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Computational and Structural Biotechnology Journal

ISSN: 2001--0370
Publisher: Research Network of Computational and Structural Biotechnology


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Robustness in experimental design: A study on the reliability of selection approaches

Author(s): Stefan Brandmaier | Igor V Tetko
Volume: 7
Issue: 9
Year: 2013
A method to predict edge strands in beta-sheets from protein sequences

Author(s): Antonin Guilloux | Bernard Caudron | Jean-Luc Jestin
Volume: 7
Issue: 9
Year: 2013
Therapeutic application of nanotechnology in cardiovascular and pulmonary regeneration

Author(s): Young Wook Chun | Spencer W Crowder | Steven C Mehl | Xingtong Wang | Hojae Bae | Hak-joon Sung
Volume: 7
Issue: 8
Year: 2013
Biochemical and Biophysical Characterization of Recombinant Yeast Proteasome Maturation Factor UMP1

Author(s): Bebiana Sá-Moura | Ana Marisa Simões | Joana Fraga | Humberto Fernandes | Isabel A. Abreu | Hugo M. Botelho | Cláudio M. Gomes | António J. Marques | R. Jürgen Dohmen | Paula C. Ramos | Sandra Macedo-Ribeiro
Volume: 7
Issue: 8
Year: 2013
A Network View on Parkinson’s Disease

Author(s): Sreedevi Chandrasekaran | Danail Bonchev
Volume: 7
Issue: 8
Year: 2013
The biological microprocessor, or how to build a computer with biological parts

Author(s): Gerd HG Moe-Behrens
Volume: 7
Issue: 8
Year: 2013
Changes in the genome-wide localization pattern of Sir3 in Saccharomyces cerevisiae during different growth stages

Author(s): Shu-Yun Tung | Kuan-Wei Lee | Jia-Yang Hong | Sue-Ping Lee | Hsiao-Hsuian Shen | Gunn-Guang Liou
Volume: 7
Issue: 8
Year: 2013
Bile acid binding protein: a versatile host of small hydrophobic ligands for applications in the fields of MRI contrast agents and bio-nanomaterials

Author(s): Katiuscia Pagano | Simona Tomaselli | Serena Zanzoni | Michael Assfalg | Henriette Molinari | Laura Ragona
Volume: 6
Issue: 7
Year: 2013
The Role of INDY in Metabolic Regulation

Author(s): Diana M Willmes | Andreas L Birkenfeld
Volume: 6
Issue: 7
Year: 2013
The role of mitochondria in the development and progression of lung cancer

Author(s): Emily R Roberts | Kelly Jean Thomas
Volume: 6
Issue: 7
Year: 2013
The role of Lipoxin A4 in Cystic Fibrosis Lung Disease

Author(s): Valérie Urbach | Gerard Higgins | Paul Buchanan | Fiona Ringholz
Volume: 6
Issue: 7
Year: 2013
The Cytotoxic Effects of Low Intensity Visible and Infrared Light on Human Breast Cancer (MCF7) cells

Author(s): P Peidaee | N Almansour | R Shukla | E Pirogova
Volume: 6
Issue: 7
Year: 2013
Probing Genome Maintenance Functions of human RECQ1

Author(s): Furqan Sami | Sudha Sharma
Volume: 6
Issue: 7
Year: 2013
Progression of 'OMICS' methodologies for understanding the pathogenicity of Corynebacterium pseudotuberculosis: the Brazilian experience

Author(s): Fernanda A Dorella | Alfonso Gala-Garcia | Anne C Pinto | Boutros Sarrouh | Camila A Antunes | Dayana Ribeiro | Flávia Aburjaile | Karina K Fiaux | Luis C Guimarães | Nubia Seyffert | Rachid A El-Aouar | Renata Silva | Syed S Hassan | Thiago LP Casto | Wanderson S Marques | Rommel Ramos | Adriana Carneiro | Pablo de Sá | Anderson Miyoshi | Vasco Azevedo | Artur Silva
Volume: 6
Issue: 7
Year: 2013
Characterization of ENU-induced Mutations in Red Blood Cell Structural Proteins

Author(s): Katrina Kildey | Robert L Flower | Thu V Tran | Robert Tunningley | Jonathan Harris | Melinda M Dean
Volume: 6
Issue: 7
Year: 2013
The albumin-binding domain as a scaffold for protein engineering

Author(s): Johan Nilvebrant | Sophia Hober
Volume: 6
Issue: 7
Year: 2013
Searching for Electrical Properties, Phenomena and Mechanisms in the Construction and Function of Chromosomes

