User Manual
Contents
1. Input and Output The inputs to RDC ANALYTIC are 1 one RDC type from N HN C N and one RDC type from C H C C measured in one alignment medium 2 the core that is the SSEs of the NMR structures with no loops on it 3 the alignment tensor computed from the core of the respective NMR structures and the experimental RDCs using singular value decomposition SVD and 4 the primary sequence of the loop to instantiate the appropriate residue specific Ramachandran map Additional experimental data e g TALOS dihedral restraints and unambiguous backbone NOEs can also be used by POOL 5 1 File Organization of RDC ANALYTIC The directory structure of RDC ANALYTIC is shown in Figure Henceforth we denote the main working directory mainDirectory in Figure 1 for POOL by a period The Java source files are located in the folders src analytic and src utilities The Java binary class files are in the folders analytic and utilities To run POOL on input data set to compute loops we create a directory call it master directory inside which the input files the output files and the log files are organized To illustrate this let us consider an example of computing the loop VAL17 ILE23 of ubiquitin Let the master directory be EXPERIMENTS 1d3z 1723 The master directory contains the file dirArch txt or a file with any name that contains the directory architecture information and passed as argument to analytic Pool2. License along with this library if not see lt http www gnu org licenses gt There are additional restrictions imposed on the use and distribution of this open source code including A this header must be included in any modification or extension of the code B you are required to cite our papers in any publications that use this code The citation for the various different modules of our software together with a complete list of requirements and restrictions are found in the document license pdf enclosed with this distribution Contact Info Bruce R Donald Duke University Department of Computer Science Levine Science Research Center LSRC Durham NC 27708 0129 USA email www cs duke edu brd lt signature of Bruce Donald gt August 04 2012 Bruce R Donald Professor of Computer Science and Biochemistry 3 Citation Requirements Any publications grant applications or patents that use RDC ANALYTIC POOL must state that RDC ANALYTIC POOL was used with a sentence such as We used the open source RDC ANALYTIC POOL software Ref to compute In addition you are required to cite our papers in any publications that use this code The primary citation corresponding to this software is 1 The papers that can be cited based on or related to this software are listed below 1 Chittaranjan Tripathy Jianyang Zeng Pei Zhou and Bruce Randall Donald Protein loop closure using orientational restraints from NMR data P
3. This file contains the information about all the input output and log file names Therefore the name of the files and directories under the master directory can be changed to or specified as any valid directory and file names by the user In our example we used the following names as supplied in dirArch txt inputDirectory input_files_1d3z e g input directory input_files inputDataDirectory input_data_files e g Input Data Directory input_files input_data_files inputParameterDirectory input_parameter_files e g Input Parameter Directory input_files input_parameter_files mainDirectory src i E analytic java utilities java analytic class utilities class docs Manual License PoolManual pdf gt PoolLicense pdf masterDirectory directoryArchitectureFile txt input_data_files coreWithEndAnchor pdb rdc_medium1 txt seq txt input_parameter_files loop txt Parameter txt output_files solutionFragments pdb log_files mostRecentLeaf pdb solutionLog txt Figure 1 Directory structure of POOL Each directory and file name in the directory masterDirectory including the master directory masterDirectory can be customized de fined or renamed by the user outputDirectory output_files logDirectory log files input data directory must contain RDC NOE information dihedral angle restraints from TALOS etc program parameter dire
