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TraDES

Trajectory Directed Ensemble Sampling. Release 5 June 2012 TraDES-2 https:/ us-east.manta.joyent.com/profhogue/public/TraDES-2/index.html. 2 Sept 2012 Beta Release of the TraDES R Analysis Package (attached at bottom of this web page). TraDES was created in the Hogue Laboratory. Formerly at the National University of Singapore, and Mount Sinai Hospital/Univeristy of Toronto. TraDES is a system for directly controlling and sampling protein conformational space. Makes Trajectory Distributions from 3D struc...

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Trajectory Directed Ensemble Sampling. Release 5 June 2012 TraDES-2 https:/ us-east.manta.joyent.com/profhogue/public/TraDES-2/index.html. 2 Sept 2012 Beta Release of the TraDES R Analysis Package (attached at bottom of this web page). TraDES was created in the Hogue Laboratory. Formerly at the National University of Singapore, and Mount Sinai Hospital/Univeristy of Toronto. TraDES is a system for directly controlling and sampling protein conformational space. Makes Trajectory Distributions from 3D struc...

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TraDES | trades.blueprint.org Reviews

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Trajectory Directed Ensemble Sampling. Release 5 June 2012 TraDES-2 https:/ us-east.manta.joyent.com/profhogue/public/TraDES-2/index.html. 2 Sept 2012 Beta Release of the TraDES R Analysis Package (attached at bottom of this web page). TraDES was created in the Hogue Laboratory. Formerly at the National University of Singapore, and Mount Sinai Hospital/Univeristy of Toronto. TraDES is a system for directly controlling and sampling protein conformational space. Makes Trajectory Distributions from 3D struc...

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trades.blueprint.org

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Tips and Hints - TraDES

http://trades.blueprint.org/home/tips-and-hints

Trajectory Directed Ensemble Sampling. Val is an ASN.1 binary file used by NCBI and TraDES. It contains the 3D structure information and can be converted into a PDB file. Valtopdb -f structure.val -m 1 -p structure.pdb. To convert a *.val file into a PDB file. See the FAQ page (Question #2) for how to convert a PDB file into a *.val file. Val2prt -f structure.val. To convert the ASN.1 binary into ascii (readable) ASN.1. Trajectory Directed Ensemble Sampling.

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Recent site activity - TraDES

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Nov 26, 2014, 5:49 PM. Christopher Hogue edited Trajectory Directed Ensemble Sampling. Nov 26, 2014, 5:43 PM. Christopher Hogue edited Trajectory Directed Ensemble Sampling. Nov 26, 2014, 5:42 PM. Christopher Hogue edited Trajectory Directed Ensemble Sampling. Oct 1, 2012, 8:07 PM. Christopher Hogue edited FAQ. Oct 1, 2012, 7:53 PM. Christopher Hogue edited Trajectory Directed Ensemble Sampling. Oct 1, 2012, 7:50 PM. Christopher Hogue attached TraDES R Analysis Package.r. Jun 5, 2012, 7:52 PM. Christophe...

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FAQ - TraDES

http://trades.blueprint.org/home/faq

Trajectory Directed Ensemble Sampling. 1 I am using the old version of TraDES. Should I upgrade to TraDES-2? Third - it is now open-source! This is the list of the new executables:. TraDES benchmarking and unit test - RUN THIS FIRST. Make *.trj files from FASTA. Make *.trj files from 3D structures in ASN.1 format. The TraDES sampling engine (formerly foldtraj). Convert ASN.1 files to PDB files (save space, use ASN.1! StrSummary - Reports on Asn.1 file contents, outputs FASTA, Ramachandran angles. RamangL...

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Trajectory Distributions - TraDES

http://trades.blueprint.org/home/trajectory-distributions

Trajectory Directed Ensemble Sampling. Controlling the Sampling of Conformational Space. The concept of the trajectory distribution may be new to many protein scientists. A trajectory distribution is simply a map of available conformational space at an amino acid residue. It can be either a Ramachandran plot with a 3rd axis which indicates the frequency or probability at that point, or it can be in a spherical form indicating placement of alpha-carbons. CLICK image to play movie. The output will be a ran...

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Ten Questions Before Grad School. Edited by Christopher Hogue. Edited by Christopher Hogue. Attachment from Christopher Hogue. Edited by Christopher Hogue. Edited by Christopher Hogue. Attachment from Christopher Hogue. Edited by Christopher Hogue. Christopher W.V. Hogue, Ph.D. Blog: http:/ bioimplement.blogspot.com/. LinkedIn: www.linkedin.com/in/cwvhogue/. Http:/ www.researcherid.com/rid/B-6726-2008. Updated 25 Oct 2014. 2 Now Open Source. - email chogue {at} blueprint.org. Xiang Wen Wei (MSc. 2013).

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SmartOS Stuff from @cwvhogue. Basic Minecraft Server on Joyent. Installation ZFS RAIDZ settings defaults. Why SmartOS in my lab? SmartOS Stuff from @cwvhogue. Why SmartOS in my lab? March 24, 2013. In my research lab at the National University of Singapore (NUS), I am Principal Investigator. Principal Sys-admin and Principal Coder. While my formal training and degree is in Biochemistry, I have been developing software since 1986, web services and REST APIs for Bioinformatics since 1996. We routinely crea...

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Trajectory Directed Ensemble Sampling. Release 5 June 2012 TraDES-2 https:/ us-east.manta.joyent.com/profhogue/public/TraDES-2/index.html. 2 Sept 2012 Beta Release of the TraDES R Analysis Package (attached at bottom of this web page). TraDES was created in the Hogue Laboratory. Formerly at the National University of Singapore, and Mount Sinai Hospital/Univeristy of Toronto. TraDES is a system for directly controlling and sampling protein conformational space. Makes Trajectory Distributions from 3D struc...

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