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--- enllacos_rmn [2014/03/21 09:28]
miquel [Metabolòmica]
+++ enllacos_rmn [2021/09/16 12:49] (current)
miquel [Solvents residuals]
@@ Line 17: / Line 17: @@
   * [[http://nmrwiki.org/ | NMR Wiki,]] is an open non-profit online NMR project (started on Nov 8th 2007). The goal of this site is to provide a collaborative informational resource to Spectroscopists, Chemists, Biologists and others using magnetic resonance techniques.
+  * [[http://www.validnmr.com/w/index.php?title=Main_Page | validNMR Wiki.]] A place to share your knowledge to benefit our NMR community. Includes:
+    * Best Practices
+    * Chemometrics (Portal Chair: Yulia Monakhova)
+    * Nomenclature (Portal Chair: John Warren)
+    * Quantitative NMR (Portal Chair: Elina Zailer)
+      * 1H High-Precision Quantification
+    * Reference Material and Data (Portal Co-chairs: Michael Maiwald and Kevin Millis)
   * [[http://sermn.uab.cat/wiki | SeRMN wiki,]] el **nostre** wiki 8-)  per tot allò que afecta al funcionament del SeRMN.
@@ Line 43: / Line 50: @@
 ==== Solvents residuals ====
-  * [[http://tigger.uic.edu/~gfp/qnmr/content/solvents/solvent.html | The Solvent Chemical Shift Finder.]] The solvent chemical shift finder is an experimental database of over 100 different solvents and reagents which might appear in an NMR spectrum. For further details consult the references,
+=== Websites ===
-    * I. C. Jones, G. J. Sharman, J. Pidgeon. Spectral Assignments and Reference Data. 1-H and 13-C NMR data to aid the identification and quantification of residual solvents by NMR spectroscopy  [[http://dx.doi.org/10.1002/mrc.1578 | Magn. Reson. Chem., 2005, 43, 497-509.]]
-    * H. E. Gottlieb, V. Kotlyar, A. Nudelman. NMR Chemical Shifts of Common Laboratory Solvents as Trace Impurities [[http://dx.doi.org/10.1021/jo971176v | J. Org. Chem., 1997, 62, 7512-7515.]]
+  * [[https://gfp.people.uic.edu/qnmr/content/solvents/solvent.html | The Solvent Chemical Shift Finder.]] The solvent chemical shift finder is an experimental database of over 100 different solvents and reagents which might appear in an NMR spectrum.
+=== References ===
+  * I. C. Jones, G. J. Sharman, J. Pidgeon. Spectral Assignments and Reference Data. 1-H and 13-C NMR data to aid the identification and quantification of residual solvents by NMR spectroscopy  [[http://dx.doi.org/10.1002/mrc.1578 | Magn. Reson. Chem., 2005, 43, 497-509.]]
+  * H. E. Gottlieb, V. Kotlyar, A. Nudelman. NMR Chemical Shifts of Common Laboratory Solvents as Trace Impurities [[http://dx.doi.org/10.1021/jo971176v | J. Org. Chem., 1997, 62, 7512-7515.]]
+  * G. R. Fulmer, A. J. M. Miller, N H. Sherden, H. E. Gottlieb, A. Nudelman, B. M. Stoltz, J. E. Bercaw, K. I. Goldberg. NMR Chemical Shifts of Trace Impurities: Common Laboratory Solvents, Organics, and Gases in Deuterated Solvents Relevant to the Organometallic Chemist. [[https://doi.org/10.1021/om100106e | Organometallics 2010, 29, 9, 2176–2179.]]
 ==== Compostos orgànics ====
@@ Line 55: / Line 69: @@
   * [[http://csearch-nmr-data.blogspot.com/ | CSEARCH NMR Database ]]
   * [[http://nmrpredict.orc.univie.ac.at/csearchlite/NMR_misinterpretation.html | NMR misinterpretation.]] Basic Misinterpretations, Typos and other Sad Events in NMR-Spectroscopy. **What is presented on this page?** This page holds examples of strange interpretation of NMR-data, either caused by missing basic knowledge about this method or caused by typos or caused by any other reason. **What is intended with this page?** The sole intention of this page is to promote massive application of computer programs to verify structural and spectral data. In NMR-Spectroscopy we are in the lucky situation, that we have already algorithms available which allow us to check our analytical data in a(n) (semi-)automatic way. Routine application of these programs would increase the quality of the chemical literature in an easy and efficient manner.
