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computers in biology and medicine

Gennady M Verkhivker
Protein kinases are versatile molecule switches that govern functional processes in signal transduction networks and regulate fundamental biological processes of cell cycle and organism development. The continuous growth of biological information and a remarkable breath of structural, genetic, and pharmacological studies on protein kinase genes have significantly advanced our knowledge of the kinase activation, drug binding and allosteric mechanisms underlying kinase regulation and interactions in signaling cascades...
October 6, 2016: Current Medicinal Chemistry
Baifan Wang, Xin Wen, Zhen Xi
Protoporphyrinogen IX oxidase (PPO, EC catalyzes the oxidation of protoporphyrinogen IX (protogen IX) to protoporphyrin IX (proto IX) in the haem/chlorophyll biosynthetic pathway. Although extensive studies of PPO have already afforded many insights into its biological function and its significance to agriculture and medicine, details of the enzymatic mechanism as well as the nature of the specific amino acids involved in substrate binding still remain largely unknown due to the lack of structural information about protogen IX binding to PPO...
October 2016: Molecular Informatics
Tyler W H Backman, Thomas Girke
BACKGROUND: Next-generation sequencing (NGS) has revolutionized how research is carried out in many areas of biology and medicine. However, the analysis of NGS data remains a major obstacle to the efficient utilization of the technology, as it requires complex multi-step processing of big data demanding considerable computational expertise from users. While substantial effort has been invested on the development of software dedicated to the individual analysis steps of NGS experiments, insufficient resources are currently available for integrating the individual software components within the widely used R/Bioconductor environment into automated workflows capable of running the analysis of most types of NGS applications from start-to-finish in a time-efficient and reproducible manner...
2016: BMC Bioinformatics
Abdellah Tebani, Carlos Afonso, Stéphane Marret, Soumeya Bekri
The rise of technologies that simultaneously measure thousands of data points represents the heart of systems biology. These technologies have had a huge impact on the discovery of next-generation diagnostics, biomarkers, and drugs in the precision medicine era. Systems biology aims to achieve systemic exploration of complex interactions in biological systems. Driven by high-throughput omics technologies and the computational surge, it enables multi-scale and insightful overviews of cells, organisms, and populations...
2016: International Journal of Molecular Sciences
Yu Zhang, Lirong Wang, Zhiwei Feng, Haizi Cheng, Terence Francis McGuire, Yahui Ding, Tao Cheng, Yingdai Gao, Xiang-Qun Xie
Given the capacity of self-renewal and multilineage differentiation, stem cells are promising sources for use in regenerative medicines as well as in the clinical treatment of certain hematological malignancies and degenerative diseases. Complex networks of cellular signaling pathways largely determine stem cell fate and function. Small molecules that modulate these pathways can provide important biological and pharmacological insights. However, it is still challenging to identify the specific protein targets of these compounds, to explore the changes in stem cell phenotypes induced by compound treatment and to ascertain compound mechanisms of action...
October 7, 2016: Journal of Chemical Information and Modeling
Henrik Vogt, Bjørn Hofmann, Linn Getz
Systems medicine, which is based on computational modelling of biological systems, is emerging as an increasingly prominent part of the personalized medicine movement. It is often promoted as 'P4 medicine' (predictive, preventive, personalized, and participatory). In this article, we test promises made by some of its proponents that systems medicine will be able to develop a scientific, quantitative metric for wellness that will eliminate the purported vagueness, ambiguity, and incompleteness-that is, normativity-of previous health definitions...
October 2016: Theoretical Medicine and Bioethics
Nasim Nikkhoo, Nichole Cumby, P Glenn Gulak, Karen L Maxwell
The timely and accurate diagnosis of infectious diseases is one of the greatest challenges currently facing modern medicine. The development of innovative techniques for the rapid and accurate identification of bacterial pathogens in point-of-care facilities using low-cost, portable instruments is essential. We have developed a novel all-electronic biosensor that is able to identify bacteria in less than ten minutes. This technology exploits bacteriocins, protein toxins naturally produced by bacteria, as the selective biological detection element...