4. typeOfRdcsToBeUsedForRefinement The formats of the input files are described below 5 2 Input Format noe txt Only a sparse set of unambiguous backbone NOEs can be used by POOL at this time These NOEs can be obtained from chemical shift analysis of small proteins or Isoleucine Leucine Valine methyl labeling strategies used for larger proteins XPLOR format for NOEs is used e g example NOE assign resid 5 and name HA resid 67 and name HN 3 555 3 555 0 876 The program requires that the interacting proton names conform with the latest PDB naming convention A line comment in the file noe txt starts with as shown above rdc_medium1 txt This file contains the RDCs in XPLOR format e g assign resid 500 and name 00 resid 500 and name Z resid 500 and name X resid 500 and name Y resid 15 and name N resid 15 and name HN 10 5000 0 0000 0 0000 ES LO ON The RDCs are read from this file seq txt This file specifies the amino acid sequence of the protein in the format residueNumber threeLetterIUPACAminoAcidName TALOS Dihedral Restraints in talos txt We use TALOS dihedral restraint format to specify dihedral restraints predicted from the analysis of the chemical shift information 5 3 Output Format The output directory is automatically created when POOL executes and the ensemble of loop conformations are written into solutionFragments pdb the file specified in dirArch txt against the tag bes
5. License for more details For full licensing details including citation requirements for the software please refer to Section 2 and Section 3 respectively This information can also be found in the document PoolLicense pdf enclosed with this package distribution POOL is designed to compute high quality protein loop backbone conformations from RDCs in one alignment medium The POOL algorithm exploits the interplay between protein backbone kinematics and the global orientational restraints derived from RDC data to naturally discretize the conformation space by polynomial root solutions and represents the candidate conformations using a tree A systematic depth first search of the conformation tree is used to enumerate all possible loop conformations that are consistent with the data POOL uses efficient pruning strategies capable of pruning the majority of the conformations that are provably not part of a valid loop thereby achieving a huge reduction in the search space POOL requires only two RDCs per residue in one alignment medium specifically one RDC type from C H C C and one RDC type from N HN C N Therefore for a loop with n residues while POOL requires about 2n RDCs in total to match with the number of degrees of freedom of the loop it performs well when only 80 90 of the 2n RDCs are present For the remaining degrees of freedom for which RDC data is not available POOL employs a finite resolution uniform sampling of
6. OO User Manual Version 1 0 Chittaranjan Tripathy and Bruce R Donald Copyright 2001 2012 Bruce Donald Lab Duke University 1 Contents 1 Introduction 3 2 License Information 3 3 Citation Requirements 4 4 Installation 5 5 Configurations Input and Output 6 5 1 File Organization of RDC ANALYTIO 2 2 o 6 5 2 Input Format eae hone ko e Be A ae oe ae we ae a oe a a a 9 5 3 Output Format 2 10 6 Examples 10 7 Utilities 11 1 Introduction POOL is a suite of programs for protein loop backbone structure determination from residual dipolar couplings RDCs only two RDCs per residue are required in one alignment medium Additional experimental data e g TALOS dihedral restraints and unambiguous backbone NOEs can be used to filter the candidate loop conformations POOL is a part of RDC ANALYTIC suite of programs for high resolution protein backbone fold determination from RDCs RDC ANALYTIC POOL is developed in the lab of Prof Bruce R Donald at Duke University RDC ANALYTIC POOL is free software and can be redistributed and or modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation either version 3 of the License or optionally any later version RDC ANALYTIC is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU Lesser General Public
7. RdcRmsdThreshold psiTypeRdcRmsdThreshold Syy Szz numberOfSearchTrees loop 17 23 1 0 5 0 6 1D3ZBB_CAHA_NHN_POF pdb 2 0 1 0 15 457906239256296 24 715711838306476 1000 computeNow 17 23 Note that here the tag CcomputeNow if not specified the loop anchors must be specified as command line arguments while invoking analytic Pool The file parameter txt looks like the following RDC Scaling Factors The flag scaleRdcTo can be set to one of the values from the following set scaled CA_HA N_HN It sets the values of the prefactors Dmax for the different types of RDCs measured If the data has already been scaled then use the flag scaled If the data are to be scaled wrt CA_HA then set the flag to CA_HA and if the data are to be scaled wrt N_HN then set the flag to N_HN We recommend to use scaled RDCs for our program or to scale the RDCs wrt CA_HA scaleRdcTo CA_HA Alignment media name for RDCs mest be medium1 medium2 etc rdcMediumName medium1 Only two RDCs in the same alignment medium required typesOfRdcsToBeUsedForAnalyticSolutions CA_HA N_HN Can be used to filter the solutions further typeOfRdcsToBeUsedForRefinement CA_HA N_HN The relative scaling of the RDCs must be specified for correct interpretation of RDC data Also the RDCs to be used can be specified here For this release typeOfRdcsToBeUsedForRef inement must be specified to have the same types as
