Software for 3D visualization and analysis of biomolecules.
DS Visualizer is an application for analysis and 3D visualization of macromolecules (proteins, RNA, DNA). Its particular strength lies in the intuitive usage as a structure analysis tool: There is no need for reading documentations, just start viewing and manipulating PDB structures in one of the best designed UIs for 3D representations. Simply expand the tree view on the left of the 3D molecule view to select chains or residues down to the single atoms. The selection can be done in the 3D view as well. Selected objects are always highlighed in both places. It's the perfect tool for also for beginners and useres who rarely work with 3D software for visualization of macromolecules.
Freely accessible program for drawing chemical structures and reaction schemes.
With ACD/ChemSketch you can draw chemical structures including organics, organometallics, polymers, and Markush structures, reactions, and schematic diagrams as well as calculate some chemical properties (e.g., molecular weight, density, molar refractivity, etc.). You can draw and view structures in 2D, or render in 3D. ACD/ChemSketch uses many standard file formats for the import and export of drawings (.mol, .cdx, .skc, .pdf, .png, .wmf, .bmp, etc.).
Software for generating IUPAC names from the structures of the compounds and vice versa.
ACD/Name generates chemical names of organic, organometallic, inorganic or biochemical compounds according to IUPAC and CAS Index rules using the structure of the molecule as input. It generates names in English, French, German and other european languages as well as InChI and SMILES strings.
Software for the prediction of physicochemical properties and ADME characteristics of chemical compounds.
With the PhysChem and ADME modules of ACD/Percepta you can rapidly predict physicochemical (aqueous solubility, logP, logD, pKa, boiling point, etc.) and ADME (blood brain barrier permeation, passive absorption, P-gp specificity etc.) properties from a chemical structure. You can employ batch modules to screen thousands of compounds and investigate the predictions by using different algorithms. In the spreadsheet view the predicted results can be sorted, filtered and color-coded using custom thresholds to facilitate the analysis.
Look up chemical acronyms and abbreviations.
"Acronyms" lists mMore than 800 acronyms of chemical substances or fragments which have been collected from about 100 chemical journals
Adobe illustrator is a vector graphics application that allows for clean and simple image creation (in 2D).
Adobe illustrator facilitates the creation of logos, drawings, typography, illustrations and, of course, figures for papers as well as group webpages and other applications. Because illustrator artwork is vector based, it can scale up and down easily for different sized screens and thus is valuable for material published on the web. It is possible to create freehand drawings as well as recolor imported photos (rendering the additional use of Photoshop unnecessary for figures). Furthermore, it is possible to import graphs from other programs, such as excel, and edit the colors, font size, and labels as appropriate for making more visually pleasing figures. When writing a paper, if one of the co-writers wants to match colors from old papers, it is possible to import the old figures, register the color, and then match all future figures for consistency.
Illustrator's free drawing app.
This app allows vector-based drawing. Free-form drawings can be designed with smooth, scalable lines and sent to Adobe Illustrator on a desktop computer. An Adobe ID is required. Tutorials and additional information are scattered across various web pages and the app thus requires learning by doing.
Photoshop’s free drawing app.
Photoshop Sketch offers various drawing tools, such as graphite pencils, ink pens or markers. Brushes are also integrated and provide additional artistic possibilities. Drawings can be sent directly to Adobe Photoshop on a desktop computer, where work can be continued. An Adobe ID is required. Tutorials and additional information are scattered across various web pages and the app thus requires learning by doing.
Altmetric is a provider of qualitative data on the online perception of research, providing an alternative to established, citation-based metrics.
Altmetric data can be accessed on a publication's website via a bookmarklet. The aggregated data is displayed as a colored donut with a number. The number is a weighed sum of different outlets and prevalence of a color indicates a dominating medium wherein the publication was mentioned. Altmetric uses policy documents, news, blogs, social media, academic networks and other sources. Links to the individual sources are provided upon clicking the donut. With your chemistry department email @chem.ethz.ch you can register/login to browse and analyze our departement's PIs' publications.
Anaconda helps to manage and run different versions of programming languages (Python, R and many more) on the same computer and to create the necessary environment to run older packages with different dependencies.
The free, open-source distribution let's you run different development enviroments (JupyterLab, JupyerNotebook, Qt Console, Spyder, Glueviz, Orange, RStudio and VS Code) with exact control of the language and package version. Ideal for scientific computing (data science, machine learning applications, large-scale data processing, predictive analytics, etc.).
antiSMASH is a tool to annotate and analyze biosynthetic gene clusters for the production of secondary metabolites from a given genome sequence.
antiSMASH is a tool that allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal and plant genomes. It does so by combining and cross-linking different tools and databases, which are commonly used for in silico analysis of genome sequences and the analysis of secondary metabolites.
