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computational structural biology

Jinbo Chen, Uwe Scholz, Ruonan Zhou, Matthias Lange
In order to access and filter content of life-science databases, full text search is a widely applied query interface. But its high flexibility and intuitiveness is paid for with potentially imprecise and incomplete query results. To reduce this drawback, query assistance systems suggest those combinations of keywords with the highest potential to match most of the relevant data records. Widespread approaches are syntactic query corrections that avoid misspelling and support expansion of words by suffixes and prefixes...
March 12, 2018: PLoS Computational Biology
Zaheer Ul-Haq, Sajda Ashraf, Majdi M Bkhaitan
Casein kinase-II, a member of protein kinase family, plays significant role in different cellular processes such as cell growth, differentiation, proliferation, gene expression and embryogenesis. Being a potent suppressor of apoptosis, it serves as a significant link for its association with various types of malignancies such as colorectal and breast cancer. To overcome its pathological role in various cancerous diseases, CK-II procures great consideration as a therapeutic target. This study aimed at understanding the binding mechanism and structural properties of benzimidazole derivatives by utilizing various computational tools including docking simulation, 3-dimensional quantitative structure activity relationships and molecular dynamic simulation...
March 12, 2018: Journal of Biomolecular Structure & Dynamics
Thomas Parr, Geraint Rees, Karl J Friston
Computational theories of brain function have become very influential in neuroscience. They have facilitated the growth of formal approaches to disease, particularly in psychiatric research. In this paper, we provide a narrative review of the body of computational research addressing neuropsychological syndromes, and focus on those that employ Bayesian frameworks. Bayesian approaches to understanding brain function formulate perception and action as inferential processes. These inferences combine 'prior' beliefs with a generative (predictive) model to explain the causes of sensations...
2018: Frontiers in Human Neuroscience
Michael Habeck, Thach Nguyen
Biological macromolecules often undergo large conformational rearrangements during a functional cycle. To simulate these structural transitions with full atomic detail typically demands extensive computational resources. Moreover, it is unclear how to incorporate, in a principled way, additional experimental information that could guide the structural transition. This article develops a probabilistic model for conformational transitions in biomolecules. The model can be viewed as a network of anharmonic springs that break, if the experimental data support the rupture of bonds...
March 9, 2018: Proteins
Alexander S Moffett, Diwakar Shukla
Eukaryotic protein kinases (PKs) are a large family of proteins critical for cellular response to external signals, acting as molecular switches. PKs propagate biochemical signals by catalyzing phosphorylation of other proteins, including other PKs, which can undergo conformational changes upon phosphorylation and catalyze further phosphorylations. Although PKs have been studied thoroughly across the domains of life, the structures of these proteins are sparsely understood in numerous groups of organisms, including plants...
March 9, 2018: Biochemical Journal
Ibai Irastorza-Azcarate, Rafael D Acemel, Juan J Tena, Ignacio Maeso, José Luis Gómez-Skarmeta, Damien P Devos
The use of 3C-based methods has revealed the importance of the 3D organization of the chromatin for key aspects of genome biology. However, the different caveats of the variants of 3C techniques have limited their scope and the range of scientific fields that could benefit from these approaches. To address these limitations, we present 4Cin, a method to generate 3D models and derive virtual Hi-C (vHi-C) heat maps of genomic loci based on 4C-seq or any kind of 4C-seq-like data, such as those derived from NG Capture-C...
March 9, 2018: PLoS Computational Biology
Carl Barton, Sandro Morganella, Øyvind Ødegård-Fougner, Stephanie Alexander, Jonas Ries, Tomas Fitzgerald, Jan Ellenberg, Ewan Birney
The 3D structure of chromatin plays a key role in genome function, including gene expression, DNA replication, chromosome segregation, and DNA repair. Furthermore the location of genomic loci within the nucleus, especially relative to each other and nuclear structures such as the nuclear envelope and nuclear bodies strongly correlates with aspects of function such as gene expression. Therefore, determining the 3D position of the 6 billion DNA base pairs in each of the 23 chromosomes inside the nucleus of a human cell is a central challenge of biology...
