Machine Learning in Bioinformatics

The machine learning field, which can be briefly defined as enabling computers make successful predictions using past experiences, has exhibited an impressive development recently with the help of the rapid increase in the storage capacity and processing power of computers. Together with many other disciplines, machin…

MOTIVATION: Identifying interactions between drug compounds and target proteins has a great practical importance in the drug discovery process for known diseases. Existing databases contain very few experimentally validated drug-target interactions and formulating successful computational methods for predicting intera…

• MEHMET GÖNEN

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• ARİF GÜLTEN

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• AKIN ÖZÇİFT

The dynamics of alpha-amylase inhibitors has been investigated using molecular dynamics (MD) simulations and two analytical approaches, the Gaussian network model (GNM) and anisotropic network model (ANM). MD simulations use a full atomic approach with empirical force fields, while the analytical approaches are based…

Peptidomimetics represent an important field in chemistry, pharmacology and material science as they circumvent the limitations of traditional peptides used in therapy. Self-structural organizations such as turns, helices, sheets and loops can be accessed by chemical modifications of amino acids or peptides. In-depth…

• İLKER AVAN

BACKGROUND: Several years after sequencing the human genome and the mouse genome, much remains to be discovered about the functions of most human and mouse genes. Computational prediction of gene function promises to help focus limited experimental resources on the most likely hypotheses. Several algorithms using dive…

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• MEHMET SOMEL

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• AYBAR CAN ACAR
• MUAMMER ALBAYRAK

SUMMARY: Molecular dynamics (MD) determines the physical motions of atoms of a biological macromolecule in a cell-like environment and is an important method in structural bioinformatics. Traditionally, measurements such as root mean square deviation, root mean square fluctuation, radius of gyration, and various energ…

• CANAN ATILGAN

SUMMARY: Molecular dynamics (MD) determines the physical motions of atoms of a biological macromolecule in a cell-like environment and is an important method in structural bioinformatics. Traditionally, measurements such as root mean square deviation, root mean square fluctuation, radius of gyration, and various energ…

• ALİ RANA ATILGAN

We propose the use of the information-theoretical entrophy, S = -sigman pi log2 pi, as a measure of variability at a given position in a set of aligned sequences. pi stands for the fraction of times the i-th type appears at a position. For protein sequences, the sum has up to 20 terms, for nucleotide sequences, up to…