+  * [[https://atb.uq.edu.au/index.py | Automated Topology Builder (ATB) and Repository]] Version 2.2. The ATB and Repository is intended to facilitate the development of molecular force fields for Molecular Dynamics or Monte Carlo simulations of biomolecular systems. Applications include: the study of biomolecule:ligand complexes, free energy calculations, structure-based drug design, the refinement of x-ray crystal complexes. This site provides:
+    * A repository for building blocks and interaction parameter files for molecules described using GROMOS force fields.
+    * An automated builder to help generate building blocks for novel molecules, compatible with the GROMOS 54A7 force field and in formats appropriate for the GROMACS, GROMOS and LAMMPS simulation packages and CNS, Phenix, CCP4 and Refmac5 X-ray refinement packages.
+    * A system topology file converter to generate AMBER topologies from GROMOS topologies.
+    * Refined geometries for molecules within the repository.
+    * Equilibrated starting coordinates for a range of biologically important systems.
 ==== Predicció de desplaçaments químics ====
-  * [[http://nmrshiftdb.nmr.uni-koeln.de/ | nmrshiftdb2 ]] is a NMR database (web database) for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. Last not least, it features peer-reviewed submission of datasets by its users. The nmrshiftdb2 software is open source, the data is published under an open content license. Please consult the documentation for more detailed information. nmrshiftdb2 is the continuation of the NMRShiftDB project with additional data and bugfixes and changes in the software.
+=== nmrshiftdb ===
-  * [[http://www.nmrdb.org/about | NMRdb]] is a web-based approach implementing a new java applet that enables to assign a chemical structure to the corresponding NMR spectrum by simply drawing lines between atoms and automatically characterized signals. Includes: [[http://www.nmrdb.org/simulator | NMR Simulator,]] [[http://www.nmrdb.org/resurector | NMR Resurrector,]] [[http://www.nmrdb.org/nemo | NMR Assigner]] and [[http://www.nmrdb.org/predictor | NMR Predictor.]]
-  * [[http://nmrpredict.orc.univie.ac.at/ | NMRPREDICT-Server]]. És un cul de sac sobre bases de dades i programes de predicció d'espectres de 13C. Per exemple,
+[[http://nmrshiftdb.nmr.uni-koeln.de/ | nmrshiftdb2 ]] is a NMR database (web database) for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. Last not least, it features peer-reviewed submission of datasets by its users. The nmrshiftdb2 software is open source, the data is published under an open content license. Please consult the documentation for more detailed information. nmrshiftdb2 is the continuation of the NMRShiftDB project with additional data and bugfixes and changes in the software.
-    * [[http://nmrpredict.orc.univie.ac.at/case/propose.php | Spectral Similarity Search,]] entra els desplaçaments químics dels teus pics a l'espectre de 13C i et trobarà estructures amb espectres semblants.
