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mskwark / PconsC3

Faster, more accurate and entirely open source method for predicting contacts in proteins
GNU General Public License v2.0
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external source of contact #1

Closed kad-ecoli closed 6 years ago

kad-ecoli commented 6 years ago

I would like to run PconsC3 locally. Unfortunately, it depends on external source of contact: PhyCMAP or CMAPpro, neither of which can be generated from standalone program. I wonder whether there is other source of contact I can used/

mskwark commented 6 years ago

PhyCMAP is (was?) a part of RaptorX package, which can be freely downloaded from authors' website (http://raptorx.uchicago.edu/download/). While the method has been tested thoroughly on phyCMAP predictions, we strongly believe that any (relatively) reliable prior on contact propensities would do just as well. It is of importance, that the method does not rely on coevolution, but rather is based on observed contact propensities of certain amino acid windows. If not phyCMAP, maybe you could consider DNcon from MULTICOM package (http://sysbio.rnet.missouri.edu/multicom_toolbox/tools.html)... But any source of contacts should work.

arneelof commented 6 years ago

PS. If you want to use something faster, better and in particular easier to install use PconsC4.

On 4 Mar 2018 01:42, "Marcin Skwark" notifications@github.com wrote:

PhyCMAP is (was?) a part of RaptorX package, which can be freely downloaded from authors' website (http://raptorx.uchicago.edu/download/). While the method has been tested thoroughly on phyCMAP predictions, we strongly believe that any (relatively) reliable prior on contact propensities would do just as well. It is of importance, that the method does not rely on coevolution, but rather is based on observed contact propensities of certain amino acid windows. If not phyCMAP, maybe you could consider DNcon from MULTICOM package (http://sysbio.rnet.missouri. edu/multicom_toolbox/tools.html)... But any source of contacts should work.

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kad-ecoli commented 6 years ago

[1] Where can I find PhyCMAP from RaptorX package? The download page contain the following files: README 0README.AUCpreD.txt 0README.DeepAlign.txt 0README.EPAD.txt 0README.MRFalign.txt 0README.RaptorX.txt 0README.data4contactPrediction.txt AUCpreD_v1.03_release.tar.gz CAL_EPAD.tar.gz CAL_TGT.tar.gz CNFpred-UserGuide.pdf CNFsearch1.66_release.zip DeepAlign_Open_v1.13.benchmark.tar.gz DeepAlign_Open_v1.134.tar.gz DeepCNF_SS_v1.02_release.tar.gz EPAD_SCOP40.tar.gz EPAD_package_v1.01.tar.gz MRFsearch0.90_release.tar.gz Mems510-PredictedContacts-byNonMPs.tar.gz RaptorX_Property_Fast_v1.01.tar.gz TGT_SCOP40.tar.gz TPL_BC40_20180228.tar.gz TPL_Remain_20180228.tar.gz TemplateLists_20180228.tar.gz nr70.tar.gz nr90.tar.gz pdb25-6767-train.release.contactFeatures.pkl pdb25-6767-valid.release.contactFeatures.pkl pdb25-test-500.release.contactFeatures.pkl pdb_BC40_20180228.tar.gz pdb_Remain_20180228.tar.gz It seems none of them is contact prediction program.

[2] Where can I find PconsC4?

arneelof commented 6 years ago

For PhyCMAP you have to contact the authors. However, I think it might be easier to use some alternative version as suggested by Marcin.

PconsC4 instuctions: if you want to use PconsC4 on an alignment (in .a3m format) it should work with the following steps:

1) Clone PconsC4: git clone https://github.com/ElofssonLab/PconsC4.git

2) Get the trained model wget https://www.dropbox.com/s/kgyz31he9q6fkoi/pconsc4_unet.python3.h5 https://www.dropbox.com/s/kgyz31he9q6fkoi/pconsc4_unet.python3.h5?dl=0 -O src/model/pconsc4_unet.python3.h5

3) Run PconsC4 on an aligment: python src/run_pconsc4.py [-o -t -s ]

Compiling the cython source code is now done automatically when running "src/run_pconsc4.py" for the first time. So no need to do it manually with the provided setup.py script anymore.

Yours

Arne

Arne Elofsson Science for Life Laboratory Tel:+46-(0)70 695 1045 Stockholm University http://bioinfo.se/ Box 1031, Email: arne@bioinfo.se 17121 Solna, Sweden Twitter: https://twitter.com/arneelof Scholar: http://scholar.google.se/citations?user=s3OCM3AAAAAJ ORCID: 0000-0002-7115-9751

On Sun, Mar 4, 2018 at 11:23 PM, Chengxin Zhang notifications@github.com wrote:

[1] Where can I find PhyCMAP from RaptorX package? The download page contain the following files: README 0README.AUCpreD.txt 0README.DeepAlign.txt 0README.EPAD.txt 0README.MRFalign.txt 0README.RaptorX.txt 0README.data4contactPrediction.txt AUCpreD_v1.03_release.tar.gz CAL_EPAD.tar.gz CAL_TGT.tar.gz CNFpred-UserGuide.pdf CNFsearch1.66_release.zip DeepAlign_Open_v1.13.benchmark.tar.gz DeepAlign_Open_v1.134.tar.gz DeepCNF_SS_v1.02_release.tar.gz EPAD_SCOP40.tar.gz EPAD_package_v1.01.tar.gz MRFsearch0.90_release.tar.gz Mems510-PredictedContacts-byNonMPs.tar.gz RaptorX_Property_Fast_v1.01.tar.gz TGT_SCOP40.tar.gz TPL_BC40_20180228.tar.gz TPL_Remain_20180228.tar.gz TemplateLists_20180228.tar.gz nr70.tar.gz nr90.tar.gz pdb25-6767-train.release.contactFeatures.pkl pdb25-6767-valid.release.contactFeatures.pkl pdb25-test-500.release.contactFeatures.pkl pdb_BC40_20180228.tar.gz pdb_Remain_20180228.tar.gz It seems none of them is contact prediction program.

[2] Where can I find PconsC4?

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kad-ecoli commented 6 years ago

git clone https://github.com/ElofssonLab/PconsC4.git Cloning into 'PconsC4'... remote: Repository not found. fatal: repository 'https://github.com/ElofssonLab/PconsC4.git/' not found

This means that either the repository does not exist on github, or your have set special permission (such as making the repository private) to forbid the public from downloading it. Is there some other way I can download PconsC4?