Journal cover: Molecular BioSystems

Molecular BioSystems

Research interfacing chemical biology with the -omic sciences and systems biology.
Impact Factor 3.183 12 Issues per Year Indexed in MEDLINE
 
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Molecular BioSystems,
01 January 2015 , Issue 1,
Page 1 to 320
Mohamed N. Triba, Laurence Le Moyec, Roland Amathieu, Corentine Goossens, Nadia Bouchemal, Pierre Nahon, Douglas N. Rutledge and Philippe Savarin
Mol. BioSyst., 2015, 11, 13-19
DOI: 10.1039/C4MB00414K, Opinion
In some cases, quality parameter values (the number of significant components, Q2, CV-ANOVA p-value,…) of PLS/OPLS models calculated with K-fold cross-validation can be strongly determined by the composition of the different validation subsets.
 
Mol. BioSyst., 2015, 11, 20-27
DOI: 10.1039/C4MB00438H, Review Article
Mathematical modeling of the coevolution of CRISPR-Cas, the prokaryotic heritable adaptive immunity system, with viruses yields many non-trivial, testable predictions.
 
Sarah R. Stockwell, Christian R. Landry and Scott A. Rifkin
Mol. BioSyst., 2015, 11, 28-37
DOI: 10.1039/C4MB00448E, Review Article
We present a conceptual framework for interpreting new experiments and current ideas on memory in the yeast galactose metabolism network.
 
Mol. BioSyst., 2015, 11, 38-59
DOI: 10.1039/C4MB00443D, Review Article
Fatty acids are primary metabolites synthesized by complex, elegant, and essential biosynthetic machinery.
 
Mol. BioSyst., 2015, 11, 60-70
DOI: 10.1039/C4MB00335G, Review Article
A review of cyanobacterial biocatalysts highlighting their metabolic features that argues for the need for systems-level metabolic engineering.
 
Mol. BioSyst., 2015, 11, 71-76
DOI: 10.1039/C4MB00436A, Method
Rapid selection of 2′,4′-BNA/FNA chimeric aptamers paves the way for further development of XNA aptamers having unconventional sugars.
 
Nicole Pearcy, Jonathan J. Crofts and Nadia Chuzhanova
Mol. BioSyst., 2015, 11, 77-85
DOI: 10.1039/C4MB00430B, Paper
At the systems level many organisms of interest may be described by their patterns of interaction, and as such, are perhaps best characterised via network or graph models.
 
Aakash Chavan Ravindranath, Nolen Perualila-Tan, Adetayo Kasim, Georgios Drakakis, Sonia Liggi, Suzanne C. Brewerton, Daniel Mason, Michael J. Bodkin, David A. Evans, Aditya Bhagwat, Willem Talloen, Hinrich W. H. Göhlmann, QSTAR Consortium, Ziv Shkedy and Andreas Bender
Mol. BioSyst., 2015, 11, 86-96
DOI: 10.1039/C4MB00328D, Paper
Integrating gene expression profiles with certain proteins can improve our understanding of the fundamental mechanisms in protein–ligand binding.
 
Rostyslav Zvanych, Nikola Lukenda, Xiang Li, Janice J. Kim, Satheeisha Tharmarajah and Nathan A. Magarvey
Mol. BioSyst., 2015, 11, 97-104
DOI: 10.1039/C4MB00406J, Paper
Metabolomic profiling, systems exploration of the biosynthesis and immunomodulatory activities of hybrid human microbiome-derived nonribosomal peptide–polyketides, mutanobactins, from Streptococcus mutans.
 
Bo Peng, Ningjing Lei, Yurong Chai, Edward K. L. Chan and Jian-Ying Zhang
Mol. BioSyst., 2015, 11, 105-114
DOI: 10.1039/C4MB00513A, Paper
Overexpression of CIP2A in lung cancer increased lactate production and CREB phosphorylation but decreased H2O2 production.
 
Zhe Li, Xiao Lu, Ling-Jun Feng, Ying Gu, Xingshu Li, Yinuo Wu and Hai-Bin Luo
Mol. BioSyst., 2015, 11, 115-125
DOI: 10.1039/C4MB00389F, Paper
Via molecular dynamics-based virtual screening, 15 novel phosphodiesterase-9A inhibitors with five non-pyrazolopyrimidinone scaffolds were discovered.
 
Tingting Zhao, Jinyuan Xu, Ling Liu, Jing Bai, Chaohan Xu, Yun Xiao, Xia Li and Liming Zhang
Mol. BioSyst., 2015, 11, 126-136
DOI: 10.1039/C4MB00478G, Paper
A computational method for identifying cancer-related lncRNAs by integrating data from the genome, regulome and transcriptome.
 
A. Marcel Willemsen, Diana M. Hendrickx, Huub C. J. Hoefsloot, Margriet M. W. B. Hendriks, S. Aljoscha Wahl, Bas Teusink, Age K. Smilde and Antoine H. C. van Kampen
Mol. BioSyst., 2015, 11, 137-145
DOI: 10.1039/C4MB00510D, Paper
This paper presents MetDFBA, a new approach incorporating experimental metabolomics time-series into constraint-based modeling. The method can be used for hypothesis testing and predicting dynamic flux profiles.
 
