Egon Willighagen › Comments

Egon Willighagen
Chemistry Development Kit - http://en.wikipedia.org/w...
Egonw: Added the missing title. {{Infobox software | name = Chemistry Development Kit | logo = [[Image:Cdklogo.svg|200px]] | screenshot = | caption = | developer = The CDK Project | released = {{Start date and age|df=yes|2001|05|11}}<ref>https://sourceforge.net/project...</ref> | frequently updated = yes<!-- Release version update? Don't edit this page, just click on the version number! --> | programming language = [[Java (programming language)]] | operating system = [[Cross-platform]] | platform = | language = | genre = [[Chemoinformatics]]/[[Molecular modelling]]/[[Bioinformatics]] | license = [[GNU Lesser General Public License]] | website = http://cdk.sourceforge.net/ }} The '''Chemistry Development Kit''' is an [[open-source]] Java library for [[Chemoinformatics]] and [[Bioinformatics]].<ref>{{cite journal |author=Steinbeck, C.; Han, Y.Q.; Kuhn, S.; Horlacher, O.; Luttmann, E.; Willighagen, E.L. |title=The Chemistry Development Kit (CDK): An open-source Java... - Egon Willighagen
Egon Willighagen
Metabonomics of human fecal extracts characterize ulcerative colitis, Crohn’s disease and healthy individuals - http://www.citeulike.org/user...
In Metabolomics, Vol. 11, No. 1. (2015), pp. 122-133, doi:10.1007/s11306-014-0677-3 This study employs spectroscopy-based metabolic profiling of fecal extracts from healthy subjects and patients with active or inactive ulcerative colitis (UC) and Crohn’s disease (CD) to substantiate the potential use of spectroscopy as a non-invasive diagnostic tool and to characterize the fecal metabolome in inflammatory bowel disease (IBD). Stool samples from 113 individuals (UC 48, CD 44, controls 21) were analyzed by 1H nuclear magnetic resonance (NMR) spectroscopy (Bruker 600 MHz, Bruker BioSpin, Rheinstetten, Germany). Data were analyzed with principal component analysis and orthogonal-projection to latent structure-discriminant analysis using SIMCA-P + 12 and MATLAB. Significant differences were found in the metabolic profiles making it possible to differentiate between active IBD and controls and between UC and CD. The metabolites holding differential power primarily belonged to a range of... - Egon Willighagen
Egon Willighagen
Ten percent of Dutch researchers take 65% of all funding. #ABBAWisdom   #WinnerTakesAll - https://plus.google.com/1041867...
Ten percent of Dutch researchers take 65% of all funding. #ABBAWisdom   #WinnerTakesAll   Toponderzoekers halen per persoon miljoenen op | Wetenschap | de Volkskrant - Egon Willighagen
Egon Willighagen
BiobankConnect: software to rapidly connect data elements for pooled analysis across biobanks using ontological and lexical indexing - http://www.citeulike.org/user...
Journal of the American Medical Informatics Association, Vol. 22, No. 1. (01 January 2015), pp. 65-75, doi:10.1136/amiajnl-2013-002577 Chao Pang, Dennis Hendriksen, Martijn Dijkstra, Joeri van der Velde, Joel Kuiper, Hans Hillege, Morris Swertz - Egon Willighagen
Egon Willighagen
Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases - http://www.citeulike.org/user...
Bioinformatics, Vol. 20, No. 13. (1 September 2004), pp. 2075-2083, doi:10.1093/bioinformatics/bth206 Motivation: Genomic research laboratories need adequate infrastructure to support management of their data production and research workflow. But what makes infrastructure adequate? A lack of appropriate criteria makes any decision on buying or developing a system difficult. Here, we report on the decision process for the case of a molecular genetics group establishing a microarray laboratory.Results: Five typical requirements for experimental genomics database systems were identified: (i) evolution ability to keep up with the fast developing genomics field; (ii) a suitable data model to deal with local diversity; (iii) suitable storage of data files in the system; (iv) easy exchange with other software; and (v) low maintenance costs. The computer scientists and the researchers of the local microarray laboratory considered alternative solutions for these five requirements and chose the... - Egon Willighagen
Egon Willighagen
Scientists have introduced very flexible and stable monolayers of gold nanoparticles made by a self-assembly process based on protein aggregation. The films were used to coat wafers up to 10 cm in diameter. - Egon Willighagen
Egon Willighagen
Edition 1.5.10-0 is out! This is the first edition updated for the CDK 1.5.x branch. Updated examples... - https://plus.google.com/1041867...