The tool not only identifies gene clusters, but also identifies related, homologous gene clusters in other species and if possible for the given class of secondary metabolite gene cluster also predicts the chemical structure of the compound that is produced.
Study app for practicing complex/exceptional mechanisms, catalytic cycles and stereochemical transformations.
The app is based on the famous collection of organic chemistry problems by Prof. D. A. Evans and problems to a specific topic can be found according to a classification hierarchy. Solutions are either integrated in the app, or, for more complex examples, only with references to the primary literature.
A free app for professional concept sketches and more. Ideal for sketching and drawing.
In Autodesk Sketchbook, sketching is at the heart of the creative process. Sketchbook comes with many powerful tools for sketching. Autodesk is market leader for CAD software, particularly for architects. Tutorials and more information are scattered across various web pages and the app thus requires learning by doing.
"Beall's List", a creation of Jeffrey Beall, includes criteria for categorizing predatory journals and lists publishers that meet those criteria.
The original list was removed by its creator, however, a copy remains accessible.
Predatory publishers provide limited publishing services while pretending a much higher standard and reputation than they actually have. When publishing in a journal for the first time, ask yourself:
- Is the journal or publisher listed in Beall’s List?
- If claiming to be an open access journal, is the journal in the DOAJ?
- Is the publisher a member of recognized professional organizations?
- Is the journal truly indexed?
- Is the journal transparent and following best practices in editorial and peer review processes, governance, and ownership?
Information on why Beall's original list disappeared can be found in the web or here.
Bioconductor is a free, open source and open development software project and focuses primarily on R. The project distributes various packages for specific R applications and genome annotation packages for microarrays.
Bioconductor offers add-on modules as R packages in order to enable the R user to analyze all types of genomic data, including Affymetrix microarrays, SAGE, nucleotide sequences, and SNP data. It is updated twice per year following the released R updates and provides bugfixes and new packages. In addition to R, Bioconductor also contributes to other programming languages.
An app for managing, browsing and reading freshly published articles and journals. Available in Android, iOS or Amazon app store.
Browzine is a digital bookshelf, in which one can organise, download and read journals avaialbe via ETH library. New articles and issues are automatically flagged, so one does not lose track. Articles can be saved and read offline at a later point in time.
The CAS Source Index (CASSI) Search Tool is an online resource for retrieving accurate bibliographic information like journal abbreviations and their full titles.
This free resource can be used to quickly and easily look up or confirm publication titles and abbreviations, as well as CODEN, ISBN, or ISSN codes. The CASSI database contains a listing of publications indexed by Chemical Abstracts Service (CAS) since 1907.
Program for drawing chemical structures and reaction schemes. The web version is called ChemDraw JS.
ChemDraw is a drawing tool for chemists and biologists to create molecules and reactions for use in laboratory reports, studies and publications and for querying chemical databases, now including SciFinder and Reaxys. ChemDraw features biopolymer tools, and conversion from and to various chemical strings such as SMILES and InChI. You can draw and view structures in 2D, or render in 3D. To download please register with your top-level domain e-mail: email@example.com
A web application for interconverting chemical identifiers.
A user friendly online application for conversion of chemical identifiers, including CAS, CHEBI, compound formulas, Human Metabolome Database HMDB, InChI, InChIKey, IUPAC name, KEGG, LipidMaps, PubChem CID+SID, SMILES and chemical synonym names. Batch convert services are supported, submitting multiple chemical identifiers of the same type and yielding a table of converted identifiers. The results can be viewed directly and/or downloaded in different formats including CSV, XLS, PDF and XML. The tool can also be queried directly using the GET method.
Flashcard app for practicing the thinking skills used for multistep organic synthesis.
The app guides through synthetic sequences in a stepwise manner, depicting starting material, reagents and product for each step as a flashcard. It features an extremely valuable "Quiz" mode wherein reagents and products are hidden under grey boxes. You can do some guesswork before looking at the solution by simply tapping. At the end of each synthesis there is a direct DOI link to the primary literature.
Copy a citation or a DOI into the field, to get to the chemicle article webiste in one click. Works with up to 10 citations simultaneously.
