Currently available methods are computationally expensive and fail to detect biologically significant local features.


Integrating multi-attribute similarity networks for robust representation of the protein space
Camoglu, Orhan; Can, Tolga; Singh, Ambuj K. (Oxford University Press (OUP), 2006-07-01)
Motivation: A global view of the protein space is essential for functional and evolutionary analysis of proteins. In order to achieve this, a similarity network can be built using pairwise relationships among proteins. However, existing similarity networks employ a single similarity measure and therefore their utility depends highly on the quality of the selected measure. A more robust representation of the protein space can be realized if multiple sources of information are used.
Integrated search and alignment of protein structures
Sacan, Ahmet; Toroslu, İsmail Hakkı; Ferhatosmanoglu, Hakan (Oxford University Press (OUP), 2008-12-15)
Motivation: Identification and comparison of similar three-dimensional (3D) protein structures has become an even greater challenge in the face of the rapidly growing structure databases. Here, we introduce Vorometric, a new method that provides efficient search and alignment of a query protein against a database of protein structures. Voronoi contacts of the protein residues are enriched with the secondary structure information and a metric substitution matrix is developed to allow efficient indexing. The ...
GLANET: genomic loci annotation and enrichment tool
Otlu, Burcak; Firtina, Can; Keles, Sunduz; Tastan, Oznur (Oxford University Press (OUP), 2017-09-15)
Motivation: Genomic studies identify genomic loci representing genetic variations, transcription factor (TF) occupancy, or histone modification through next generation sequencing (NGS) technologies. Interpreting these loci requires evaluating them with known genomic and epigenomic annotations.
Finding differentially expressed genes for pattern generation
Abul, O; Alhajj, R; Polat, Faruk; Barker, K (Oxford University Press (OUP), 2005-02-15)
Motivation: It is important to consider finding differentially expressed genes in a dataset of microarray experiments for pattern generation.
CellTrack: an open-source software for cell tracking and motility analysis
Sacan, Ahmet; Ferhatosmanoglu, Hakan; Coskun, Huseyin (Oxford University Press (OUP), 2008-07-15)
Motivation: Cell motility is a critical part of many important biological processes. Automated and sensitive cell tracking is essential to cell motility studies where the tracking results can be used for diagnostic or curative decisions and where mathematical models can be developed to deepen our understanding of the mechanisms underlying cell motility.
Citation Formats
A. Sacan, O. Ozturk, H. Ferhatosmanoglu, and Y. Wang, “LFM-Pro: a tool for detecting significant local structural sites in proteins,” BIOINFORMATICS, pp. 709–716, 2007, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/67849.