Author(s): Ivan Kanev | Wai-Ning Mei | Akira Mizuno | Kristi DeHaai | Jennifer Sanmann | Michelle Hess | Lois Starr | Jennifer Grove | Bhavana Dave | Warren Sanger
Volume: 6
Issue: 7
Year: 2013
Study of Uremic Toxin Fluxes Across Nanofabricated Hemodialysis Membranes Using Irreversible Thermodynamics

Author(s): Assem Hedayat | Jerzy Szpunar | N A P Kiran Kumar | Rob Peace | Hamdi Elmoselhi | Ahmed Shoker
Volume: 6
Issue: 7
Year: 2013
Biomarker signature identification in “omics” data with multi-class outcome

Author(s): Vincenzo Lagani | George Kortas | Ioannis Tsamardinos
Volume: 6
Issue: 7
Year: 2013
Biomarker Identification in Breast Cancer: Beta-Adrenergic Receptor Signaling and Pathways to Therapeutic Response

Author(s): Liana E. Kafetzopoulou | David J. Boocock | Gopal Krishna R. Dhondalay | Desmond G. Powe | Graham R. Ball
Volume: 6
Issue: 7
Year: 2013
Tribology of bio-inspired nanowrinkled films on ultrasoft substrates

Author(s): Juergen M. Lackner | Wolfgang Waldhauser | Lukasz Major | Christian Teichert | Paul Hartmann
Volume: 6
Issue: 7
Year: 2013
ChromatoGate: A Tool for Detecting Base Mis-Calls in Multiple Sequence Alignments by Semi-Automatic Chromatogram Inspection

Author(s): Nikolaos Alachiotis | Emmanouella Vogiatzi | Pavlos Pavlidis | Alexandros Stamatakis
Volume: 6
Issue: 7
Year: 2013
MD simulation studies to investigate iso-energetic conformational behaviour of modified nucleosides m2G and m22G present in tRNA

Author(s): Rohit S Bavi | Susmit B Sambhare | Kailas D Sonawane
Volume: 5
Issue: 6
Year: 2013
Automated detection of structural alerts (chemical fragments) in (eco)toxicology

Author(s): Alban Lepailleur | Guillaume Poezevara | Ronan Bureau
Volume: 5
Issue: 6
Year: 2013
Current progress in Structure-Based Rational Drug Design marks a new mindset in drug discovery

Author(s): Valère Lounnas | Tina Ritschel | Jan Kelder | Ross McGuire | Robert P Bywater | Nicolas Foloppe
Volume: 5
Issue: 6
Year: 2013
A frequency-based linguistic approach to protein decoding and design: Simple concepts, diverse applications, and the SCS Package

Author(s): Kenta Motomura | Morikazu Nakamura | Joji M. Otaki
Volume: 5
Issue: 6
Year: 2013
Molecular Dynamics Computer Simulations of Multidrug RND Efflux Pumps

Author(s): Paolo Ruggerone | Attilio V Vargiu | Francesca Collu | Nadine Fischer | Christian Kandt
Volume: 5
Issue: 6
Year: 2013
Methods for Similarity-based Virtual Screening

Author(s): Thomas Greve Kristensen | Jesper Nielsen | Christian Nørgaard Storm Pedersen
Volume: 5
Issue: 6
Year: 2013
Multivariate linear QSPR/QSAR models: Rigorous evaluation of variable selection for PLS

Author(s): Kurt Varmuza | Peter Filzmoser | Matthias Dehmer
Volume: 5
Issue: 6
Year: 2013
Chemical Structure Identification in Metabolomics: Computational Modeling of Experimental Features

Author(s): Lochana C Menikarachchi | Mai A Hamdalla | Dennis W Hill | David F Grant
Volume: 5
Issue: 6
Year: 2013
Small world network strategies for studying protein structures and binding

Author(s): Neil R Taylor
Volume: 5
Issue: 6
Year: 2013
Comparison and Enumeration of Chemical Graphs

Author(s): Tatsuya Akutsu | Hiroshi Nagamochi
Volume: 5
Issue: 6
Year: 2013
Fusing similarity rankings in ligand-based virtual screening

Author(s): Peter Willett
Volume: 5
Issue: 6
Year: 2013
Targeted, LCMS-based Metabolomics for Quantitative Measurement of NAD+ Metabolites

Author(s): Samuel AJ Trammell | Charles M Brenner
Volume: 4
Issue: 5
Year: 2013
Integrated LC-MS/MS system for plant metabolomics

