[Bronwen Dekker]

Nature Protocols is an on-line Journal that launched in June 2006.

http://www.nature.com/nprot/index.html

Two new categories will be added to the browse list soon: 'Chemical Modifications' and 'Synthetic Chemistry'.

If you would like to see a list of the protocols that have already been published that fit in these categories you can visit: http://natprotchem.blogspot.com/.

While a site licence is required to see the peer-reviewed content, the Network Protocols are completely free. At the moment, though, there are no chemistry Network Protocols.

If you are interested you can participate in this project by:
-suggesting methods that we should commission (comment here or on the blog)
-uploading one of your methods (http://www.natureprotocols.com/authors.php#research)
-commenting on a published method

I am sure that you have lots of excellent ideas and look forward to hearing from you soon!

[Mitch]

After perusing the sample pdfs, it does seem it would make it easier for chemists to publish protocols that might actually work! I like how the format includes the subtle information that is often left out.

What are Network Protocols?

[Bronwen Dekker]

The ‘Protocols Network’ is made up of protocols that are uploaded by researchers and are not further styled, peer reviewed or copy edited, but posted live soon after submission. They do not look quite as professional as the peer-reviewed content, but they are free.

Here are two examples:

NOESY-Based Strategy for Assignments of Backbone and Side Chain Resonances of Large Proteins without Deuteration
http://www.natureprotocols.com/2006/11/09/noesybased_strategy_for_assign.php

Live-cell assay to detect the dynamics of protein interactions
http://www.natureprotocols.com/2006/06/30/livecell_assay_to_detect_the_d.php

The easiest way to find them is to browse by the categories in the website. You would then see two lists of manuscripts in your chosen category (under these headings):
(1) Nature Protocols
(2) Protocols Network

Also, if you did a search for, for example, 'nmr' on the site, you would get both manuscript types.

[Bronwen Dekker]

Just to let you know that we have finally published something on the 'Protocols Network' that could be thought of as chemistry.

The title is:
Development of QSAR models using C-QSAR program: a regression program that has dual databases of over 21,000 QSAR models

The link is:
http://www.natureprotocols.com/2007/03/05/development_of_qsar_models_usi_1.php.

Update (4 April 2007):

It has now become part of my job to look after the Network Protocols. I have quickly gone through all of them to find ones that are 'good examples'. I thought I would put this list here for those people who are still coming to look at this topic every now and then. It is rather a long list of mostly biological stuff...    But hopefully something will catch your eye.

http://www.natureprotocols.com/2006/12/21/seeing_is_believing_in_vivo_fu_1.php
Seeing is believing: In vivo functional real-time imaging of transplanted islets using positron emission tomography (PET) - This one contains the synthesis of the radiotracer -

AutoMotif Server: A Computational Protocol for Identification of Post-Translational Modifications in Protein Sequences.
http://www.natureprotocols.com/2007/03/23/automotif_server_a_computation.php

Large Scale Vitreous Fluid Proteomics using 1D SDS-PAGE, Tandem Mass Spectrometry, and a Relational Database
http://www.natureprotocols.com/2007/03/08/large_scale_vitreous_fluid_pro.php

AFPredictor: A computational screening protocol for antifreeze/ice-structuring proteins
http://www.natureprotocols.com/2006/08/17/afpredictor_a_computational_sc.php

http://www.natureprotocols.com/2006/09/29/rat_chromaffin_cells_primary_c.php
Rat Chromaffin cells primary cultures: Standardization and quality assessment for single-cell assays
 
http://www.natureprotocols.com/2006/06/30/livecell_assay_to_detect_the_d.php
Live-cell assay to detect the dynamics of protein interactions

http://www.natureprotocols.com/2007/01/29/detection_of_placental_rna_all.php
Detection of placental RNA allelic ratio in maternal plasma by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

http://www.natureprotocols.com/2006/11/09/noesybased_strategy_for_assign.php
NOESY-Based Strategy for Assignments of Backbone and Side Chain Resonances of Large Proteins without Deuteration

