Although the structures of many beta-barrel membrane proteins are available, our knowledge principles that govern their energetics and oligomerization states is incomplete. Here we describe a computational method to study transmembrane (TM) domains proteins. Our based on physical interaction model, simplified conformational space for efficient enumeration, an empirical potential function from detailed combinatorial analysis. Using this method, can identify weakly stable regions in TM domain,...

As an increasing amount of protein-protein interaction (PPI) data becomes available, their computational interpretation has become important problem in bioinformatics. The alignment PPI networks from different species provides valuable information about conserved subnetworks, evolutionary pathways and functional orthologs. Although several methods have been proposed for global network alignment, there is a pressing need that produce more accurate alignments terms both topological...

β-Barrel membrane proteins are found in the outer of gram-negative bacteria, mitochondria, and chloroplasts. They important for pore formation, anchoring, enzyme activity. These also often responsible bacterial virulence. Due to difficulties experimental structure determination, they sparsely represented protein databank. We have developed a computational method predicting structures transmembrane (TM) domains β-barrel proteins. Based on physical principles, our can predict TM domain novel...

A routine approach to inferring functions for a gene set is by using function enrichment analysis based on GO, KEGG or other curated terms and pathways. However, such requires the existence of overlapping genes between query those annotated GO/KEGG. Furthermore, GO/KEGG databases only maintain very restricted vocabulary. Here, we have developed tool called "CoCiter" literature co-citations address limitations in conventional analysis. Co-citation widely used ranking articles predicting...

Regulation of cell growth and division has a fundamental role in tissue formation, organ development, cancer progression. Remarkable similarities the topological distributions were found variety proliferating epithelia both animals plants. At same time, there are species with significantly varied frequency hexagonal cells. Moreover, local topology been shown to be disturbed on boundary between quiescent cells, where cells have fewer sides than natural epithelia. The mechanisms regulating...

Understanding an enzyme's function is one of the most crucial problem domains in computational biology. Enzymes are a key component all organisms and many industrial processes as they help fighting diseases speed up essential chemical reactions. They have wide applications therefore, discovery new enzymatic proteins can accelerate biological research commercial productivity. Biological experiments, to determine function, time-consuming resource expensive.In this study, we propose novel...

Objective The mitotic activity index is an important prognostic factor in the diagnosis of cancer. task mitosis detection difficult as nuclei are microscopic size and partially labeled, there many more non-mitotic compared to ones. In this paper, we highlight challenges current pipelines propose a method tackle these challenges. Methods Our proposed methodology inspired from recent research on deep learning extensive analysis dataset training pipeline. We first used MiDoG′22 for training,...

Significance <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:mi>β</mml:mi> </mml:math> -Barrel membrane proteins ( MPs) are drawing increasing attention because of their promising potential in bionanotechnology. However, structures notoriously hard to determine experimentally. Here we develop a method achieve accurate prediction MP structures, including those for which no has been attempted before. The is general and can be applied genome-wide structural MPs,...

Abstract Long non-coding RNAs (lncRNAs), which were once considered as transcriptional noise, are now in the limelight of current research. LncRNAs play a major role regulating various biological processes such imprinting, cell differentiation, and splicing. The mutations lncRNAs involved complex diseases. Identifying lncRNA-disease associations has gained lot attention predicting it efficiently will lead towards better disease treatment. In this study, we have developed machine learning...

Knowledge of the transfer free energy amino acids from aqueous solution to a lipid bilayer is essential for understanding membrane protein folding and predicting structure. Here we report computational approach that can calculate transmembrane region outer β-barrel proteins (OMPs) by combining an empirical function with reduced discrete state space model. We quantitatively analyzed energies 20 acid residues at center OmpLA. Our results are in excellent agreement experimentally derived...

Abstract Motivation: Biological molecules perform their functions through interactions with other molecules. Structure alignment of interaction interfaces between biological complexes is an indispensable step in detecting structural similarities, which are keys to understanding evolutionary histories and functions. Although various structure methods have been developed successfully access the similarities protein structures or certain types interfaces, existing tools cannot directly align...

Abstract The Gene Ontology (GO) is a controlled vocabulary that captures the semantics or context of an entity based on its functional role. Biomedical entities are frequently compared to each other find similarities help in data annotation and knowledge transfer. In this study, we propose GOntoSim, novel method determine similarity between genes. GOntoSim quantifies pairs GO terms, by taking graph structure information content nodes into consideration. Our measure ancestors terms...

Regulation of cell growth and division plays fundamental roles in tissue morphogenesis. However, the mechanisms regulating elongation through are still not well understood. The wing imaginal disc Drosophila provides a model system that has been widely used to study Here we use recently developed two-dimensional cellular wing. We simulate effects directional cues on elongation. also computationally analyze role reduced size. Our simulation results indicate oriented divisions, mechanical...

Abstract Motivation: The inherent promiscuity of small molecules towards protein targets impedes our understanding healthy versus diseased metabolism. This also poses a challenge for the pharmaceutical industry as identifying all is important to assess (side) effects and repositioning opportunities drug. Results: Here, we present novel integrated structure- system-based approach drug-target prediction (iDTP) enable large-scale discovery new molecules, such drugs, co-factors metabolites...

Geometric and mechanical properties of individual cells interactions among neighboring are the basis formation tissue patterns. Understanding complex interplay is essential for gaining insight into embryogenesis, development, other emerging behavior. Here we describe a cell model an efficient geometric algorithm studying dynamic process in 2D (e.g. epithelial tissues). Our approach improves upon previous methods by incorporating as well detailed description growth process, with all...

COVID-19 an outbreak of a novel corona virus originating from Wuhan, China in December 2019 has now spread across the entire world and been declared pandemic by WHO. Angiotensin converting enzyme 2 (ACE2) is receptor protein that interacts with spike glycoprotein host to facilitate entry coronavirus (SARS-CoV-2) hence causing disease (COVID-19). Our experimental design based on bioinformatics approach combines sequence, structure consensus tools label coding single nucleotide polymorphism...

Enzymes are critical proteins in every organism. They speed up essential chemical reactions, help fight diseases, and have a wide use the pharmaceutical manufacturing industries. Wet lab experiments to figure out an enzyme's function time consuming expensive. Therefore, need for computational approaches address this problem becoming necessary. Usually, enzyme is extremely specific performing its function. However, there exist enzymes that can perform multiple functions. A multi-functional...

Regulation of proliferation is required for normal development tissues and prevention cancer formation. Continuous control leads to regular shaped cells forming characteristic tissue patterns. Epithelial serve as a model system studying morphogenesis. Several groups have studied epithelial morphogenesis using topological or geometric models, with various assumptions. In this study, we developed method simulate the dynamic process proliferating epithelia an off-lattice cellular model. Our...