Edition 1.5.10-0 is out! This is the first edition updated for the CDK 1.5.x branch. Updated examples for the new API. This link is for the paperback version, but there is an eBook (PDF) version for download too. Koop Groovy Cheminformatics with the Chemistry Development Kit door Egon Willighagen (Paperback) online via Lulu NL. Ga naar de Lulu Marktplaats voor productinformatie, beoordelingen en recensies. - Egon Willighagen
Egon Willighagen
Developing a Molecular Roadmap of Drug-Food Interactions - http://www.citeulike.org/user...
PLoS Comput Biol, Vol. 11, No. 2. (10 February 2015), e1004048, doi:10.1371/journal.pcbi.1004048 Recent research has demonstrated that consumption of food -especially fruits and vegetables- can alter the effects of drugs by interfering either with their pharmacokinetic or pharmacodynamic processes. Despite the recognition of such drug-food associations as an important element for successful therapeutic interventions, a systematic approach for identifying, predicting and preventing potential interactions between food and marketed or novel drugs is not yet available. The overall objective of this work was to sketch a comprehensive picture of the interference of ~ 4,000 dietary components present in ~1800 plant-based foods with the pharmacokinetics and pharmacodynamics processes of medicine, with the purpose of elucidating the molecular mechanisms involved. By employing a systems chemical biology approach that integrates data from the scientific literature and online databases, we gained... - Egon Willighagen
Egon Willighagen
Reshared post from Wikidata: - https://plus.google.com/1041867...
Original Post from Wikidata: Our glossary needs some serious simplification to make it easier to understand. Can you help? Wikidata is a knowledge base that anyone can edit. Before you get started, it is a good idea to familiarize yourself with the Wikidata Glossary. That way, editors can "speak the same language" (so to say). We hope that this will help to improve discussion and communication amongst editors. - Egon Willighagen
Egon Willighagen
Scientific Data, Vol. 2 (17 February 2015), doi:10.1038/sdata.2015.4 - Egon Willighagen
Egon Willighagen
Trends in Biochemical Sciences, Vol. 10, No. 3. (March 1985), pp. 109-110, doi:10.1016/0968-0004(85)90266-x Paul Srere - Egon Willighagen
Egon Willighagen
Egonw: Pymol and Rasmol are (or have older version that are) open source. {{infobox biodatabase |title = Protein Data Bank |logo = [[File:Database.png]] |description = {{ubl | [[Protein structure]] | [[X-ray crystallography]] | [[Nuclear magnetic resonance spectroscopy of proteins|NMR Structure Determination]]}} |scope = |organism = |center = |laboratory = |author = |pmid = |released = |standard = |format = [[Protein Data Bank (file format)|PDB]] |url = {{Plainlist| * {{URL|http://www.wwPDB.org/}} * {{URL|http://www.pdbe.org}} * {{URL|http://www.rcsb.org/pdb}} * {{URL|http://www.pdbj.org}} }} |download = |webservice = |sql = |sparql = |webapp = |standalone = |license = |versioning = |frequency = |curation = |bookmark = |version= }} The '''Protein Data Bank''' ('''PDB''') is a repository for the three-dimensional structural data of large biological molecules, such as [[protein]]s and [[nucleic acid]]s. (See also [[crystallographic database]].) The data, typically obtained by [[X-ray... - Egon Willighagen
Egon Willighagen
Egonw: Replaced another citation with a DOI. A '''metabolon''' is a temporary structural-functional complex formed between sequential enzymes of a metabolic pathway, held together by noncovalent interactions, and structural elements of the cell such as integral membrane proteins and proteins of the cytoskeleton. The concept of structural-metabolic cellular complexes was first conceived in 1970 by A. M. Kuzin of the USSR Academy of Sciences,<ref>Kuzin A. M. Structural – metabolic hypothesis in radiobiology. Moscow: Nauka Ed., 1970.- 50 p.</ref> and adopted in 1972 by P. A. Srere of the University of Texas for the enzymes of the Tricarboxilic Acids (Szent Györgyi-Krebs) Cycle.<ref>Srere P. A. Is there an organization of Krebs cycle enzymes in the mitochondiral matrix? In: Energy Metabolism and the Regulation of Metabolic Processes in Mitochondria, R. W. Hanson and W.A. Mehlman (Eds.). New York: Academic Press. 1972. p.79-91.</ref> This hypothesis was well accepted in the former USSR and... - Egon Willighagen