http://www.natureprotocols.com/2006/10/13/determination_of_neopterin_and.php
Determination of neopterin and biopterin by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) in rat and human plasma, cell extracts and tissue homogenates

http://www.natureprotocols.com/2006/12/15/purification_of_a_protein_comp.php
Purification of a protein complex that associates with chromatin

http://www.natureprotocols.com/2006/09/15/northern_blot_analysis_of_mrna.php
Northern Blot analysis of mRNA from mammalian polyribosomes

http://www.natureprotocols.com/2006/09/01/analysis_of_branch_migration_a.php
ANALYSIS OF BRANCH MIGRATION ACTIVITIES OF PROTEINS USING SYNTHETIC DNA SUBSTRATES

http://www.natureprotocols.com/2006/12/12/application_of_direct_current.php
Application of direct current electric fields to cells and tissues in vitro and modulating wound electric field in vivo

http://www.natureprotocols.com/2006/11/17/thymosin_4_t4induced_outgrowth.php
Thymosin beta-4 (Tbeta-4)-induced Outgrowth and Differentiation of Vasculogenic Precursor Cells from Adult Epicardium

http://www.natureprotocols.com/2006/08/25/neural_stem_cell_culture_neuro.php
Neural Stem Cell Culture: Neurosphere generation, microscopical analysis and cryopreservation

http://www.natureprotocols.com/2007/03/05/development_of_qsar_models_usi_1.php
Development of QSAR models using C-QSAR program: a regression program that has dual databases of over 21,000 QSAR models

http://www.natureprotocols.com/2006/07/19/rnai_screens_in_c_elegans_in_a.php
RNAi screens in C. elegans in a 96-well liquid format and their application to the systematic identification of genetic interactions

http://www.natureprotocols.com/2006/06/30/automated_imagingbased_highthr.php
Automated imaging-based high-throughput screening for small molecules that reverse cellular senescence

http://www.natureprotocols.com/2007/01/29/detection_of_autoantibodies_wi.php
Detection of autoantibodies with self-assembling radiolabeled antigen tetramers

http://www.natureprotocols.com/2006/09/15/western_blot_analysis_of_subce.php
Western blot analysis of sub-cellular fractionated samples using the Odyssey Infrared Imaging System

http://www.natureprotocols.com/2006/06/23/metabolic_biotinylation_of_mam.php
Metabolic biotinylation of mammalian cell receptors for imaging


http://www.natureprotocols.com/2006/11/09/oscillating_current_stimulatio.php
Oscillating current stimulation – Slow oscillation stimulation during sleep

http://www.natureprotocols.com/2007/01/10/functional_analyses_for_sitesp.php
Functional analyses for site-specific phosphorylation of a target protein in cells

http://www.natureprotocols.com/2006/11/03/mechanical_tracing_of_protein.php
Mechanical tracing of protein function in the Drosophila ear

http://www.natureprotocols.com/2006/07/19/rnai_screens_in_c_elegans_in_a.php
RNAi screens in C. elegans in a 96-well liquid format and their application to the systematic identification of genetic interactions


http://www.natureprotocols.com/2007/02/14/production_of_neuronpreferenti.php
Production of neuron-preferential lentiviral vectors

http://www.natureprotocols.com/2007/01/24/placenta_specific_gene_manipul.php
Placenta specific gene manipulation by transducing zona-free blastocyst using lentiviral vector

http://www.natureprotocols.com/2007/03/20/doublelabel_immunofluorescent.php
Double-label immunofluorescent staining of CD38 and oxytocin in the mouse hypothalamus

http://www.natureprotocols.com/2006/10/02/nucleofection_and_adoptive_tra.php
Nucleofection and adoptive transfer of primary mouse T lymphocytes

http://www.natureprotocols.com/2007/02/14/simplified_behavioural_tests_f.php
Simplified behavioural tests for transient social memory in male mice and dams

http://www.natureprotocols.com/2006/10/02/removal_of_ccr5_ligands_and_in.php
Removal of CCR5 ligands and induction of pro-resolving lipid mediators by apoptotic neutrophils during resolution