2016: PloS One
Paolo Decuzzi
Since the launch of multiple research initiatives on nanotechnology applied to medicine in the early 2000s, a plethora of nanomedicines have been developed that exhibit great therapeutic efficacy in preclinical models but yet minimal impact in daily clinical practice. The successful and complete clinical fruition of nanomedicines requires addressing three major technical challenges: improving loading efficacy and on-command release, modulating recognition and sequestration by immune cells, and maximizing accumulation at biological targets...
September 27, 2016: ACS Nano
Syed Lal Badshah, Yahia Nasser Mabkhot
This commentary highlights the recent article published in Nature, June 2016, titled: "Proteome-wide covalent ligand discovery in native biological systems". They screened the whole proteome of different human cell lines and cell lysates. Around 700 druggable cysteines in the whole proteome were found to bind the electrophilic fragments in both active and inactive states of the proteins. Their experiment and computational docking results agreed with one another. The usefulness of this study in terms of bringing a change in medicinal chemistry is highlighted here...
2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Cesar Pichardo-Almarza, Vanessa Diaz-Zuccarini
Current computational and mathematical tools are demonstrating the high value of using systems modeling approaches (e.g. Quantitative Systems Pharmacology) to understand the effect of a given compound on the biological and physiological mechanisms related to a specific disease. This review provides a short survey of the evolution of the mathematical approaches used to understand the effect of particular cholesterol-lowering drugs, from pharmaco-kinetic (PK) / pharmaco-dynamic (PD) models, through physiologically base pharmacokinetic models (PBPK) to QSP...
September 4, 2016: Current Pharmaceutical Design
Chao Wang, Xiaokui Huo, Xiangge Tian, Min Xu, Peipei Dong, Zhilin Luan, Xiaobo Wang, Baojing Zhang, Bo Zhang, Shanshan Huang, Sa Deng, Xiaochi Ma
BACKGROUND AND PURPOSE: Herbs which are widely used as food and medicine, are involved in many physiopathological processes. Melatonin is a human hormone, synthesized and secreted by the pineal gland, with a range of biological functions. Here, we have evaluated the potential influences of components extracted from common herbs on melatonin metabolism in humans. EXPERIMENTAL APPROACH: An in vivo pharmacokinetic study involving 12 healthy subjects, in vitro incubations with human liver microsomes (HLMs) and recombinant human cytochrome P (CYP) isoenzymes and an in silico quantitative structure-activity relationship (QSAR) model analysis using comparative molecular field analysis and comparative molecular similarity indices analysis methods were employed to explore these interactions...
September 2, 2016: British Journal of Pharmacology
Muhammad Ammad-Ud-Din, Suleiman A Khan, Disha Malani, Astrid Murumägi, Olli Kallioniemi, Tero Aittokallio, Samuel Kaski
MOTIVATION: A key goal of computational personalized medicine is to systematically utilize genomic and other molecular features of samples to predict drug responses for a previously unseen sample. Such predictions are valuable for developing hypotheses for selecting therapies tailored for individual patients. This is especially valuable in oncology, where molecular and genetic heterogeneity of the cells has a major impact on the response. However, the prediction task is extremely challenging, raising the need for methods that can effectively model and predict drug responses...
September 1, 2016: Bioinformatics
Zhongming Zhao, Yunlong Liu, Yufei Huang, Kun Huang, Jianhua Ruan
The 2015 International Conference on Intelligent Biology and Medicine (ICIBM 2015) was held on November 13-15, 2015 in Indianapolis, Indiana, USA. ICIBM 2015 included eight scientific sessions, three tutorial sessions, one poster session, and four keynote presentations that covered the frontier research in broad areas related to bioinformatics, systems biology, big data science, biomedical informatics, pharmacogenomics, and intelligent computing. Here, we present a summary of the 10 research articles that were selected from ICIBM 2015 and included in the supplement to BMC Systems Biology...