8. align two structures and extract information such as backbone RMSD for ranges of residues with or without alignment and compute the magnitudes rotation and translation for align ment we provide the utility StructureAligner To learn more about the command the options type java utilities StructureAligner help For example to run the StructureAligner utility you can use the following command or something similar for your set up java utilities StructureAligner pdbfile EXPERIMENTS experimentsToTestUtilities 1ghh 1GHHModel1 pdb pdbfile EXPERIMENTS experimentsToTestUtilities 1ghh 1GHHModel2 pdb atomtypes N CA C ranges 2 12 72 80 To simulate RDCs using a structure and an alignment tensor we provide the utility RDCSimulator To learn more about the command the options type java utilities RDCSimulator help For example to run the RDCSimulator utility you can use the following command or some thing similar for your set up To run the RDCSimulator utility you can use the following command something similar for your set up java utilities RDCSimulator masterdir EXPERIMENTS experimentsToTestUtilities loyc pdbfile EXPERIMENTS experimentsToTestUtilities loyc loyc_afh pdb Szz 8 8465e 04 Sxx_yy 1 2187e 03 Sxy 6 5320e 04 Sxz 6 0936e 05 Syz 3 4005e 04 rdctypes N_HN CA_C 11 e To test the fit of RDC data with structural coordinates we provide the utility OrientationalRestraintAndStructureFitter To learn more a
9. bout the command the options type java utilities OrientationalRestraintAndStructureFitter help For example to run the OrientationalRestraintAndStructureFitter utility you can use the following command or something similar for your set up java utilities OrientationalRestraintAndStructureFitter masterdir EXPERIMENTS experimentsToTestUtilities 1ghh pdbfile EXPERIMENTS experimentsToTestUtilities 1ghh 1GHHModel1And2 pdb rdctypes N_HN CA_C CA_HA printbackcomputedrdcsincsrosettaformat printbackcomputedrdcsinxplorformat ranges 20 30 printbackboneinpof printbackbonedihedrals 12
10. ctory must contain 1 the set of parameters to be used for the program and 2 the RDC scaling factor information i e how your RDCs are mutually comparable RDC and CSA Files in Mediumi rdc_mediuml txt RDC and CSA Files in Medium2 null RDC and CSA Files in Medium2 rdc_medium2 txt programParameterFile parameter txt SSeInfoFile sse txt sequenceFile seq txt loopConfigurationFile loop txt dihedralRestraintFile talos txt noeRestraintFile noe txt Warning not recommended to change the settings below bestFragmentPdbFile solutionFragments pdb solutionTreeLogFile solutionLog txt mostRecentFragmentCorrespondingToALeaf mostRecentLeaf pdb Note that in the above specifications of file and directory names the part left to the colon symbol is a tag used by the program and the part right to the colon symbol is the user supplied name For example above the input directory is specified to be input_files_1d3z It has two sub directories namely input_data_files and input_parameter_files input_parameter_files contains the input data files and the core of the protein The directory input_parameter_files contains two files loop txt and parameter txt The file loop txt contains the specification of the loop as shown below Format is Cloop beginResidueNumber endResidueNumber closureDistanceThreshold gridResolutionForPhiPsi DepthAtWhichStericCheckerTurnsOn pdbFileContainingGlobalFold phiType
11. cture Determination from NMR Data Journal of Computational Biology 13 7 1276 1288 2006 7 Lincong Wang and Bruce Randall Donald Analysis of a Systematic Search Based Algorithm for Determining Protein Backbone Structure from a Minimal Number of Residual Dipolar Couplings In Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference CSBO4 Stanford CA pages 319 330 2004 4 Installation Since POOL is written in Java it requires JDK 1 7 Henceforth it is assumed that JDK 1 7 has already been installed To install POOL 1 Unpack the tar file in a directory of your choice Then go to the sub directory that contains the directory structure shown in Figure 1 2 The Java files are in the directory src analytic and the class files after compilation will be in the following directory analytic To compile the Java files type the following two commands javac d classpath javax vecmath Jampack Jampack src analytic java J P J P P y J javac d classpath javax vecmath Jampack Jampack src utilities java For convenience we have provided a shell script with the name compile sh Executing this script will compile the Java files 3 This completes installation and POOL is ready for use 4 To run the program type the following command java analytic Pool lt arguments gt The lt arguments gt that are supplied to POOL can be found by typing java analytic Pool help 5 Configurations