Mol. BioSyst., 2015, 11, 146-158
DOI: 10.1039/C4MB00471J, Paper
Derived consensus regulatory interaction model between key signaling proteins in mammary epithelial cells has shown that STAT3 is central to the crosstalk between proliferation and pro-survival pathways.
 
Shoiab Bukhari, Taseem A. Mokhdomi, Naveed A. Chikan, Asif Amin, Hilal Qazi, Sajad H. Wani, Asrar H. Wafai, Sumira Tyub, Farhat Mustafa, Masood S. Mir, Nisar A. Chowdri and Raies A. Qadri
Mol. BioSyst., 2015, 11, 159-169
DOI: 10.1039/C4MB00506F, Paper
Utilizing immunogenic property of antigens, an in-house affinity-reagent was developed to capture tumor associated antigens
 
Liqi Li, Sanjiu Yu, Weidong Xiao, Yongsheng Li, Wenjuan Hu, Lan Huang, Xiaoqi Zheng, Shiwen Zhou and Hua Yang
Mol. BioSyst., 2015, 11, 170-177
DOI: 10.1039/C4MB00340C, Paper
Mitochondrion, a tiny energy factory, plays an important role in various biological processes of most eukaryotic cells.
 
Mol. BioSyst., 2015, 11, 178-189
DOI: 10.1039/C4MB00486H, Paper
The domino effect illustrates that libraries of purvalanol-A are attuned to fill the allosteric binding site of HTLV-1 PR through molecular recognition and shows proper binding of ligand pharmacophoric features in receptor contours.
 
Cyril C. Curtain, Nigel M. Kirby, Haydyn D. T. Mertens, Kevin J. Barnham, Robert B. Knott, Colin L. Masters, Roberto Cappai, Agata Rekas, Vijaya B. Kenche and Timothy Ryan
Mol. BioSyst., 2015, 11, 190-196
DOI: 10.1039/C4MB00356J, Paper
Size exclusion chromatography with small angle X-ray scattering and ensemble optimisation modelling reveals conformers in random pool of α-synuclein.
 
Tai-Chung Huang, Santosh Renuse, Sneha Pinto, Praveen Kumar, Yi Yang, Raghothama Chaerkady, Brian Godsey, Joshua T. Mendell, Marc K. Halushka, Curt I. Civin, Luigi Marchionni and Akhilesh Pandey
Mol. BioSyst., 2015, 11, 197-207
DOI: 10.1039/C4MB00585F, Paper
The integration of transcriptomics and proteomics analysis identifies novel targets of a tumor suppressor miRNA, miR-145, in pancreatic cancer.
 
Gabbianelli Rosita, Carloni Manuel, Marmocchi Franco, Nasuti Cinzia, Fedeli Donatella, Laudadio Emiliano, Massaccesi Luca and Galeazzi Roberta
Mol. BioSyst., 2015, 11, 208-217
DOI: 10.1039/C4MB00491D, Paper
Permethrin and its metabolites affect the structure and activity of Cu/Zn superoxide dismutase (SOD), as it results from intrinsic fluorescence, 8-ANS fluorescence techniques and in silico studies.
 
Jungkweon Choi, Dae Won Cho, Sachiko Tojo, Mamoru Fujitsuka and Tetsuro Majima
Mol. BioSyst., 2015, 11, 218-222
DOI: 10.1039/C4MB00551A, Paper
Although the reduction dynamics of ferric Cyt-c occur within a time range of a few microseconds, the ligand binding and exchange of heme, accompanied by one-electron reduction, depends on the initial configuration of the heme.
 
Mol. BioSyst., 2015, 11, 223-231
DOI: 10.1039/C4MB00383G, Paper
Using molecular dynamics simulations, we investigate the relationship between the conformational changes of BoNT/A-RBD:SV2C-LD and the interfacial interactions.
 
Christoph B. Messner, Günther K. Bonn and Thomas S. Hofer
Mol. BioSyst., 2015, 11, 232-238
DOI: 10.1039/C4MB00424H, Paper
Hybrid quantum mechanical/molecular mechanical simulations have been used to study the structural and dynamical properties of a La(III)–phosphopeptide complex.
 
Ruth Isserlin, Daniele Merico, Dingyan Wang, Dajana Vuckovic, Nicolas Bousette, Anthony O. Gramolini, Gary D. Bader and Andrew Emili
Mol. BioSyst., 2015, 11, 239-251
DOI: 10.1039/C4MB00265B, Paper
An integrative bioinformatic and experimental approach to elucidate potential miRNA targets for further study and validation. The incorporation of multiple data sources can help address the high false positive rate of miRNA target predictions.
 
Yan Wang, Qing-Chuan Zheng, Chui-Peng Kong, Ye Tian, Jiuyu Zhan, Ji-Long Zhang and Hong-Xing Zhang
Mol. BioSyst., 2015, 11, 252-261
DOI: 10.1039/C4MB00381K, Paper
The structural alignment for the representative structure of Hep system (yellow color) and crystal structure (gray color). The small figure on the right top of TOC is from PCA analysis. The first frame from PCA is in blue color and the last frame from PCA is colored in red. The other two small figures of TOC show the detailed of 4-mer heparin and 0GX in the Hep system.
 

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