2016: BMC Systems Biology
E B Speltz, N Sawyer, L Regan
The ability to design new protein-protein interactions (PPIs) has many applications in biotechnology and medicine. The goal of designed PPIs is to achieve both high affinity and specificity for the target protein. A great challenge in protein design is to identify such proteins from an enormous number of potential sequences. Many computational and experimental methods have been developed to contend with this challenge. Here we describe one particularly powerful approach-semirational design-that combines design and selection...
2016: Methods in Enzymology
Cristina da Costa Oliveira, Clarice de Carvalho Veloso, Renata Cristina Mendes Ferreira, Gisele Avelar Lage, Lúcia Pinheiro Santos Pimenta, Igor Dimitri Gama Duarte, Thiago Roberto Lima Romero, Andrea de Castro Perez
Peltatoside is a natural compound isolated from leaves of Annona crassiflora Mart., a plant widely used in folk medicine. This substance is an analogue of quercetin, a flavonoid extensively studied because of its diverse biological activities, including analgesic effects. Besides, a previous study suggested, by computer structure analyses, a possible quercetin-CB1 cannabinoid receptor interaction. Thus, the aim of this work was to assess the antinociceptive effect of peltatoside and analyze the cannabinoid system involvement in this action...
August 30, 2016: Planta Medica
D Kilburg, E Gallicchio
We review computational models and software tools in current use for the study of protein-peptide interactions. Peptides and peptide derivatives are growing in interest as therapeutic agents to target protein-protein interactions. Protein-protein interactions are pervasive in biological systems and are responsible for the regulation of critical functions within the cell. Mutations or dysregulation of expression can alter the network of interactions among proteins and cause diseases such as cancer. Protein-protein binding interfaces, which are often large, shallow, and relatively feature-less, are difficult to target with small-molecule inhibitors...
2016: Advances in Protein Chemistry and Structural Biology
Stephen Nayfach, Katherine S Pollard
Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches...
August 25, 2016: Cell
Margherita Brindisi, Caterina Cavella, Simone Brogi, Angela Nebbioso, Johanna Senger, Samuele Maramai, Alfonso Ciotta, Concetta Iside, Stefania Butini, Stefania Lamponi, Ettore Novellino, Lucia Altucci, Manfred Jung, Giuseppe Campiani, Sandra Gemma
AIM: Histone deacetylases (HDACs) regulate the expression and activity of numerous proteins involved in the initiation and progression of cancer. Currently, three hydroxamate-containing HDAC pan-inhibitors have been approved as antitumor agents. RESULTS: We herein present the development of a series of novel phenylpyrrole-based derivatives stemmed from combined computational and medicinal chemistry efforts to rationally modulate HDAC1/6 isoform selectivity. In vitro activity on HDAC1 and HDAC6 isoforms and the effects of selected analogs on histone H3 and α-tubulin acetylation levels were determined...
September 2016: Future Medicinal Chemistry
Kun Huang, Yunlong Liu, Yufei Huang, Lang Li, Lee Cooper, Jianhua Ruan, Zhongming Zhao
We summarize the 2015 International Conference on Intelligent Biology and Medicine (ICIBM 2015) and the editorial report of the supplement to BMC Genomics. The supplement includes 20 research articles selected from the manuscripts submitted to ICIBM 2015. The conference was held on November 13-15, 2015 at Indianapolis, Indiana, USA. It included eight scientific sessions, three tutorials, four keynote presentations, three highlight talks, and a poster session that covered current research in bioinformatics, systems biology, computational biology, biotechnologies, and computational medicine...
2016: BMC Genomics
Marco Persico, Antonio Di Dato, Nausicaa Orteca, Paola Cimino, Ettore Novellino, Caterina Fattorusso
Computer-aided drug discovery plays a strategic role in the development of new potential therapeutic agents. Nevertheless, the modeling of biological systems still represents a challenge for computational chemists and at present a single computational method able to face such challenge is not available. This prompted us, as computational medicinal chemists, to develop in-house methodologies by mixing various bioinformatics and computational tools. Importantly, thanks to multi-disciplinary collaborations, our computational studies were integrated and validated by experimental data in an iterative process...
September 2016: Molecular Informatics
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