Author(s): Yuji Sawada | Masami Yokota Hirai
Volume: 4
Issue: 5
Year: 2013
Data Mining Methods for Omics and Knowledge of Crude Medicinal Plants toward Big Data Biology

Author(s): Farit M. Afendi | Naoaki Ono | Yukiko Nakamura | Kensuke Nakamura | Latifah K. Darusman | Nelson Kibinge | Aki Hirai Morita | Ken Tanaka | Hisayuki Horai | Md. Altaf-Ul-Amin | Shigehiko Kanaya
Volume: 4
Issue: 5
Year: 2013
Statistical methods for the analysis of high-throughput metabolomics data

Author(s): Jörg Bartel | Jan Krumsiek | Fabian J. Theis
Volume: 4
Issue: 5
Year: 2013
LC-MS-based Metabolomics of Xenobiotic-induced Toxicities

Author(s): Chi Chen | Sangyub Kim
Volume: 4
Issue: 5
Year: 2013
Untargeted metabolomics: an emerging approach to determine the composition of herbal products

Author(s): Mauro Commisso | Pamela Strazzer | Ketti Toffali | Matteo Stocchero | Flavia Guzzo
Volume: 4
Issue: 5
Year: 2013
Metabolomics in the identification of biomarkers of dietary intake

Author(s): Aoife O’Gorman | Helena Gibbons | Lorraine Brennan
Volume: 4
Issue: 5
Year: 2013
LC-MS metabolomics from study design to data-analysis – using a versatile pathogen as a test case

Author(s): Maya Berg | Manu Vanaerschot | Andris Jankevics | Bart Cuypers | Rainer Breitling | Jean-Claude Dujardin
Volume: 4
Issue: 5
Year: 2013
Error Analysis and Propagation in Metabolomics Data Analysis

Author(s): Hunter N B Moseley
Volume: 4
Issue: 5
Year: 2013
Computational Tools for the Secondary Analysis of Metabolomics Experiments

Author(s): Sean Cameron Booth | Aalim Weljie | Raymond Joseph Turner
Volume: 4
Issue: 5
Year: 2013
Bioprocess systems engineering: transferring traditional process engineering principles to industrial biotechnology

Author(s): Michalis Koutinas | Alexandros Kiparissides | Efstratios N Pistikopoulos | Athanasios Mantalaris
Volume: 3
Issue: 4
Year: 2012
Engineering Microbes for Plant Polyketide Biosynthesis

Author(s): Francois-Xavier Lussier | David Colatriano | Zach Wiltshire | Jonathan E. Page | Vincent J. J. Martin
Volume: 3
Issue: 4
Year: 2012
Escherichia coli redox mutants as microbial cell factories for the synthesis of reduced biochemicals

Author(s): Jimena Alicia Ruiz | Alejandra de Almeida | Manuel Santiago Godoy | Mariela Paula Mezzina | Gonzalo Nahuel Bidart | Beatriz Silvia Méndez | Maria Julia Pettinari | Pablo Ivan Nikel
Volume: 3
Issue: 4
Year: 2012
Emerging engineering principles for yield improvement in microbial cell design

Author(s): Santiago Comba | Ana Arabolaza | Hugo Gramajo
Volume: 3
Issue: 4
Year: 2012
Systems biology and metabolic engineering of Arthrospira cell factories

Author(s): Amornpan Klanchui | Tayvich Vorapreeda | Wanwipa Vongsangnak | Chiraphan Kannapho | Supapon Cheevadhanarak | Asawin Meechai
Volume: 3
Issue: 4
Year: 2012
Microbial Consortia Engineering for Cellular Factories: in vitro to in silico systems

Author(s): Hans C Bernstein | Ross P Carlson
Volume: 3
Issue: 4
Year: 2012
Beyond de-foaming: the effects of antifoams on bioprocess productivity

Author(s): Sarah Jayne Routledge
Volume: 3
Issue: 4
Year: 2012
Engineered fluorescent proteins illuminate the bacterial periplasm

Author(s): Thorben Dammeyer | Philip Tinnefeld
Volume: 3
Issue: 4
Year: 2012
Analyzing the genomic variation of microbial cell factories in the era of “New Biotechnology”

Author(s): Markus Herrgård | Gianni Panagiotou
Volume: 3
Issue: 4
Year: 2012
Metabolic engineering of biocatalysts for carboxylic acids production

Author(s): Ping Liu | Laura R Jarboe
Volume: 3
Issue: 4
Year: 2012
Dissecting complex polyketide biosynthesis