12. roteins Structure Function and Bioin formatics 80 2 433 453 2012 2 Chittaranjan Tripathy Jianyang Zeng Pei Zhou and Bruce Randall Donald Protein loop closure using orientational restraints from NMR data In Vineet Bafna and S Sahinalp editors Proceedings of the 15th Annual International Conference on Research in Computational Molec ular Biology RECOMB Vancouver BC Canada volume 6577 of Lecture Notes in Computer Science pages 483 498 Springer Berlin Heidelberg 2011 3 Anna Yershova Chittaranjan Tripathy Pei Zhou and Bruce Randall Donald Algorithms and Analytic Solutions using Sparse Residual Dipolar Couplings for High Resolution Automated Protein Backbone Structure Determination by NMR The Ninth International Workshop on the Algorithmic Foundations of Robotics WAFR 68 355 372 2010 4 Jianyang Zeng Jeffrey Boyles Chittaranjan Tripathy Lincong Wang Anthony Yan Pei Zhou and Bruce Randall Donald High resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations Journal of Biomolecular NMR 45 3 265 281 2009 5 Bruce R Donald and Jeffrey Martin Automated NMR Assignment and Protein Structure De termination using Sparse Dipolar Coupling Constraints Progress in Nuclear Magnetic Resonance Spectroscopy 55 2 101 127 2009 6 Lincong Wang Ramgopal R Mettu and Bruce R Donald A Polynomial Time Algorithm for De Novo Protein Backbone Stru
13. tFragmentPdbFile In addition a directory is created to keep the log files for the execution of POOL The log file solutionLog txt and mostRecentLeal pdb respectively hold the progress of the execution of POOL and the fragment corresponding to the most recently evaluated leaf node of a solution tree 6 Examples This distribution comes with seven examples of how to prepare the input files and run POOL on proteins For ubiquitin two examples experimental NMR data is used For the rest five proteins since no NMR data is available simulated RDCs are used These loops vary in size i e the number of residues in the loop from 6 to 12 Specifically the lengths of the seven loops are 6 7 8 12 12 12 and 12 To invoke POOL for each of these loops the following commands can be issued in parallel without any problem in any order java analytic Pool masterdir EXPERIMENTS 1d3z_17_23 10 java java java java java java analytic Pool masterdir EXPERIMENTS 1d3z_7_12 analytic Pool masterdir EXPERIMENTS 1ds1 analytic Pool masterdir EXPERIMENTS 1dqz analytic Pool masterdir EXPERIMENTS 1cnv analytic Pool masterdir EXPERIMENTS 1dysA analytic Pool masterdir EXPERIMENTS 1oyc 7 Utilities For convenience we provide some basic utilities that comes with RDC ANALYTIC POOL To facilitate faster learning of the use of these utilities we provide examples in the directory EXPERIMENTS experimentsToTestUtilities To
14. the Ramachandran map is used for that dihedral degree of freedom For the cases with less RDC data POOL may take longer to compute the loop conformations since dihedral angles for which RDCs are missing are sampled uniformly thereby increases the time complexity of the tree search Also in this case the solutions can be less accurate For loops with moderate amount of dynamics POOL can be used to compute ensembles of loop conformations from RDCs This document contains license information citations required upon using the software and the details of how to install and use POOL 2 License Information The source header below must be included in any modification or extension of the source code of RDC ANALYTIC Source Header This file is part of RDC ANALYTIC RDC ANALYTIC Protein Backbone Structure Determination Software Version 1 0 Copyright C 2001 2012 Bruce Donald Lab Duke University RDC ANALYTIC is free software you can redistribute it and or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation either version 3 of the License or at your option any later version RDC ANALYTIC is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU Lesser General Public License for more details You should have received a copy of the GNU Lesser General Public
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