Egon Willighagen
Egonw: Reverted to deprecated template as that at least fills in the unknowns. A '''metabolon''' is a temporary structural-functional complex formed between sequential enzymes of a metabolic pathway, held together by noncovalent interactions, and structural elements of the cell such as integral membrane proteins and proteins of the cytoskeleton. The concept of structural-metabolic cellular complexes was first conceived in 1970 by A. M. Kuzin of the USSR Academy of Sciences,<ref>Kuzin A. M. Structural – metabolic hypothesis in radiobiology. Moscow: Nauka Ed., 1970.- 50 p.</ref> and adopted in 1972 by P. A. Srere of the University of Texas for the enzymes of the Tricarboxilic Acids (Szent Györgyi-Krebs) Cycle.<ref>Srere P. A. Is there an organization of Krebs cycle enzymes in the mitochondiral matrix? In: Energy Metabolism and the Regulation of Metabolic Processes in Mitochondria, R. W. Hanson and W.A. Mehlman (Eds.). New York: Academic Press. 1972. p.79-91.</ref> This hypothesis was... - Egon Willighagen
Egon Willighagen
Egonw: Added a few DOIs. A '''metabolon''' is a temporary structural-functional complex formed between sequential enzymes of a metabolic pathway, held together by noncovalent interactions, and structural elements of the cell such as integral membrane proteins and proteins of the cytoskeleton. The concept of structural-metabolic cellular complexes was first conceived in 1970 by A. M. Kuzin of the USSR Academy of Sciences,<ref>Kuzin A. M. Structural – metabolic hypothesis in radiobiology. Moscow: Nauka Ed., 1970.- 50 p.</ref> and adopted in 1972 by P. A. Srere of the University of Texas for the enzymes of the Tricarboxilic Acids (Szent Györgyi-Krebs) Cycle.<ref>Srere P. A. Is there an organization of Krebs cycle enzymes in the mitochondiral matrix? In: Energy Metabolism and the Regulation of Metabolic Processes in Mitochondria, R. W. Hanson and W.A. Mehlman (Eds.). New York: Academic Press. 1972. p.79-91.</ref> This hypothesis was well accepted in the former USSR and further developed... - Egon Willighagen
Egon Willighagen
Egonw: /* References */ A '''metabolon''' is a temporary structural-functional complex formed between sequential enzymes of a metabolic pathway, held together by noncovalent interactions, and structural elements of the cell such as integral membrane proteins and proteins of the cytoskeleton. The concept of structural-metabolic cellular complexes was first conceived in 1970 by A. M. Kuzin of the USSR Academy of Sciences,<ref>Kuzin A. M. Structural – metabolic hypothesis in radiobiology. Moscow: Nauka Ed., 1970.- 50 p.</ref> and adopted in 1972 by P. A. Srere of the University of Texas for the enzymes of the Tricarboxilic Acids (Szent Györgyi-Krebs) Cycle.<ref>Srere P. A. Is there an organization of Krebs cycle enzymes in the mitochondiral matrix? In: Energy Metabolism and the Regulation of Metabolic Processes in Mitochondria, R. W. Hanson and W.A. Mehlman (Eds.). New York: Academic Press. 1972. p.79-91.</ref> This hypothesis was well accepted in the former USSR and further developed... - Egon Willighagen
Egon Willighagen
Egonw: /* References */ A '''metabolon''' is a temporary structural-functional complex formed between sequential enzymes of a metabolic pathway, held together by noncovalent interactions, and structural elements of the cell such as integral membrane proteins and proteins of the cytoskeleton. The concept of structural-metabolic cellular complexes was first conceived in 1970 by A. M. Kuzin of the USSR Academy of Sciences,<ref>Kuzin A. M. Structural – metabolic hypothesis in radiobiology. Moscow: Nauka Ed., 1970.- 50 p.</ref> and adopted in 1972 by P. A. Srere of the University of Texas for the enzymes of the Tricarboxilic Acids (Szent Györgyi-Krebs) Cycle.<ref>Srere P. A. Is there an organization of Krebs cycle enzymes in the mitochondiral matrix? In: Energy Metabolism and the Regulation of Metabolic Processes in Mitochondria, R. W. Hanson and W.A. Mehlman (Eds.). New York: Academic Press. 1972. p.79-91.</ref> This hypothesis was well accepted in the former USSR and further developed... - Egon Willighagen
Egon Willighagen
On the Accuracy of Density Functional Theory to Predict Shifts in Nuclear Magnetic Resonance Shielding Constants due to Hydrogen Bonding - http://www.citeulike.org/user...