The Chemistry Reference Resolver takes as input a text reference to a published article in a variety of formats and then finds and displays the corresponding publication by pointing the users to the webpage where the citation is hosted. It can also be used to retrieve patents and safety data sheets or look up a chemical at Aldrich via its CAS number. The search bar add-on is especially fast: Just copy in a reference and get to the article, without having to load the website. Using the Chrome extension, references can be resolved by selecting and right click.
Tool for converting various textual identifiers for molecular structures (InChI, SMILES, Mol)
ChemSpider InChI Web Services is an online converter for textual identifiers of molecules. The following conversions are possible: InChIKeyToInChI, InChIKeyToMol, InChIToInChIKey, InChIToMol, InChIToSMILES, IsValidInChIKey, MolToInChI, MolToInChIKey, SMILESToInChI
Citavi is a reference management software package, used to create/manage literature databases and quickly adding references and bibliographies when writing theses and publications. For Windows or as a VM for iOS and Linux.
In Citavi you can process your collected pdfs with highlighter and comments, and tagging with keywords can help to retrieve your information at a later point. A remarkable feature is the Knowledger Organizer, which facilitates working with ideas, corresponding text snippets and their references. Supports MS Word and various TeX editors. ETH library regularly offers hands-on training sessions.
DeepL is an online translation tool that delivers better results than google translate.
DeepL translates texts quicly and precisely, using an unspecified neuronal networks approach. Supported languages are German, English, French, Spanish, Dutch and Polish.
Doodle is an online polling tool for setting dates/times for events and plan/coordinate activities. Helps to reduce unneccesary email traffic.
You can create polls e.g. giving a list of possible dates for a meeting and distribute them via link. You can opt to get email updates for every person that has just completed the poll. The currently most popular choices are nicely highlighted in real-time and the final result can be exported as an excel file. Doodle is also useful for other things: For instance, when coordinating who contributes what to the party, you can create custom choices like snacks, salad, cake or soft drinks. Everyone looking at the poll immediately knows what is already taken care of.
Doodle offers possibilities to connect to Outlook, Google Calendar and iCal.
DuckDuckGo is a search engine that does not collect personal information and thus also avoids biased retrieval caused by the filter bubble.
DuckDuckGo is a combination of meta search engine and web crawler. A unique feature is Instant Answers, available for certain types of queries.
Look up even obscure journal titles and abbreviations that you find nowhere else and get to the publisher.
The Electronic Journals Library University of Regensburg provides a comprehensive catalogue of journals including publication history and more info. It lists even journals that have long since ceased to exist or are now published under another name.
This online training resource offers short courses in field-independent skills such as research preparation, writing, publishing, peer-reviewing and science communication.
Learn about a broad variety of topics such as writing grant applications, research data management, manuscript preparation, writing skills, technical or book writing, scientific publishing, ethics, finding the right journal, fundamentals of peer-review, social impact of science and ensuring visibility.
EndNote is a reference management software package, used to create/manage literature databases and quickly adding references and bibliographies when writing theses and publications. Available as web-based, iPhone or desktop version.
In EndNote you can process your collected pdfs with Highlighter and Notes, and tagging with keywords can help to retrieve your information at a later point. Endnote databases, attached files and annotations can be synchronized across many devices. Supports MS Word, OpenOffice and BibTeX (via export). Can connect to databases like PubMed and Web of Science.
Many valuable features are restricted in the free online-only version EndNote basic. EndNote can be licensed via the ETH IT-Shop. ETH library regularly offers hands-on training sessions.
A comprehensive gene set enrichment analysis web server.
Software for analyzing gene sets generated by genome-wide experiments. Enrichr program contains a large collection of diverse gene set libraries available for analysis and download.
It is a comprehensive resource for curated gene sets and a search engine that collects biological knowledge including GO terms, pathways, transcriptional profiles.
If you enter gene sets from your analysis, the Enrichr program interprets it and shows the results about GO terms (biological Process, Cellular Component, Molecular Function), KEGG pathways, Genes associated with NIH grants, Transcription factors and so on. It is free, includes many accumulated genomics, transcriptomics and proteomics data and hase nice visualization of enrichment results.
Online tool for reference management, data analysis and information synthesis. Ideal for all processes involving large numbers of articles as encountered in the literature review process, writing systematic reviews and meta-analyses. Subscription on a monthly basis.
In addition to common tools that are necessary for electronic search, bibliographic management, categorizing, collaborating, screening, coding, data analysis and visual presentation of the outcomes, some advanced features including text mining, term extraction and data clustering are also provided by the software.
A news aggregator that collects updates from your favourite newspaper, websites, blogs, Twitter and RSS feeds without you needing to visit the page. For browser, Android and iOS.
