Current Bioinformatics - Volume 7, Issue 2, 2012

Proteins and their interactions play vital roles in living organisms. Elucidating the mechanism of protein folding as well as the recognition of proteins with other molecules (proteins, nucleic acids and carbohydrates and ligands) are intriguing and challenging problems in computational and molecular biology. The problem of protein folding, stability and interactions has been viewed through several perspectives using experim Read More

The rapidly growing structure databases enhance the probability of finding identical sequences sharing structural similarity. Structure prediction methods are being used extensively to abridge the gap between known protein sequences and the solved structures which is essential to understand its specific biochemical and cellular functions. In this work, we plan to study the ambiguity between sequence-structure relat Read More

Prediction of protein 3D structure from solely its amino acid sequence is one of the most challenging problems in structural bioinformatics, where the 3D structure reconstruction from observed constraints is the key step. In this paper, we propose a novel protocol called Glocal to recover a protein’s 3D coordinates based on a given 2D contact map by combining both global and local optimization schemes achieved by the sw Read More

The attachment of glycosylphosphatidylinositol (GPI) is one of the most important post-translational modifications of proteins and plays an important role in promoting biochemical activities in eukaryotic cells. GPIanchored proteins (GPI-APs) are characterized by GPI-anchor attachment signals of hydrophobic residues and small residues near the GPI-anchoring site (ω-site). Here, we describe a new method for predicting Read More

G protein-coupled receptors (GPCRs) are integral membrane proteins with seven trans-membrane helices. Belonging to the largest family of cell surface receptors, GPCRs are among the most frequent targets of therapeutic drugs. Unfortunately, since they are difficult to crystallize and most of them will not dissolve in normal solvents, so far the number of GPCRs with three-dimensional structure determined is very limited. Thi Read More

Free energy of unfolding (ΔGu) is the difference between the free energy values of the folded and unfolded structures of a protein. A successful model describing both folding/unfolding rates of proteins should be able to provide considerable insight on free energy of unfolding. In our earlier works, we have shown that Long-range Order (LRO) correlates well with both folding/unfolding rates of two-state proteins. In the presen Read More

Protein thermostabilization has been the focus of recent research due to growing interest in the production of enzymes that can operate at temperatures that are industrially beneficial. Understanding the determinants of thermostabilization at the level of sequence and structure is important to design such enzymes. A bioinformatical approach was used to determine the extent by which reduced amino acid alphabet Read More

The structural analysis of protein-protein interactions and the prediction of their functional properties are important areas in modern structural bioinformatics. First, we review concepts for classifying protein-protein interactions, and for analyzing the geometry and composition of binding interfaces. Next, computational methods are discussed that allow predicting hot-spot residues and the kinetics and the rmodynamics of Read More

It has been well established that the elastic character of DNA plays an important role in protein-DNA binding specificity. In this work, we have analyzed the role of elasticity to understand the binding specificity of protein-RNA complexes. We have developed a sequence dependent stiffness scale for the trinucleotides in RNA and revealed the similarities and differences compared with DNA. We found that the stiffness of 15 tri Read More

Background: Metal atoms are involved in many biological mechanisms, such as protein structure stability, apoptosis and aging. Therefore, identifying metal-binding sites in proteins is an important issue in helping biologists better understand the workings of these mechanisms. Methods: We propose a method based on Position Specific Scoring Matrix (PSSM) profiles and additional information (conservation score and solve Read More

Viral diseases cause severe damage to human lives than any other microbes. Hepatitis is the inflammation of liver and currently six strains of viral hepatitis are identified. Infection by Hepatitis B Virus (HBV) and Hepatitis C Virus (HCV) causes serious mortality, morbidity and becomes a global health problem. Human Immunodeficiency Virus (HIV) is increasing in the world, with an estimation of 5.7 million cases of HIV infection i Read More

Mass spectrometry based proteomics analysis can produce many thousands of spectra in a single experiment, and much of this data, frequently greater than 50%, cannot be properly evaluated computationally. Therefore a number of strategies have been developed to aid the processing of mass spectra and typically focus on the identification and elimination of noise, which can provide an immediate improvement in the anal Read More

Bottom-up proteomics (mass spectrometry analysis of peptides obtained by proteolysis and separated by liquid chromatography, (LC-MS/MS)) is one of the most frequently used techniques for identifying and characterizing proteins in biological samples. A key element of the analysis is database searching when the mass spectra of the peptides are compared with a database of theoretically computed (or experimental) Read More