http://www.hindawi.com The latest articles from Hindawi Publishing Corporation © 2013 , Hindawi Publishing Corporation . All rights reserved. Tue, 14 May 2013 14:32:08 +0000 http://www.hindawi.com/isrn/comp.bio/2013/391018/ Sexual stages of Plasmodium such as zygote, ookinete, and young oocysts express 25 kDa surface protein P25, which along with P28 proteins protect the parasite from harmful environment inside mosquito midgut. Vaccines against these proteins induce antibodies in vertebrate host capable to inhibit parasite development in mosquito midgut and thus preventing the transmission of parasite from mosquito to other human host. Transmission-blocking vaccines help reduce malaria burden. The purpose of this study was in silico structural characterization of P25 family proteins and to predict their phylogenetic relationships with other proteins. Results indicate that members of P25 family have four EGF domains arranged in triangular fashion with major variations lying in the loop regions. All 22 cysteines are conserved forming 11 disulphide bonds. The C-loop of EGF domain IV in P25 proteins is smaller in comparison to P28 proteins. B loop of EGF domain II showed maximum RMSD variations followed by loops of EGF domain III. P25 proteins are tile-like triangular flat proteins that protect the parasite inside mosquito midgut. Obtained structures will help in understanding the biology of the parasite inside the mosquito midgut. These structures may also help in designing transmission-blocking vaccine against malaria in absence of experimentally determined structures. Babita Sharma and Manoj Kumar Jaiswal Copyright © 2013 Babita Sharma and Manoj Kumar Jaiswal. All rights reserved. Mon, 22 Apr 2013 10:47:45 +0000 http://www.hindawi.com/isrn/comp.bio/2013/417634/ HomoKinase database is a comprehensive collection of curated human protein kinases and their relevant biological information. The entries in the database are curated by three criteria: HGNC approval, gene ontology-based biological process (protein phosphorylation), and molecular function (ATP binding and kinase activity). For a given query protein kinase name, the database provides its official symbol, full name, other known aliases, amino acid sequences, functional domain, gene ontology, pathways assignments, and drug compounds. In addition, as a search tool, it enables the retrieval of similar protein kinases with specific family, subfamily, group, and domain combinations and tabulates the information. The present version contains 498 curated human protein kinases and links to other popular databases. Suresh Subramani, Saranya Jayapalan, Raja Kalpana, and Jeyakumar Natarajan Copyright © 2013 Suresh Subramani et al. All rights reserved. Sun, 31 Mar 2013 09:59:40 +0000 http://www.hindawi.com/isrn/comp.bio/2013/640125/ Molecular dynamic simulations are used for investigating various aspects of biological processes. Such simulations often require intensive computer power; therefore several solutions were developed to minimize the computer power needed, including the usage of elevated temperatures. Yet, such simulations are still not commonly used by the wide scientific community of chemists and biochemists. For about two years now, the molecular simulations suite GROMACS enables conducting simulations using implicit solvent models to further decrease runtimes. In order to quantify the saving in computer power, and to confirm the validity of the models, we followed the simple dissolution process of a single NaCl molecule. The results reveal approximately 350-fold decrease in real-world runtime when using an implicit solvent model and an elevated temperature, compared to using explicit water molecules and simulating at room temperature. In addition, in a wide range of temperatures, the dissolution times of NaCl are distributed, as expected, exponentially, both in explicit and in implicit solvent models, hence confirming the validity of the simulation approach. Hopefully, our findings will encourage many scientists to take advantage of the recent progress in the molecular dynamics field for various applications. Ifat Shub, Ehud Schreiber, and Yossef Kliger Copyright © 2013 Ifat Shub et al. All rights reserved. Thu, 28 Mar 2013 18:31:37 +0000 http://www.hindawi.com/isrn/comp.bio/2013/362973/ Scabies is among the infestations almost forgotten due to its association with poor communities. We formulate a deterministic model to assess the possible impact vaccination will have on scabies control. The Descartes’s rule of signs is used to show the nature of the endemic equilibria. Analysis of the reproduction number and numerical simulations suggest that vaccination in addition to treatment will help greatly in reducing the spread of scabies infestation. This suggests there is a strong need for researchers to come up with a possible vaccine in that order to effectively control scabies especially among the disadvantaged communities. C. P. Bhunu, S. Mushayabasa, and T. G. Monera Copyright © 2013 C. P. Bhunu et al. All rights reserved. Thu, 28 Mar 2013 13:56:55 +0000 http://www.hindawi.com/isrn/comp.bio/2013/428378/ Background and Aim. Despite tangible progress in recent years, substantial therapeutic challenges remain unexplored in nephropathy, particularly in diabetic patient. Addressing these challenges requires identification of novel drugs and development of noninvasive and cost-effective methods to select the most appropriate therapeutic option for the disease. Angiopathic nephropathy is one of the complications of diabetes mellitus and is becoming the single most important reason for end-stage renal disease in the western world. This study has investigated the inhibitory effect of a library naturally occurring nonprotein compounds that inhibit angiotensin converting enzyme (ACE). Materials and Methods. Docking studies of ACE protein with natural compounds and synthetic commercial drug perindopril were done using AutoDock, FlexX, and Hex. Toxicity predictions were carried out using OpenTox. Quantum mechanical properties were studied using GAMESS. Results. Pelargonidin-3-glucoside could be used as a potent renoprotective drug candidate, which inhibits ACEII. It has low toxicity and its quantum mechanical properties are comparable to those of commercial drugs. Talambedu Usha, Pranav Tripathi, Veena Pande, and Sushil Kumar Middha Copyright © 2013 Talambedu Usha et al. All rights reserved. Thu, 07 Mar 2013 11:17:56 +0000 http://www.hindawi.com/isrn/comp.bio/2013/467943/ Microbial evolution is complex and is influenced by many sources of variation. Experimental evolution is no exception, although it is more controlled, easily replicated, and typically devoid of interactions between species. Mathematical modeling of the evolutionary process can help in understanding the underlying mechanisms that drive outcome of such experiments. These models can be complex and parameter rich, limiting their feasibility for statistical inference. In this paper, we introduce the use of Approximate Bayesian Computation (ABC) as a tool for statistical inference in the study of experimental evolution. ABC is a fast and simple method for fitting complex models to data. We utilize this method, coupled with a mechanistic model of experimental evolution, to study the evolution process of bacteriophage ϕX174 under benign selection pressure. Our results highlight three mutation-selection scenarios that could explain this process: high mutation/low selection pressure, low mutation/high selection pressure, and low mutation/low selection pressure, with posterior support of 19%, 9.5%, and 71.5% for each of these scenarios, respectively. Sequence data support the first candidate. Though surprising, this scenario was not improbable based on our analysis. Zaid Abdo, Mathew Stein, Andrzej Wojtowicz, and Kim M. Pepin Copyright © 2013 Zaid Abdo et al. All rights reserved.