rohithmohan / aesop-r Goto Github PK
View Code? Open in Web Editor NEWold AESOP R framework
old AESOP R framework
AESOP Clustering Framework (Aug. 16, 2013) ------------------------------------------- This README file describes the contents and usage of the AESOP Clustering Framework. Contents of AESOP_clust ------------------------ + README (This file) + aesop_description.pdf = Theory and structure behind the AESOP framework + Directories ------------ - Source = Source code for AESOP framework, plus additional utilities to aid calculations * AESOP.r = Source code containing AESOP framework functions * pdb_align_hom.r = Utility script for superimposing protein structures containing different sequences * pdb_align.r = Utility script for superimposing protein structures containing the same sequence * chimera_images.r = Utility script for making isopotential contours - examples = AESOP examples + barnase_alascan = Clustering example for alanine-scan of a single chain, barnase * Results (Folder) = Contains example output files for comparison * bn_bs.pdb = PDB structure for the barnase-bastar complex (1BRS) * barnase_alascan.r = AESOP script for performing electrostatic similarity clustering of barnase alanine-scan mutants + barnase_barstar_alascan = Example for alanine-scan of a complex with clustering and solvation free energies of association * Results (Folder) = Contains example output files for comparison * barnase_barstar.pdb = PDB structure for the barnase-bastar complex (1BRS) * bnbs_alascan.r = AESOP script for performing electrostatic similarity clustering and calculating solvation free energies of association for barnase-barstar alanine-scan mutants + c3d_perturb_map = Example for perturbation map of complement C3d * Results (Folder) = Contains example output files for comparison * c3d.pdb = PDB structure for the complement C3d (1C3D) * c3d_esi_dist.r = AESOP script for generating perturbation map of + LTP_homology = Clustering example for homologous lipid transfer proteins (LTP) * Results (Folder) = Contains example output files for comparison * LTP_pdb (Folder) = Contains 20 PDB structures for LTP and LTP-like proteins from Arabidopsis * LTP_esd_clust.r = AESOP script for performing electrostatic similarity clustering of LTPs * chimera_images.r = Utility script for making isopotential contours for each LTP protein * pdb_align_hom.r = Utility script for superimposing protein structures containing different sequences + sumo_charge_reverse = Example for charge-reversal scan of SUMO4 in complex with SENP2 (clustering and free energies) * Results (Folder) = Contains example output files for comparison * senp2_sumo4.pdb = PDB file for the SENP2-SUMO4 complex (model) * sumo_qrev.r = AESOP script for performing electrostatic similarity clustering and calculating solvation free energies of association for SENP2-SUMO4 charge-reversal scan mutants + sumo_mut_comb = Example for generating combinations of mutations based on list allowed mutations for SENP2-SUMO4 (clustering and free energies) * Results (Folder) = Contains example output files for comparison * senp2_sumo4.pdb = PDB file for the SENP2-SUMO4 complex (model) * sumo_mut_comb.r = AESOP script for performing electrostatic similarity clustering and calculating solvation free energies of association for mutation combinations + c3d_mutants_list / cr2_mutants_list = Example for generating generating a list of specific mutations for C3d-CR2 (clustering and free energies) * Results (Folder) = Contains example output files for comparison * c3d_cr2.pdb = PDB file for the C3d-CR2 complex (model) * c3dmuts.xls / cr2muts.xls = Excel file for the C3d/CR2 sequence number and mutant (up to triple mutants) * c3d_mut_list.r / cr2_mut_list.r = AESOP script for performing electrostatic similarity clustering and calculating solvation free energies of association for specified list of SUMO4 mutants External Software Needed for AESOP: ----------------------------------- The following list of software must be installed prior to using the AESOP Framework. SCWRL4 is need for non-alanine mutations. The last two programs are needed only for the chimera_images (UCSF Chimera) and pdb_align_hom (MUSCLE) utilities, which have been included to aid in the visualization of results and in the super-positioning of homologous protein structures. Please visit the links below and follow the instructions provided by each website on how to install the programs. Where the programs are installed is not of importance, however the path to MUSCLE executable must be added to the PATH environmental variable. The paths to all other programs will simply be set in the AESOP scripts. At this time the AESOP Framework has only been tested for UNIX platforms (Mac and Linux), since PDB2PQR is unable to installed on Windows. Those wishing to implement the AESOP framework on a Windows machine will need to use the Cygwin environment (http://www.cygwin.com/). ======================================================== R for Statistical Computing - http://www.r-project.org/ Bio3D - http://mccammon.ucsd.edu/~bgrant/bio3d/ APBS - http://www.poissonboltzmann.org/apbs/ PDB2PQR - http://www.poissonboltzmann.org/pdb2pqr/ UCSF Chimera - http://www.cgl.ucsf.edu/chimera/ (Needed for chimera_images to make isopotential contours) **MUSCLE - http://www.drive5.com/muscle/ (Needed for pdb_align_hom to select atoms to be used in fitting) ** Only needed for optional utilities for structure alignment and visualization ======================================================== One additional R package is also needed. It can be installed by executing the following command while in the R environment: install.packages("stringr") Setup and execution of AESOP: ----------------------------------- After installing the above required software, the paths of these programs must be updated in the AESOP_paths.r file, which can be found in the source directory. To run an AESOP script, open the R environment and navigate to the correct working directory. Finally, the source command is used to execute the the AESOP script. Please see the aesop_description.pdf, and the included examples for more details. ***NOTE*** To avoid potential problems, it is best to use cleaned PDB files as input, meaning only including ATOM lines. PDB files do not need to be renumbered, but if multiple chain are present in the PDB file, chain identifiers need to be used.
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.