Items and sources can be searched, organized, read or marked as "read later". Connections to other tools like Evernote, OneNote, Trello or Slack are available.
Using " Find e-journal ", you easily get access all e-journals that are available at ETH Zurich.
You can locate a specific journal via "A-Z title search" or a "Category" search. If you have the reference details (such as volume and page number or DOI) you can use "Fetch Item" to link directly to the full text. You will also find information in which years are licensed. Note that only electronic journals are included. When searching for print journals, please consult CLICAPS.
Retrieve the DOI (Digital Object Identifier) for a given article e.g. by means of title and author name.
CrossRef is an international association of scholarly publishers that develops shared infrastructure to support more effective scholarly communications. The network covers over 60 million journal articles and other content items (books chapters, data, theses, technical reports) from thousands of scholarly and professional publishers around the globe. CrossRef currently provides a number of ways to locate a DOI: If you have bibliographic data for an item and would like to find the DOI, please use "Bibliographic metadata search". If you only have an article title and author, please use the "article title" search section of this form. If you have the text of a bibliographic reference, please use "Simple Text Query".
The world's largest library of book summaries. Expand your knowledge with 5-page summaries that you can read in 10 minutes or less. Main focus is business, but there is a broad selection of other books, too.
Compressed Knowledge: The best of knowledge in concise summaries that include all basic facts and statements of the latest, sharpest and most relevant books. The summaries are mainly available in English and German, nut also Spanish, Russian, Chinese, French and Portuguese.
Google Books allows a full text search of more than 30 millions of books as well as journals/magazines.
The books are either out of copyright or have been scanned in collaboration with major libraries. With a glance, you can see where and how often your search terms appear in the book. If the book is out of copyright, or the publisher has given permission, you'll be able to see a preview of the book, and in some cases the entire text. If it's in the public domain, you are free to download a PDF copy. If you find a book you like, click on the "Buy this book" and "Borrow this book" links to see where you can buy or borrow the print book, like e.g. in the Info Center.
Google Images is the most comprehensive search engine for image content on the web.
In addition to the keyword search, Google Image has a reversed image search. By clicking on the camera icon, an image or the URL to an image can be uploaded and a search for websites that contain this image can be performed. If this particular image cannot be found, links to similar images are displayed.
A web service for visualizing the occurence over time of a phrase consisting of n words (n-gram).
You can also specify wildcards in queries, search for inflections, perform case insensitive search, look for particular parts of speech, or add, subtract, and divide ngrams.
A free search engine for the scholarly literature and case law.
To keep up with current developments, you can create alerts for search terms. Legal proceedings can be found under case law.
The free online translation service from Google translates text and web pages in seconds and from 103 languages.
When Google Translate generates a translation, it looks for patterns in hundreds of millions of documents to help decide on the best translation for you. By detecting patterns in documents that have already been translated by human translators, Google Translate can make intelligent guesses as to what an appropriate translation should be. This process of seeking patterns in large amounts of text is called "statistical machine translation". Since the translations are generated by machines, not all translations will be perfect. The more human-translated documents that Google Translate can analyse in a specific language, the better the translation quality will be. This is why translation accuracy will sometimes vary across languages.
Analyze the popularity of google search queries as a function of time.
You can enter your own search terms, look at current hot trends (the top 20), check summaries from past years trends or the past week and look at geographical data associated with the searches.
ImageJ is a freely available, Java-based image processing program for scientific image analysis.
ImageJ was developed with an open architecture that can be extended using Java plug-ins and is equipped with a macro recorder. The many plugins make it possible to solve image processing and analysis problems, from three-dimensional live-cell imaging and radiological image processing to data comparison between several imaging systems and automated hematology systems. The plugin architecture and the integrated development environment make ImageJ a popular platform for image processing.
The IUPAC Gold Book is compiled by the International Union of Pure and Applied Chemistry and is the primary source of definitions and standards in chemistry.
The compendium compiles the definitions of terms described in the various IUPAC glossaries and other IUPAC nomenclature documents. It is text and structure searchable and has links between related terms and concepts. In recognition of the contribution of Victor Gold, initiator of the first edition, the compendium is also referred to as the „Gold Book“.
Find the perfect Journal (Elsevier only) for your manuscript.
Paste in title and abstract and the almighty algorithm will find the perfect spot for your opus magnum. The list of suggested journals includes typical timeline for refereeing, rejection rate, some impact metrics, open access fees and the expected embargo period.