Author(s): Patrick Caffrey
Volume: 3
Issue: 4
Year: 2012
Metabolic modelling in the development of cell factories by synthetic biology

Author(s): Paula Tuulia Jouhten
Volume: 3
Issue: 4
Year: 2012
Genome-based Modeling and Design of Metabolic Interactions in Microbial Communities

Author(s): Radhakrishnan Mahadevan | Michael A Henson
Volume: 3
Issue: 4
Year: 2012
Developing a yeast cell factory for the production of terpenoids

Author(s): Sotirios C Kampranis | Antonios Michael Makris
Volume: 3
Issue: 4
Year: 2012
Optimization of enzyme parameters for fermentative production of biorenewable fuels and chemicals

Author(s): Laura R Jarboe | Ping Liu | Kumar Babu Kautharapu | Lonnie O. Ingram
Volume: 3
Issue: 4
Year: 2012
Metabolic engineering of Corynebacterium glutamicum aimed at alternative carbon sources and new products

Author(s): Ahmed Zahoor | Steffen Nikolaus Lindner | Volker Fritz Wendisch
Volume: 3
Issue: 4
Year: 2012
The Biochemistry of Vitreoscilla hemoglobin

Author(s): Benjamin C. Stark | Kanak L. Dikshit | Krishna R. Pagilla
Volume: 3
Issue: 4
Year: 2012
Converting Cells into Cellular Factories

Author(s): Hal Alper
Volume: 3
Issue: 4
Year: 2012
Computational approaches for rational design of proteins with novel functionalities

Author(s): Manish Kumar Tiwari | Ranjitha Singh | Raushan Kumar Singh | In-Won Kim | Jung-Kul Lee
Volume: 2
Issue: 3
Year: 2012
Emerging role of N- and C-terminal interactions in stabilizing (β/α)8 fold with special emphasis on Family 10 xylanases

Author(s): Amit Bhardwaj | Pranjal Mahanta | Suryanarayanarao Ramakumar | Amit Ghosh | Sadhu Leelavathi | Vanga Siva Reddy
Volume: 2
Issue: 3
Year: 2012
Editorial Note: Advances in Enzymology and Enzyme Engineering

Author(s): Paul Christakopoulos | Evangelos Topakas
Volume: 2
Issue: 3
Year: 2012
A structural overview of GH61 proteins – fungal cellulose degrading polysaccharide monooxygenases

Author(s): Leila Lo Leggio | Ditte Welner | Leonardo De Maria
Volume: 2
Issue: 3
Year: 2012
From Molecular Phylogenetics to Quantum Chemistry: Discovering Enzyme Design Principles through Computation

Author(s): Troy Wymore | Charles L. Brooks III
Volume: 2
Issue: 3
Year: 2012
Computational tools for rational protein engineering of aldolases

Author(s): Michael Widmann | Jürgen Pleiss | Anne K Samland
Volume: 2
Issue: 3
Year: 2012
Technology Prospecting on Enzymes: Application, Marketing and Engineering

Author(s): Shuang Li | Xiaofeng Yang | Shuai Yang | Muzi Zhu | Xiaoning Wang
Volume: 2
Issue: 3
Year: 2012
Cellulose degradation by oxidative enzymes

Author(s): Maria Dimarogona | Evangelos Topakas | Paul Christakopoulos
Volume: 2
Issue: 3
Year: 2012
Directed evolution: selection of the host organism

Author(s): Azadeh Pourmir | Tyler W Johannes
Volume: 2
Issue: 3
Year: 2012
Engineering Non-Heme Mono- and Dioxygenases for Biocatalysis

Author(s): Adi Dror | Ayelet Fishman
Volume: 2
Issue: 3
Year: 2012
Recent advances in rational approaches for enzyme engineering

Author(s): Kerstin Steiner | Helmut Schwab
Volume: 2
Issue: 3
Year: 2012
Computational Enzyme Design: Advances, hurdles and possible ways forward

Author(s): Mats Linder
Volume: 2
Issue: 3
Year: 2012
Computer-Aided Protein Directed Evolution: a Review of Web Servers, Databases and other Computational Tools for Protein Engineering

Author(s): Rajni Verma | Ulrich Schwaneberg | Danilo Roccatano
Volume: 2
Issue: 3
Year: 2012
Computational protein design approaches with significant biological outcomes: progress and challenges

Author(s): Xiaoman Li | Ziding Zhang | Jiangning Song
Volume: 2
Issue: 3
Year: 2012
Structural and mechanistic fundamentals for designing of cellulases