-    * Aquest enllaç està estretament relacionat amb el programa [[http://www.modgraph.co.uk/product_nmr_pricing.htm | comercial]] del mateix nom [[http://www.modgraph.co.uk/product_nmr_version3.htm | NMRPredict]]
+=== NMRdb ===
-  * [[http://www.acdlabs.com/resources/ilab/ | ACD/Labs i-Lab.]] Reduce the need for labor intensive experimental testing and literature searches, by using the [[https://ilab.acdlabs.com/ | online ACD/I-Lab prediction engine]] to predict physicochemical properties, NMR spectra and chemical shifts, and ADME toxicities. The browser-based I-Lab software also assesses prediction reliability and includes searchable content databases. I-Lab predictions are made using the same advanced algorithms that power our full desktop software suites, giving you the same highly accurate predictions without the need for individual software installations. A site license allows unlimited predictions for all of your organization’s users, while the I-Lab for Intranets API can be implemented on servers behind your own firewalls. **How It Works:** Predictions are generated from structures, input in a variety of forms. Draw a structure in the I-Lab interface, paste a structure from ACD/ChemSketch, upload a SMILES string, or look up a compound in the built-in dictionary. Select a module to predict the property or spectra of interest, or generate a systematic name or structure for the molecule. Generate a report by saving the results to a PDF. **Available prediction modules:** Physicochemical Properties, ADME Properties, Toxicity Properties, NMR Spectra and Chemical Shifts Nomenclature. **I-Lab is also available for individual users as a [[http://www.acdlabs.com/resources/ilab/pricing.php | credit-based system]].**
+[[http://www.nmrdb.org/about | NMRdb]] is a web-based approach implementing a new java applet that enables to assign a chemical structure to the corresponding NMR spectrum by simply drawing lines between atoms and automatically characterized signals. Includes: [[http://www.nmrdb.org/simulator | NMR Simulator,]] [[http://www.nmrdb.org/resurector | NMR Resurrector,]] [[http://www.nmrdb.org/nemo | NMR Assigner]] and [[http://www.nmrdb.org/predictor | NMR Predictor.]]
+:info: There is a [[http://www.nmrdb.org/new_predictor | new HTML5 version of NMR Predictor]] that does not use the Java applet.
+=== NMRPREDICT-Server ===
+[[http://nmrpredict.orc.univie.ac.at/ | NMRPREDICT-Server]]. És un cul de sac sobre bases de dades i programes de predicció d'espectres de 13C. Per exemple,
+  * [[http://nmrpredict.orc.univie.ac.at/case/propose.php | Spectral Similarity Search,]] entra els desplaçaments químics dels teus pics a l'espectre de 13C i et trobarà estructures amb espectres semblants.
+  * Aquest enllaç està estretament relacionat amb el programa [[http://www.modgraph.co.uk/product_nmr_pricing.htm | comercial]] del mateix nom [[http://www.modgraph.co.uk/product_nmr_version3.htm | NMRPredict]]
+=== ACD/Labs i-Lab ===
+[[http://www.acdlabs.com/resources/ilab/ | ACD/Labs i-Lab.]] Reduce the need for labor intensive experimental testing and literature searches, by using the [[https://ilab.acdlabs.com/ | online ACD/I-Lab prediction engine]] to predict physicochemical properties, NMR spectra and chemical shifts, and ADME toxicities. The browser-based I-Lab software also assesses prediction reliability and includes searchable content databases. I-Lab predictions are made using the same advanced algorithms that power our full desktop software suites, giving you the same highly accurate predictions without the need for individual software installations. A site license allows unlimited predictions for all of your organization’s users, while the I-Lab for Intranets API can be implemented on servers behind your own firewalls. **How It Works:** Predictions are generated from structures, input in a variety of forms. Draw a structure in the I-Lab interface, paste a structure from ACD/ChemSketch, upload a SMILES string, or look up a compound in the built-in dictionary. Select a module to predict the property or spectra of interest, or generate a systematic name or structure for the molecule. Generate a report by saving the results to a PDF. **Available prediction modules:** Physicochemical Properties, ADME Properties, Toxicity Properties, NMR Spectra and Chemical Shifts Nomenclature. **I-Lab is also available for individual users as a [[http://www.acdlabs.com/resources/ilab/pricing.php | credit-based system]].**
 ==== Predicció de propietats químiques ====
   * [[http://www.organic-chemistry.org/prog/peo/ | OSIRIS Property Explorer.]] The OSIRIS Property Explorer is an integral part of Actelion's inhouse substance registration system. It lets you draw chemical structures and calculates on-the-fly various drug-relevant properties whenever a structure is valid. Prediction results are valued and colour coded. Properties with high risks of undesired effects like mutagenicity or a poor intestinal absorption are shown in red. Whereas a green color indicates drug-conform behaviour.
