Current Bioinformatics - Volume 7, Issue 4, 2012

About 15 years ago, the steered molecular dynamics (SMD) was used to probe binding of ligand to biomolecule surfaces but in terms of drug design this approach has only recently attached attention of researchers. The main idea of using SMD to screen out leads is based on the hypothesis that the larger is the force needed to unbind a ligand from a receptor the higher its binding affinity. Thus, instead of binding free energy, the Read More

In order to obtain structural information about intermolecular interactions between a protein target and a drug we could either solve the structure by experimental techniques (protein crystallography or nuclear magnetic resonance), or simulate the protein-drug complex computationally. Molecular docking is a computer simulation methodology that can predict the conformation of a protein-drug complex, with relatively hi Read More

Amantadine is a specific anti-influenza a drug that inhibits viral replication by binding to the M2 channel and preventing proton conductance. The increasing resistance to amantadine in strains of the influenza A virus that infect both animals and humans has been highlighted frequently. Resistance is usually caused by one of several single mutations in the M2 channel, but variants with double mutations have also been re Read More

The shikimate pathway is found in microorganisms, fungi, plants and also in several apicomplexan parasites. This metabolic pathway consists of seven enzymes and converts the primary metabolites phosphoenolpyruvate and erythrose-4-phosphate to chorismate, the last common precursor for the three aromatic amino acids Phe, Tyr, and Trp and other aromatic compounds. The significance of targeting the enzymes of this p Read More

Caspases belong to the family of cysteinyl aspartate–a specific proteases which control the programmed cell death process, or apoptosis. In this paper, we have performed a structural bioinformatics analysis of the conserved domains and residues, WebLogo generation and active sites identification related to apoptosis activator and apoptosis executioner caspase-cascades. Here, we have also shown conservation patter Read More

Caspases are very important molecules which are playing a key role for apoptosis. Deregulation of apoptosis contributes to the pathogenesis of many human diseases. Therefore, the regulation of this protein can be controlled for the therapeutic purpose. To determine molecular evolution, in silico of proteins is popular a method for certain laboratories and biotechnology companies. It may help to detect that mutations often o Read More

Orphan nuclear receptors (oNRs) provide huge opportunities for the discovery of new drug targets. Identifying novel and perhaps unexpected types of ligands for oNRs may gain insight into potentially new principles of physiology. Recently, the network-based approaches are playing an increasingly important role in identifying and validating novel ligands for nuclear receptors. This review describes current progresses in Read More

Sequence classification is one of the most fundamental machine learning tasks in computational biology nowadays. With the wide availability of large corpora of annotated sequences, the use of supervised learning techniques can greatly speed up the process of identifying new sequences sharing certain function or properties. Many methods have been proposed over the years and we hope to provide an introduction to so Read More

If structures of proteins of whole organisms were available, metabolomic models could be developed, drug targets could be identified, issues of affinity versus specificity could be sorted out and side effects and toxicity brought under control etc. all with greater levels of reliability. Advances in whole genome sequencing projects, annotation algorithms, growing protein sequence information with over half a million entries in the Read More

Designing ontology to represent gene function is of vital importance for meeting the major challenge of integrating sequence data with the increasing amount of data from functional analyses of genes. Given that genes are expressed in temporally and spatially characteristic patterns, their products quite often reside in specific cellular compartments and may be part of one or more multi-component complexes. Genes Read More

Transcriptional regulation is a key step to control the level of mRNA formed. Recent view of transcriptional regulation has evolved from a one-dimensional mode, i.e. RNA Polymerase II assembles with general transcription factors, and cis-regulatory elements (CREs) interact with transcription factors, to a much complex multiple-dimensional mode, involving combinatorial interactions between transcription factors Read More

Emerging and re-emerging viral infections are a threat to human health and a cause of global concern. Several viral vaccines have been successfully developed using conventional methods. However, there are many viruses for which vaccines need to be developed on priority basis. Furthermore, the challenges viz, varying efficacy of existing vaccines also need to be addressed as viruses are known to evolve at a high Read More

Bunyaviridae family consists of vector borne lethal viruses, stands out as the largest virus family with its 350 members. One such virus of this family, Crimean- Congo hemorrhagic fever virus (CCHFV) is transmitted through bites of ixodid ticks or by direct contact with blood from infected animals. Crimean-Congo haemorrhagic fever (CCHF) is a severe disease in humans which is endemic in large parts of the world with a hi Read More

Malaria is a serious infectious disease that causes over one million deaths yearly. It is caused by a group of protozoan parasites in the genus Plasmodium. No effective vaccine is currently available and the elevated levels of resistance to drugs in use underscore the pressing need for novel antimalarial targets. In this review, we survey omics centered developments in Plasmodium biology, which have set the stage for a quan Read More

Since most molecular studies on death of cells in tissues have been carried out on isolated cell populations due to known difficulties manifested by interactions with surrounding cells, a novel means of investigating general principles governing cellular functions under oxidative stress conditions is needed in order to shed more light on the background of cancer disease. It is believed that relevant signal transmission may be discover Read More

Sequence alignment is a basic field in bioinformatics, especially the sequence alignment of remotely homologue proteins is a hot spot. In our previous work, we developed a new score matrix named transformation matrix which can greatly enhance the quality of the alignment of distant protein sequences. Here, by using the transformation score matrix, we assessed the statistical significance of the local sequence alignm Read More

MicroRNAs (miRNAs) are short RNA molecules that regulate the post-transcriptional expression of their target genes – messenger RNAs (mRNAs). Although miRNAs are known to down-regulate the translation or the cleavage of mRNAs, the miRNA-mediated regulation mechanisms still remain largely unknown. Therefore, in order to achieve a better understanding of the biological function of the miRNAs, a critical step is to ident Read More