Author(s): Sandro Roberto Marana
Volume: 2
Issue: 3
Year: 2012
Lipase improvement: goals and strategies

Author(s): Arnau Bassegoda | Silvia Cesarini | Pilar Diaz
Volume: 2
Issue: 3
Year: 2012
Approaches to engineer stability of beetle luciferases

Author(s): Mikhail Koksharov | Natalia Ugarova
Volume: 2
Issue: 3
Year: 2012
Rational approaches for engineering carbon-carbon bond forming enzymes

Author(s): Perrin Baker | Stephen Seah
Volume: 2
Issue: 3
Year: 2012
Thumb-loops up for catalysis: a structure/function investigation of a functional loop movement in a GH11 xylanase

Author(s): Gabriel Paës | Juan Cortés | Thierry Siméon | Michael J. O'Donohue | Vinh Tran
Volume: 1
Issue: 2
Year: 2012
Assessment of Automated Analyses of Cell Migration on Flat and Nanostructured Surfaces

Author(s): Cristian Grădinaru | Joanna M Łopacińska | Johannes Huth | Hans A Kestler | Henrik Flyvbjerg | Kristian Molhave
Volume: 1
Issue: 2
Year: 2012
In silico evidence of signaling pathways of notch mediated networks in leukemia

Author(s): Kaiser Jamil | Archana Jayaraman | Raghunatha Rao | Surya Narayana G. Raju
Volume: 1
Issue: 2
Year: 2012
Integration of QSAR and SAR methods for the mechanistic interpretation of predictive models for carcinogenicity

Author(s): Natalja Fjodorova | Marjana Novič
Volume: 1
Issue: 2
Year: 2012
Limiting factors in single particle cryo electron tomography

Author(s): Mikhail Kudryashev | Daniel Castaño-Díez | Henning Stahlberg
Volume: 1
Issue: 2
Year: 2012
Measuring the shapes of macromolecules – and why it matters

Author(s): Jie Li | Paul Mach | Patrice Koehl
Volume: 8
Issue: 12
Year: 2013
Reconstruction of SAXS Profiles from Protein Structures

Author(s): Daniel K Putnam | Edward W Lowe Jr | Jens Meiler
Volume: 8
Issue: 11
Year: 2013
Structure-based Methods for Computational Protein Functional Site Prediction

Author(s): Dukka B KC
Volume: 8
Issue: 11
Year: 2013
Inverted Topologies in Membrane Proteins: A Mini-Review

Author(s): Amanda M Duran | Jens Meiler
Volume: 8
Issue: 11
Year: 2013
A Sieve-Raft Hypothesis for the regulation of endothelial fenestrations

Author(s): Victoria C. Cogger | Ute Roessner | Alessandra Warren | Robin Fraser | David G. Le Couteur
Volume: 8
Issue: 11
Year: 2013
Autophagy in Plasmodium, a multifunctional pathway?

Author(s): Adelaide U.P. Hain | Jürgen Bosch
Volume: 8
Issue: 11
Year: 2013
Frequency of dipeptides and antidipeptides

Author(s): Oliviero Carugo
Volume: 8
Issue: 11
Year: 2013
From plant genomes to protein families: computational tools

Author(s): Manuel Martinez
Volume: 8
Issue: 10
Year: 2013
Capturing RNA-dependent pathways for cryo-EM analysis

Author(s): Justin R Tanner | Katherine Degen | Brian L Gilmore | Deborah F Kelly
Volume: 1
Issue: 1
Year: 2012
STRUCTURAL BIOLOGY OF THE INTRINSIC CELL DEATH PATHWAY: WHAT DO WE KNOW AND WHAT IS MISSING?

Author(s): Erinna Faith Lee | Walter Douglas Fairlie
Volume: 1
Issue: 1
Year: 2012
The Use of Hammett Constants to Understand the Non-Covalent Binding of Aromatics

Author(s): Michael Lewis | Christina Bagwill | Laura K. E. Hardebeck | Selina Wireduaah
Volume: 1
Issue: 1
Year: 2012
Genetic code redundancy and its influence on the encoded polypeptides

Author(s): Paige S Spencer | Jose M. Barral
Volume: 1
Issue: 1
Year: 2012
Structure-Function Of The Tumor Suppressor BRCA1

Author(s): Serena L. Clark | Ana M. Rodriguez | Russell R. Snyder | Gary D.V. Hankins | Darren Boehning
Volume: 1
Issue: 1
Year: 2012
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