+  * [[https://openmolecules.org/datawarrior/ | DataWarrior, ]] an Open-Source Program for Data Visualization and Analysis with Chemical Intelligence. By [[https://openmolecules.org/ | openmolecules.org]] DataWarrior combines dynamic graphical views and interactive row filtering with chemical intelligence:
+    * Scatter plots, box plots, bar charts and pie charts not only visualize numerical or category data, but also show trends of multiple scaffolds or compound substitution patterns.
+    * Chemical descriptors encode various aspects of chemical structures, e.g. the chemical graph, chemical functionality from a synthetic chemist’s point of view or 3-dimensional pharmacophore features. These allow for fundamentally different types of molecular similarity measures, which can be applied for many purposes including row filtering and the customization of graphical views.
+    * DataWarrior supports the enumeration of combinatorial libraries as the creation of evolutionary libraries. Compounds can be clustered and diverse subsets can be picked.
+    * Calculated compound similarities can be used for multidimensional scaling methods, e.g. Kohonen nets.
+    * Physicochemical properties can be calculated, structure activity relationship tables can be created and activity cliffs be visualized.
 ==== Metabolòmica ====
@@ Line 135: / Line 174: @@
 ===== Programari d'interés =====
+  * [[https://www.nmrbox.org/ | NMRbox is a resource for biomolecular NMR (Nuclear Magnetic Resonance) software.]] It provides tools for finding the software you need, documentation and tutorials for getting the most out of the software, and cloud-based virtual machines for executing the software.
   * [[http://rnmr.nmrfam.wisc.edu/ | rNMR]] is an open source software package for visualizing and interpreting one and two dimensional NMR data. In contrast to most existing 2D NMR software, rNMR is specifically designed for high-throughput assignment and quantification of small molecules. As a result, rNMR supports extensive batch manipulation of plotting parameters and has numerous tools for expediting repetitive resonance assignment and quantification tasks.
   * [[http://www2.ccc.uni-erlangen.de/services/spinus/ | SPINUS (Structure-based Predictions In NUclear magnetic resonance Spectroscopy)]] is an on-going project for the development of structure-based tools for fast prediction of NMR spectra. SPINUS - WEB currently accepts molecular structures via a Java molecular editor, and estimates 1H NMR chemical shifts and coupling constants. The predictions are obtained from ensembles of previously trained feed-forward neural networks, and corrected with data from an additional memory.
@@ Line 145: / Line 185: @@
   * [[http://www.martindalecenter.com/Calculators3B_1_MO.html#CHEM-NMR | Martindales Center]] conté un munt d'enllaços d'interès per RMN i MRI, però no he tingut temps de comprovar la seva vàlua i utilitat.
   * [[http://www.organic-chemistry.org/ | Organic Chemistry Portal.]] The Organic Chemistry Portal offers an overview of recent topics, interesting reactions, and information on important chemicals for organic chemists.
+  * [[https://www.emolecules.com/ | eMolecules]] empowers researchers to explore uncharted chemical and biological space and deliver more efficient drug discovery programs. Our promise to drug discovery researchers is that we will aim to facilitate:
+    * **exploration** of unchartered chemical and biological space with our database of over 8 million compounds available from our global network of trusted suppliers.
+    * **evaluation** of the best source of molecules for their projects based upon suppliers' availability, delivery time and pricing data which we normalize, update and curate monthly.
+    * **expedition** of their drug discovery programs by reducing the barriers, time and costs associated to acquiring molecules.
+  * El portal de la [[https://organicchemistrydata.org/links/ | Division of Organic Chemistry,]] American Chemical Society inclou uns apartats sobre RMN que procedeixen en gran part de la "Prof. Hans Reich's collection of various topics on NMR. Most of this content originated from his Chem 605 Course at the University of Wisconsin - Madison.".
+    * [[https://organicchemistrydata.org/links/#general-nmr | General NMR]]
+    * [[https://organicchemistrydata.org/links/#nmr-data | NMR Data]]
+    * [[https://organicchemistrydata.org/links/#multinuclear-nmr-data | Multinuclear NMR Data]]

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