J. Chem. Theory Comput., Vol. 4, No. 2. (16 January 2008), pp. 267-277, doi:10.1021/ct700285j We present the first systematic investigation of shifts in the nuclear magnetic resonance (NMR) shielding constant due to hydrogen bonding using either the series of wave function based methods, Hartree?Fock (HF), second-order M?ller-Plesset perturbation theory (MP2), Coupled Cluster Singles and Doubles (CCSD) and CCSD extended with an approximate description of triples (CCSD(T)), or Density Functional Theory (DFT) employing either the B3LYP, PBE0, or KT3 exchange correlation (xc) functionals. The molecular systems considered are (i) the water dimer and (ii) formaldehyde in complex with two water molecules. Specially for the 17O in formaldehyde we observe significant differences between the DFT and CCSD(T) predictions. However, the extent of these deviations depends crucially on the applied xc functional. Compared to CCSD(T) we find the KT3 functional to provide accurate results, whereas both... - Egon Willighagen
Egon Willighagen
New Strategies in the Development of Antimicrobial Coatings: The Example of Increasing Usage of Silver and Silver Nanoparticles - http://www.citeulike.org/user...
Polymers, Vol. 3, No. 1. (26 January 2011), pp. 340-366, doi:10.3390/polym3010340 Bacterial infection from medical devices is a major problem and accounts for an increasing number of deaths as well as high medical costs. Many different strategies have been developed to decrease the incidence of medical device related infection. One way to prevent infection is by modifying the surface of the devices in such a way that no bacterial adhesion can occur. This requires modification of the complete surface with, mostly, hydrophilic polymeric surface coatings. These materials are designed to be non-fouling, meaning that protein adsorption and subsequent microbial adhesion are minimized. Incorporation of antimicrobial agents in the bulk material or as a surface coating has been considered a viable alternative for systemic application of antibiotics. However, the manifestation of more and more multi-drug resistant bacterial strains restrains the use of antibiotics in a preventive strategy. The... - Egon Willighagen
Egon Willighagen
Egonw: Added my VIAF ID. Small molecule scientists. Background in chemoinformatics, now in metabolomics. Blog: http://chem-bla-ics.blogspot.com/ Interests: semantic chemistry web (microformats, RDF(a), etc), chemistry etc. Things I'm involved in on WikiPedia: [[Chemistry Development Kit]], [[Bioclipse]], [[WikiPathways]], [[Journal of Cheminformatics]]. {{Authority control|ORCID=0000-0001-7542-0286|VIAF=282582124}} - Egon Willighagen
Egon Willighagen
Too many journals? Towards a theory of repeated rejections and ultimate acceptance - http://www.citeulike.org/user...
In Scientometrics (2015), pp. 1-5, doi:10.1007/s11192-015-1527-4 Under a set of reasonable assumptions, it is shown that all manuscripts submitted to any journal will ultimately be published, either by the first journal or by one of the following journals to which a manuscript is resubmitted. This suggests that low quality manuscripts may also be published, which further suggests that there may be too many journals. Jan Oosterhaven - Egon Willighagen
Egon Willighagen
Polymeric Nanoparticles for Non-Viral Gene Therapy Extend Brain Tumor Survival In Vivo - http://www.citeulike.org/user...
ACS Nano (2 February 2015), doi:10.1021/nn504905q Biodegradable polymeric nanoparticles have the potential to be safer alternatives to viruses for gene delivery; however, their use has been limited by poor efficacy in vivo. In this work, we synthesize and characterize polymeric gene delivery nanoparticles and evaluate their efficacy for DNA delivery of herpes simplex virus type I thymidine kinase (HSVtk) combined with the prodrug ganciclovir (GCV) in a malignant glioma model. We investigated polymer structure for gene delivery in two rat glioma cell lines, 9L and F98, to discover nanoparticle formulations more effective than the leading commercial reagent Lipofectamine? 2000. The lead polymer structure, poly(1,4-butanediol diacrylate-co-4-amino-1-butanol) end-modified with 1-(3-aminopropyl)-4-methylpiperazine, is a poly(beta-amino ester) (PBAE) and formed nanoparticles with HSVtk DNA that were 138 ± 4 nm in size and 13 ± 1 mV in zeta potential. These nanoparticles containing HSVtk DNA... - Egon Willighagen
Egon Willighagen
A New Publicly Available Chemical Query Language, CSRML, to support Chemotype Representations for Application to Data Mining and Modeling - http://www.citeulike.org/user...
J. Chem. Inf. Model. (3 February 2015), doi:10.1021/ci500667v Chemotypes are a new approach for representing molecules, chemical substructures and patterns, reaction rules, and reactions. Chemotypes are capable of integrating types of information beyond what is possible using current representation methods (e.g., SMARTS patterns) or reaction transformations (e.g., SMIRKS, reaction SMILES). Chemotypes are expressed in the XML-based Chemical Subgraphs and Reactions Mark-up Language (CSRML), and can be encoded not only with connectivity and topology, but also with properties of atoms, bonds, electronic systems, or molecules. The CSRML language has been developed in parallel with a public set of chemotypes, i.e., the ToxPrint chemotypes, which are designed to provide excellent coverage of environmental, regulatory and commercial-use chemical space, as well as to represent chemical patterns and properties especially relevant to various toxicity concerns. A software application, ChemoTyper... - Egon Willighagen
Egon Willighagen
A M.Sc. thesis can be cited too, if stored and available! +Samuel Lampa's thesis resulted in this reuse... - https://plus.google.com/1041867...