JupyterLab is a browser-based interactive programming interface for several coding languages that can help developing and running reproducible computation for scientific applications.
The name JuPyteR stems from the three principal languages Julia, Python and R, but meanwhile, many other languages are available as well. Functionalities of Jupyter include notebooks, terminal, text editor, file browser, rich outputs, Markdown and export to numerous formats (HTML, TeX, PDF, etc.)
A free and open-source data analytics, reporting and integration platform.
KNIME can collect different types of data via import or webscraping. These can be processed in various ways and finally visualized or exported. A reusable workflow can be quickly created by drag-and-drop and linking so-called nodes (processing unit). To implement more complex applications, it is possible to integrate Python, R or Wekascripts. For chemical applications there is integration with JChem/Marvin and Schrödinger.
Kudos is a Web Service that helps authors to enrich and share their publications with the goal of increasing usage and impact.
Authors can describe their research in plain language, add supplementary information, and then communicate it via social media channels or email. The effect of these actions can be measured via a wide range of metrics.
The Kudos dashboard provides statistics about downloads, citation count, Altmetric score, and many more metrics. It is also an overview of the articles including the additional context and resources that were added by the user.
There is a special registration URL for D-CHAB members. Please contact Dr. Joachim Schnabel.
Online dictionaries for 8 languages.
Online dictionaries German-English, -French, -Spanish-, -Italian, -Chinese,- Russian, -Portuguese and -Polish including a forum to discuss translations.
Dictionary and search in 100 million translations.
Linguee is a unique combination of an editorial dictionary and a search engine. The search results are divided into two parts in Linguee. Left you see clear results from the editorial reliable dictionary. This gives you a quick overview of the translation options. On the right are set examples from other sources that give you an impression of how your keyword is translated in context.
With more than 400 millions registered users, LinkedIn is the largest business-oriented social networking service to maintain your contacts, find new business contacts or search for a job.
When you join LinkedIn, you can showcase your work and yourself to get spotted by employers or headhunters, stay in touch with (former) colleagues and business partners, find professionals with certain qualifications, get access to people, jobs, news, updates, and insights based on your network.
Note: Carefully adjust settings to avoid sending or getting unneccessary notifications (spam mail).
Web tool for the processing/visualization of 3D molecule structures.
Fast web application for 3D visualization of molecules and other related data. It provides standard visualizations of molecules (cartoons, surfaces, ball and stick, etc.), assemblies, symmetry partner, electron density and cryoEM maps. By an integrated PDBe API you can view and explore validation and annotation data. You can directly load molecules into the viewer by just entering the pdb code. Parts of the molecules can be selected by a powerful python-based selection syntax.
Program for drawing chemical structures and reaction schemes. The web version is called Marvin JS.
With MarvinSketch you can create structural drawings for a broad range of chemical compounds and save (SMILES, mol, cdx, InChI) or export (jpg, png, eps) them in different formats. After registering on their website, you can get a free 2 year academic licence.
Mendely is a freely available reference management software package, used to create/manage literature databases and quickly adding references and bibliographies when writing theses and publications. Available as web-based, desktop and mobile version.
In Mendely you can process your collected pdfs with highlighter, sticky notes and comments, and tagging with keywords can help to retrieve your information at a later point. Mendely databases, attached files and annotations can be synchronized across many devices and with other people. Supports MS Word, OpenOffice, LibreOffice and BibTeX (via export).
Mendeley also tries to suggest potentially interesting literature via algorithm, offers a social network and platforms for job and grant search.
The Mendeley Institutional Edition which has been licensed by the ETH Bibliothek is a premium version of Mendeley in which the core Mendeley capabilities are enhanced (sharing libraries) and more cloud space is available (100 GB). ETH library regularly offers hands-on training sessions.
Crystal structure visualization, exploration and analysis tool.
It enables you to
- generate packing diagrams.
- define and visualise Miller planes.
- build and explore networks of intermolecular contacts.
- display space-group symmetry elements.
- calculate and display voids.
- generate publication-quality images.
MesReNova is a user-friendly software for the processing, analysis, simulation and presentation of NMR and LC/GC/MS data.
With Mnova you can
- Handle NMR data from different manufacturers (Agilent, Bruker, JEOL, PicoSpin, Magritek, Nanalysis, Oxford Instruments, and more).
- Perform high quality analysis of spectra (deconvolution, peak picking, integration, multiplet analysis, etc.).
- Process your data automatically (1H, 13C, DEPTs or any other 1D NMR as well as any 2D NMR correlations, such as HSQC, HMBC, NOESY, COSY, TOCSY, etc.).