March 9, 2018: PLoS Computational Biology
Michael Hucka, Frank T Bergmann, Andreas Dräger, Stefan Hoops, Sarah M Keating, Nicolas Le Novère, Chris J Myers, Brett G Olivier, Sven Sahle, James C Schaff, Lucian P Smith, Dagmar Waltemath, Darren J Wilkinson
Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations...
March 9, 2018: Journal of Integrative Bioinformatics
Yeonjoon Kim, Jaewook Kim, Kyung Yup Baek, Woo Youn Kim
Microhydration of biomolecules is an important structural factor associated with their biological processes. However, there is no general way to elucidate stable hydrated structures even for simple amino acids because of the high complexity of chemical space increasing rapidly with the number of water molecules. Here, we propose a very efficient computational method to selectively sample the most stable structures of microhydrated molecules. The key idea is to utilize the unique structural patterns of H-bond networks obtained from their energetic features, i...
March 9, 2018: Physical Chemistry Chemical Physics: PCCP
Carolina Horta Andrade, Bruno Junior Neves, Cleber Camilo Melo-Filho, Juliana Rodrigues, Diego Cabral Silva, Rodolpho Campos Braga, Pedro Vitor Lemos Cravo
Only ~1% of all drug candidates against Neglected Tropical Diseases (NTDs) have reached clinical trials in the last decades, underscoring the need for new, safe and effective treatments. In such context, drug repositioning, which allows finding novel indications for approved drugs whose pharmacokinetic and safety profiles are already known, is emerging as a promising strategy for tackling NTDs. Chemogenomics is a direct descendent of the typical drug discovery process that involves the systematic screening of chemical compounds against drug targets in high-throughput screening (HTS) efforts, for the identification of lead compounds...
March 8, 2018: Current Medicinal Chemistry
Tiago Simões, Daniel Lopes, Sérgio Dias, Francisco Fernandes, João Pereira, Joaquim Jorge, Chandrajit Bajaj, Abel Gomes
Detecting and analyzing protein cavities provides significant information about active sites for biological processes (e.g., protein-protein or protein-ligand binding) in molecular graphics and modeling. Using the three-dimensional structure of a given protein (i.e., atom types and their locations in 3D) as retrieved from a PDB (Protein Data Bank) file, it is now computationally viable to determine a description of these cavities. Such cavities correspond to pockets, clefts, invaginations, voids, tunnels, channels, and grooves on the surface of a given protein...
December 2017: Computer Graphics Forum: Journal of the European Association for Computer Graphics
Lukas Everding, Jörg Conradt
In order to safely navigate and orient in their local surroundings autonomous systems need to rapidly extract and persistently track visual features from the environment. While there are many algorithms tackling those tasks for traditional frame-based cameras, these have to deal with the fact that conventional cameras sample their environment with a fixed frequency. Most prominently, the same features have to be found in consecutive frames and corresponding features then need to be matched using elaborate techniques as any information between the two frames is lost...
2018: Frontiers in Neurorobotics
Luis A Camuñas-Mesa, Yaisel L Domínguez-Cordero, Alejandro Linares-Barranco, Teresa Serrano-Gotarredona, Bernabé Linares-Barranco
Convolutional Neural Networks (ConvNets) are a particular type of neural network often used for many applications like image recognition, video analysis or natural language processing. They are inspired by the human brain, following a specific organization of the connectivity pattern between layers of neurons known as receptive field. These networks have been traditionally implemented in software, but they are becoming more computationally expensive as they scale up, having limitations for real-time processing of high-speed stimuli...
2018: Frontiers in Neuroscience
Saeideh Jalali, Amir Zarrinhaghighi, Saman Sadraei, Younes Ghasemi, Amirhossein Sakhteman, Pouya Faridi
Background The plant Nardostachys jatamansi from Valerianaceae family is a well known antidepressant plant and has historically been used in traditional medicine. As N. jatamansi contains many different compounds, to identify its mechanisms of action, we need a network-based study. Network-based studies are becoming an increasingly important tool in understanding the mechanisms of actions of drugs. Systems pharmacology (SP) and bioinformatics are two emerging tools that use computation to develop an understanding of drug actions in molecular and cellular levels...