A M.Sc. thesis can be cited too, if stored and available! +Samuel Lampa's thesis resulted in this reuse from Jan Wielemaker et al. in Amsterdam: "The Blipkit [18] system is a comprehensive system for querying and transforming data in bioinformatics. Blipkit’s RDF support in terms of performance and expressiveness was evaluated by Lampa [15]. Lampa stresses the enhanced maintainability of Prolog queries due to reuse of query fragments represented as predicates (Figure 18 in [15])." http://uu.diva-portal.org/smash... BTW, did you see those download counts?? If only DIVA used DOIs... Lampa, Samuel. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. (Prof. Jarl Wikberg, Bioclipse group). 2010 (English)Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis ... - Egon Willighagen
Egon Willighagen
Well, clearly the +American Chemical Society hasn't solved the cookie issue with their journals yet,... - https://plus.google.com/1041867...
Well, clearly the +American Chemical Society hasn't solved the cookie issue with their journals yet, but this is a paper by a large group of well-known cheminformaticians. The work seems interesting and will get back on the details. This is certainly a paper I like to review (in my blog and probably +Publons... it's about a proposed standard for substructure search specification. The CDK is used via the +KNIMETV nodes for the MACCS keys. The CDK website is cited, but none of the papers. Not for KNIME either, BTW. An Error Occurred Setting Your User Cookie. Your browser is currently set to not accept cookies. Please enable cookies in your web browser to continue. How do I enable cookies? For most browsers, the cookies settings are located under Preferences or Internet Options. - Egon Willighagen
Egon Willighagen
Reshared post from Egon Willighagen: - https://plus.google.com/1041867...
Original Post from Egon Willighagen: Well, clearly the +American Chemical Society hasn't solved the cookie issue with their journals yet, but this is a paper by a large group of well-known cheminformaticians. The work seems interesting and will get back on the details. This is certainly a paper I like to review (in my blog and probably +Publons... it's about a proposed standard for substructure search specification. The CDK is used via the +KNIMETV nodes for the MACCS keys. The CDK website is cited, but none of the papers. Not for KNIME either, BTW. An Error Occurred Setting Your User Cookie. Your browser is currently set to not accept cookies. Please enable cookies in your web browser to continue. How do I enable cookies? For most browsers, the cookies settings are located under Preferences or Internet Options. - Egon Willighagen
Egon Willighagen
A Quick Guide for Building a Successful Bioinformatics Community - http://www.citeulike.org/user...
PLoS Comput Biol, Vol. 11, No. 2. (5 February 2015), e1003972, doi:10.1371/journal.pcbi.1003972 “Scientific community” refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role in many bioinformatics activities. Communities may be linked to a specific location or institute, or involve people working at many different institutions and locations. Education and training is typically an important component of these communities, providing a valuable context in which to develop skills and expertise, while also strengthening links and relationships within the community. Scientific communities facilitate: (i) the exchange and development of ideas and expertise; (ii) career development; (iii) coordinated funding activities; (iv) interactions and engagement with professionals from other fields; and (v) other activities beneficial to individual participants, communities, and... - Egon Willighagen
Egon Willighagen
Programming: Pick up Python - http://www.citeulike.org/user...
Nature, Vol. 518, No. 7537. (4 February 2015), pp. 125-126, doi:10.1038/518125a Jeffrey Perkel - Egon Willighagen
Egon Willighagen
Our research school has a new logo. - https://plus.google.com/1041867...
Our research school has a new logo. As of January 2015 NUTRIM's name was changed into NUTRIM School of Nutrition and Translational Research in Metabolism. - Egon Willighagen
Egon Willighagen
Reshared post from Greg Landrum: - https://plus.google.com/1041867...
I like the $$$$ at the end... pharma product, I assume? :) Original Post from Greg Landrum: The new ChEMBL is here. Excellent! We are pleased to announce the release of ChEMBL_20. This version of the database was prepared on 14th January 2015 and contains: 1715135 compound records; 1463270 compounds (of which 1456020 have mol files); 13520737 activities; 1148942 assays; 10774 targets; 59610 source documents ... - Egon Willighagen
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