- Build high quality, publication-ready spectra whilst working up the data.
With your ETH ChemDraw licence, you can get a free licence to MestreNova Lite. For a full licence of MestreNova contact your institutes NMR facility.
openBIS is an Open Source Biology Information System, developed by the Scientific IT Services (SIS) group at ETH.
openBIS kann auch als elektronisches Laborjournal in verschiedenen biologischen Kontexten verwendet werden, solange die Handhabung chemischer Strukturen nicht erforderlich ist. Das openBIS Software-Framework kann leicht an die folgenden Technologien angepasst werden: High Content Screening, Proteomik, Metabolomik und Tiefensequenzierung.
Orange is an GUI-based open-source software for data and text mining.
The widget-based interface enables the rapid creation of reusable workflows and Python scripts can be integrated to implement more complex applications. Standard algorithms for data reading, manipulation and cleansing, modeling, (un-/supervised) machine learning, validation and visualization are available. Interactive visualization of multivariate data sets enables explorative data analysis. There are also possibilities for text analysis and bioinformatics applications.
ORCID provides researches with an unique numeric identifier (think dog tag), to set them apart from people bearing the same name, or to ensure that older publications are found, when a researcher is active at a new institution.
The ORCID Identifier can be used when submitting new manuscripts, so that your ORCID, publication list will be automatically updated. You can import earlier publications via Crossref or Scopus and it is possible to create a detailed profile in ORCID.
Advanced scientific graphing and data analysis software.
With over 100 built-in 2D and 3D graph types their point-and-click customization Origin makes it easy to create publication-quality figures. Origin allows the user to automatically update data and parameters, create templates for repetitive tasks, perform batch operations, connect with other programs (MATLAB, LabVIEW, Microsoft Excel) or create custom routines using scripting and C languages, embedded Python, or the R console. Origin also provides various tools for linear, polynomial and nonlinear curve and surface fitting. Additionally it is very helpful in peak analysis, signal processing and spectra fitting. Origin is available from the ETH IT-Shop.
Overleaf is a web service for collaborative work on LaTeX documents. Free of charge via NETZ-Login.
In Overleaf several authors can work on the same document at the same time and all of them see the latest version. Comments can be added and changes can be tracked. Other valuable functions are the real-time preview and LaTeX error tracking. Integration of Dropbox, Github & Mendeley is possible.
One of our favorites, both for sketching, drawing and painting, ideally with an Apple Pencil.
The app Procreate has received the Apple Design award and is an App Store Essential. It ranks among the most powerful drawing and painting apps but is, nevertheless, intuitive to use and optimized for the iPad Pro and the Apple Pencil. The – not free – app is also ideal for artistic illustrations and cover design. The app comes with all kinds of pens, pencils, brushes, canvas, export and import functionalities and many options for customization.
The free handbook with 453 (Artist) respectively 261 pages (Pocket) is not really necessary to use the app – but an excellent service.
PROSS (Protein Repair One-Stop Shop) is a database-based algorithm for the prediction of stabilizing mutations for unstable proteins and is free to academic users.
Starting point of the process is a pdb-file of the protein. Thereof, a multiple sequence alignment is conducted whereby different parameters can be set, e.g. residues crucial for ligand binding or protein-protein interaction considered not being changeable or reducing the multiple sequence alignment to specific taxa. Resulting design suggestions containing different predicted substitutions are subsequently scored in regard of Rosetta scoring functions. For each design fasta and pdb output files are generated. In addition the used multiple sequence alignment and the resulting scoring file are provided for download.
Besides bibliographic information, Publons provides verified information about scientific peer review.
Publons stellt den Verlagen Tools zur Verfügung, um Peer-Reviewer zu finden, sammelt Details über das globale Peer-Review-Verhalten und stellt Schulungsressourcen für Nachwuchsforscher zur Verfügung.
PubPeer enables scientist to search for their publications or their peers publications and provide feedback and/or start a conversation anonymously.
Articles can be searched by DOI, PMID, arXiv ID, keyword or author. PubPeer has also contributed in revealing scientific misconduct.
Software for 3D visualization and analysis of biomolecules.
PyMOL is an open-source, molecular visualization system working with all data formats in structural biology (PDB etc). PyMOL can produce high-quality 3D images of small molecules and biological macromolecules, such as proteins. Students can obtain a licence freen of charge.
Qinsight is a biomedical semantic search engine for PubMed and related content that uses artificial intelligence.
