Drugs bind to their target proteins, which interact with downstream effectors and ultimately perturb the transcriptome of a cancer cell. These perturbations reveal information about their source, i.e., drugs' targets. Here, we investigate whether these perturbations and protein interaction networks can uncover drug targets and key pathways. We performed the first systematic analysis of over 500...

BACKGROUND Prediction of interaction sites within the membrane protein complexes using the sequence data is of a great importance, because it would find applications in modification of molecules transport through membrane, signaling pathways and drug targets of many diseases. Nevertheless, it has gained little attention from the protein structural bioinformatics community. METHODS In this stu...

Pseudokinases, the catalytically impaired component of the kinome, have recently been found to share more properties with active kinases than previously thought. In many pseudokinases, ATP binding and even some activity is preserved, highlighting these proteins as potential drug targets. In both active kinases and pseudokinases, binding of ATP or drugs in the nucleotide-binding pocket can stabi...

Bacterial conjugation is a mechanism for horizontal DNA transfer with potential for universal DNA delivery. The conjugal machinery can be separated into three functional modules: the relaxosome, the coupling protein, and a type IV protein secretion system. Module interchangeability among different conjugative systems opens up the possibility of "a la carte" engineering of DNA delivery into virt...

protein secretory systems are found in all living organisms including gram negative bacteria, and eukaryotic cell’s organelles that are derived from these bacteria. unlike all other living organisms, gram negative bacteria have different protein secretory systems. at least there are four different independent secretory systems, which are responsible to transport the secreted proteins to the mil...

nanotechnology has changed our lives dramatically and influenced every sector of the research, engineering and also business community. nanotechnology is a rapidly growing science of producing and utilizing nano-sized particles, that measure in nanometer. in other words, nanotechnology is the art of characterizing, manipulating and organizing matter systemically, at the nanometer scale, which h...

nowadays, environment-sensitive smart drug delivery systems have found diverse applications in pharmaceutical science and technology. these systems can respond to the environment stimuli such as temperature, pressure, ph, light, electrical and magnetical fields and etc. they can release the proper amount of drug in human body. among these systems, special attention and much research works have ...

1. Background Protein-protein interaction networks Proteins are linear chain biomolecules that are the basis of functional networks in all organisms. They include classes that regulate other proteins (e.g. kinases), classes that regulate gene expression (e.g. transcription factors), and classes that control response to disease (e.g. immunoglobulins). Aspects of their social networks have been e...

Understanding the pathways by which viral capsid proteins assemble around their genomes could identify key intermediates as potential drug targets. In this work, we use computer simulations to characterize assembly over a wide range of capsid protein-protein interaction strengths and solution ionic strengths. We find that assembly pathways can be categorized into two classes, in which intermedi...

Cancer development is a multi-step process that leads to uncontrolled tumor cell growth. Multiple pathways are involved; typically some signalling and regulatory pathways are activated, while others are suppressed. Systematically exploring these networks of proteins will lead to better understanding of disease initiation and progression. Integrating these data with microRNA regulatory networks ...