March 5, 2018: Current Drug Metabolism
Saad Raza, Syed Sikander Azam
Conformational flexibility and generalized structural features are responsible for specific phenomena existing in biological pathways. With advancements in computational chemistry, novel approaches and new methods are required to compare the dynamic nature of biomolecules, which are crucial not only to address dynamic functional relationships but also to gain detailed insights into the disturbance and positional fluctuation responsible for functional shifts. Keeping this in mind, axial frequency distribution (AFD) has been developed, designed, and implemented...
March 6, 2018: Journal of Molecular Modeling
Crhisllane Rafaele Dos Santos Vasconcelos, Túlio de Lima Campos, Antonio Mauro Rezende
BACKGROUND: Systematic analysis of a parasite interactome is a key approach to understand different biological processes. It makes possible to elucidate disease mechanisms, to predict protein functions and to select promising targets for drug development. Currently, several approaches for protein interaction prediction for non-model species incorporate only small fractions of the entire proteomes and their interactions. Based on this perspective, this study presents an integration of computational methodologies, protein network predictions and comparative analysis of the protozoan species Leishmania braziliensis and Leishmania infantum...
March 6, 2018: BMC Bioinformatics
Antonio Benedetto, Pietro Ballone
Empirical evidence and conceptual elaboration reveal and rationalise the remarkable affinity of organic ionic liquids for biomembranes. Cations of the so-called room-temperature ionic liquids (RTILs), in particular, are readily absorbed into the lipid fraction of biomembranes, causing a variety of observable biological effects, including generic cytotoxicity, broad anti-bacterial potential, and anti-cancer activity. Chemical-physics analysis of model systems made of phospholipid bilayers, RTIL ions and water confirm and partly explain this evidence, quantifying the mild destabilising effect of RTILs on structural, dynamical and thermodynamic properties of lipids in biomembranes...
March 6, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
Franco Tassi, Stefano Fazi, Simona Rossetti, Paolo Pratesi, Marco Ceccotti, Jacopo Cabassi, Francesco Capecchiacci, Stefania Venturi, Orlando Vaselli
Volcanic lakes are characterized by physicochemical favorable conditions for the development of reservoirs of C-bearing greenhouse gases that can be dispersed to air during occasional rollover events. By combining a microbiological and geochemical approach, we showed that the chemistry of the CO2- and CH4-rich gas reservoir hosted within the meromictic Lake Averno (Campi Flegrei, southern Italy) are related to the microbial niche differentiation along the vertical water column. The simultaneous occurrence of diverse functional groups of microbes operating under different conditions suggests that these habitats harbor complex microbial consortia that impact on the production and consumption of greenhouse gases...
2018: PloS One
Alexandre Barrozo, Qinghua Liao, Mauricio Esguerra, Gaël Marloie, Jan Florián, Nicholas H Williams, Shina Caroline Lynn Kamerlin
β-Phosphoglucomutase (β-PGM) has served as an important model system for understanding biological phosphoryl transfer. This enzyme catalyzes the isomerization of β-glucose-1-phosphate to β-glucose-6-phosphate in a two-step process proceeding via a bisphosphate intermediate. The conventionally accepted mechanism is that both steps are concerted processes involving acid-base catalysis from a nearby aspartate (D10) side chain. This argument is supported by the observation that mutation of D10 leaves the enzyme with no detectable activity...
March 6, 2018: Organic & Biomolecular Chemistry
Qianli Huang, Ming-An Sun, Ping Yan
In recent years, transcriptome sequencing has become very popular, encompassing a wide variety of applications from simple mRNA profiling to discovery and analysis of the entire transcriptome. One of the most common aims of transcriptome sequencing is to identify genes that are differentially expressed (DE) between two or more biological conditions, and to infer associated pathways and gene networks from expression profiles. It can provide avenues for further systematic investigation into potential biologic mechanisms...
2018: Methods in Molecular Biology
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