Qinsight does not search directly using the keywords and terms entered, but uses Quantum Logic Linguistic™ Technology to find the information relevant to the query. Qinsight uses an extensive ontology (with verbs) and engines for Entity Identification, Concept Identification, Linguistics, Key Concept Identification, and Relevance. In addition to Pubmed, Qinsight you searches in NIH Grant Applications and US Patents.
R is an open-source script-based programming language for which extensive additional packages for various special applications and fields are available.
R offers a variety of options for importing, wrangling, processing and visualizing different types of data. ALL possible types of statistics can be easily executed. RStudio is the recommended standard graphical user interface. Since R is only one letter, using the CRAN acronym helps googling problems with the software.
Learn Named Reactions, understand mechanisms, look at examples from Reaxys and test your knowledge with ReactionFlash for Android and portable Apple devices.
In organic chemistry, reactions – usually named after their discoverers – are a fundamental part of every chemist's toolkit. ReactionFlash helps you learn and understand named reactions: from the famous ones, to those you have forgotten, to those only a Nobel Prize Winner knows! Not only does the app give you the reaction, it also shows you mechanism, published examples from Reaxys, and even allows you to test your skills with the ReactionFlash Quiz. Why spend laborious hours making your own reaction flash cards when ReactionFlash gives you all you need and makes learning fun?
ReaCube Papers is a reference management software package, used to create/manage literature databases and quickly adding references and bibliographies when writing theses and publications. Available in an annual subscription model (USD 36) as web-based, mobile, Kindle or desktop version.
In Papers you can process your collected pdfs with Highlighter and Notes, and tagging with keywords can help to retrieve your information at a later point. Pdfs cannot only be processed in the app, but also in the web application. Papers databases, attached files and annotations can be synchronized across many devices and with other people (up to 25), with unlimited storage space in the cloud. Supports MS Word, OpenOffice, Overleaf and Manuscript with BibTeX. Can connect to databases like PubMed/Google Scholar/Dimensions/Crossref/arXiv.
An app for managing, browsing and reading freshly published articles and journals. Available in Android or iOS app store.
Researcher is a digital periodical shelf where you can organize, access and read journals. New articles or issues are automatically marked so that you don't lose track. Articles can be saved and read offline at a later date. There are interfaces to Mendeley, Zotero, ORCID and integration of Unpaywall.
ResearchGate is the largest academic social networking site and researchers to share papers, ask and answer questions, and find collaborators.
Users can upload research information (papers, data, chapters, negative results, patents, research proposals, methods, presentations, and software code). Users may also follow the activities of other users and engage in discussions with them. RG shows also the h-index of a scientist, in addition to the proprietary RG score, which depends on the activity in the network.
Note: Carefully adjust settings to avoid sending or getting unnecessary notifications (spam mail).
Get to the article with a known DOI.
The International DOI Foundation (IDF) manages the DOI (Digital Object Identifier) system and also provides retrieval tools. Type or paste a DOI number into the text box and click Go. Your browser will take you to the Web page (URL) associated with that DOI.
Blog listing background information to retracted articles from 2010 onwards.
If you find anything suspicious in a paper you can contact the authors and they might investigate. There is also a list of papers they are already looking into.
Startpage (formerly Ixquick) is a powerful search engine employing the most advanced metasearch technology without collecting or sharing any personal information. Start using this search enginge to avoid biased retrieval caused by the filter bubble.
Startpage is a powerful meta-search engine which simultaneously searches multiple popular search engines like Google, Yahoo, Gigablast, Yandex and internet databases to gather and display the most comprehensive and accurate web results. No IP addresses are stored, no personal data is gathered or passed on to third parties, and no identifying cookies are placed on your browser. Startpage also offers secure SSL encryption, a proxy option that allows anonymous web surfing, full third-party certification, and numerous other privacy features.
STRING provides functional protein association networks from information about physical and functional interactions between proteins.
Data from various sources are aggregated using an easy to use web-based interface. After entering a protein name/sequence, a network of different types of interactions (color-coded) is displayed: experimentally verified, based on the genetic context (neighborhood, fusions, co-occurrence), derived from textmining, due to co-expression or based on protein homology.
The network can be recentered on other proteisn, and further information can be displayed for each individual protein (gene names, protein domains, 3D structures, etc.). Links to further databases are provided (e.g. NCBI, KEGG, UniProt, PDB). There are different viewing functionalities across species like neighborhood (adjacent genes of similar proteins) or fusion (identify fusion proteins). The data can be exported in various formats and an API for developers is available. It is even possible to download the raw data that is used by STRING to generate the network; they are provided under a Creative Commons license.
Free short link service.
There is no data collection and additionally the links are checked for malware.
Among our favorite apps, especially for drawing, illustrating and tracing.
The app Sketches is a sketching app that was developed particularly for mobile devices, featuring a comprehensive set of tools. Sketches is ideal for converting relevant information from photos into a drawing. The free version allows to use more than 4 layers. Sketches is also ideal for artistic techniques, like water color and acrylic painting. Online tutorials can be found on Vimeo.
Synonym and Antonym Finder.
Incorporating some of history’s finest English associations, the free online thesaurus combines the authoritative labor of lexicographers with innovative technology for one of the most comprehensive and efficient language tools available online today. Professionals, students, and many others return to the Thesaurus.com to find the perfect synonym, antonym, or simply as a source of word inspiration.
Short link service for ETH URLs.
To view user numbers, just add a plus sign to the short link.
Online unit converter.
A free online conversion tool to easily convert between different units of measurement in more than 70 categories. The Unit Conversion Tool software is also available for download (USD 30.-).
Software for 3D visualization, animation and analysis of (large biological) molecules.
VMD is designed for modeling, visualization, and analysis of biological systems but it may also be used to view molecules in general, as it can read various coordinate files to display the contained structure. VMD provides a wide variety of methods for rendering and coloring molecules. Molecular scenes can be saved in various formats or exported to external rendering tools such as POV-Ray, Tachyon and others.
VOSviewer is a free software tool for constructing and visualizing bibliometric networks.
These networks may for instance include journals, researchers, or individual publications, and they can be constructed based on citation, bibliographic coupling, co-citation, or co-authorship relations. VOSviewer also offers text mining functionality that can be used to construct and visualize co-occurrence networks of important terms extracted from a body of scientific literature.
WolframAlpha introduces a fundamentally new way to get knowledge and answers – not by searching the web, but by doing dynamic computations based on a vast collection of built-in data, algorithms, and methods.
WolframAlpha is based on the software Mathematica. The search engine works particularly well for content from exact sciences and is available also as an app.
User-friendly tool for creation of word clouds from documents such as articles or abstracts.
The cloud gives greater prominence to words that appear more frequently in the source text. You can tweak your clouds with different fonts, layouts, and color schemes. The images you create with Wordle can be printed or saved.
With Wordpress a blog can be created in no time and with little effort. Blogs can be public or restrict access to people with a login.
The blogs can be used for various purposes: As a themed blog for an interested audience, as a forum for the discussion of current literature, as a platform for the exchange of like-minded people, as an archive of read articles, travel or photo diaries, etc... Each ETH member can run up to 5 blogs free of charge.
All about words: word of the day, vocabulary portal for over 229 languages.
The international vocabulary portal (in English) allows you to look up words in 229 different languages. The dictionary (over 100,000 words and phrases in German and English) will tell you how often a particular word has been used.
Browser-based application for drawing chemical structures and reaction schemes.
Xemistry Web Sketcher does not rely on Java, plug-Ins or any other browser- or platform-dependent components; program intelligence is concentrated on the server and conveniently maintained there. The client side works on any browser without the need to configure, install or download any code. Conversion to and from SMILES strings is possible as well as image export to various formats including vectorgraphics.
Free your mind from having to remember all of the day-to-day (routine) tasks by letting this tool do it for you and focus your brain power on important things like scientific research.
If you find it exhausting to keep track of all your activities in your studies, research, hobbies and household, this tool could be a relief. Zendone is one of many GTD ("Get Things Done") apps that allow you to set alarms for routine tasks (e.g. checking the latest publications in your area, cleaning your home), store flashes of inspiration whenever they hit you, and track the progress of your various projects. What's special about this tool is the seamless integration of Evernote and Google Calendar deadlines. The combination helps to preserve the sense of control over the things that need to be done, the challenges that need to be solved before they get out of hand, and life in general.
Zotero is a reference management software package, used to create/manage literature databases and quickly adding references and bibliographies when writing theses and publications. Available as web-based, iPhone or desktop version.
In Zotero you can process your collected pdfs with Highlighter and Notes, and tagging with keywords can help to retrieve your information at a later point. Pdfs cannot only be processed in the app, but also in the web application. Papers databases, attached files and annotations can be synchronized across many devices and with other people. Supports MS Word, OpenOffice, LibreOffice and BibTeX (via export). Can connect to databases like PubMed/Google Scholar/Dimensions/Crossref/arXiv.