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MolShaCS User Manual

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3. Here the volume of each atom is described as a Gaussian functionc 2 I A 6 The pictures below show in one dimension what MolShaCS performes in three dimensions MolShaCS MolShaCS ee ee ee ee IUAM IAA a Step 1 b Step 2 MolShaCS MolShaCS ee ee ILAA c Step 3 d Step 4 Figure 3 1 A score is computed by summing the overlap of Gassians that describe atomic shape A maximal score is obtained when molecules are super posed At r the shape volume is defined as 9 10 CHAPTER 3 THEORY pilr pieap a r Ha 3 1 where R is the atomic coordinate p is the Gaussian amplitude and a is the atomic radius dependent decay factor 3Pi noi 3 2 Qi T The overlap of Gaussians among two molecules named A and B can be given by Van X irao 3 3 ieAjeB That formulations is the classical description of molecular shape based on Gaussian density and the use of the overlap of Gaussians to estimate the molec ular overlap It has been described since early nineties and is already imple mented with some flavours in different programs dedicated to molecular sim ilarity identification such as ROCS 4 6 ShaEP 7 etc MolShaCS differs from these softwares in the way it includes the molecular charge distribution in the overlap computation In MolShaCS two other terms are included in equation 3 3 accounting for the overlap of positiv
4. of molecular data sets Journal of Computer Aided Molecular Design 6 513 520 1992 E E Hodgkin A C Good and W G Richards Utilization of gaussian func tions for the rapid evaluation of molecular similarity Journal of Chemical Information and Computer Sciences 32 188 191 1992 E G Birgin and J M Martinez Improving ultimate convergence of an aug mented lagrangian method Optimization Methods Software 23 177 195 2008 J A Grant and B T Pickup A gaussian description of molecular shape Journal of Physical Chemistry 99 3503 3510 1995 E E Hodgkin and W G Richards Molecular similarity based on electro static potential and electric field International Journal of Quantum Chem istry 1 105 110 1987 M A Gallardo J A Grant and B T Pickup A fast method of molecular shape comparison A simple application of a gaussian description of molec ular shape Journal of Computational Chemistry 17 1653 1666 1996 J S Puranen M J Vainio and M S Johnson Shaep molecular overlay based on shape and electrostatic potential Journal of Chemical Information and Modeling 49 492 502 2009 K Svanberg A class of globally convergent optimization methods based on conservative convex separable approximations Siam Journal on Optimiza tion 12 555 573 2001 17 18 BIBLIOGRAPHY Chapter 6 GNU Public License 3 0 20 CHAPTER 6 GNU PUBLIC LICENSE 3 0 Copyright 2007 Free Software Foundation Inc http fsf org
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9. MolShaCS Manual Alessandro S Nascimento September 2012 Contents 1 Introduction 1 1 What is MolShaCS 2 License terms w Theory 4 Getting and Installing 4 1 Compiling MolShaCS 4 1 1 Installing necessary libraries 4 1 2 Compiling without the GUI 4 1 3 Compiling with GUI 4 2 Building MolShaCS for Windows Systems 5 Using MolShaCS 5 1 Sample Run 6_ GNU Public License 3 0 13 13 13 14 14 14 15 15 19 CONTENTS Chapter 1 Introduction 1 1 What is MolShaCS MolShaCS Molecular Shape and Charge Similarity is a computational tool dedicated to overlay and compute a similarity index among two small molecules MolShaCS currently can handle only SYBYL MOL2 file format and it is desir able for the molecules to have atomic charges defined since MolShaCS will use the charge distribution of the molecules together with molecular shape to overlay and compute the similarity index For molecular overlay and similarity index computation MolShaCS uses a Gaussian description of the molecule shape and charge distribution The overlay is achieved by numerical optimization of the sum of Gaussians that describe molecular shape and charge Once the overlay is optimized the similarity index is computed using a Hodgking s like index 5 MolShaCS can be used as an important tool for small molecule identifica tions in different contexts including i virtua
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13. com The program is distributed as pre built binaries and source code 4 1 Compiling MolShaCS MolShaCS can be compiled from source code in two ways using Qt libraries to build the GUI or without the GUI 4 1 1 Installing necessary libraries MolShaCS uses a couple of libraries within its engine GNU Scientific Library GSL NLOT and ZLIB libraries have to be built prior to program compilation Building from repositories On Ubuntu systems GSL and ZLIB libraries can be built using sudo apt get install libgsl0 dev zlibig dev Building GSL Alternativelly to the repository install GSL source code can be downloaded from GSL webpage The package contains instructions for compilation Building NLOPT NLOPT can be downloaded from NLOPT webpage The libraries are easilly built with the following commands assuming you have GNU C compiler gcc and c compiler g configure with cxx make sudo make install The libraries are installed by default in usr local lib for linux systems 13 14 CHAPTER 4 GETTING AND INSTALLING Building ZLIB Alternativelly to the repository install zlib can de obtained from ZLIB webpage Instructions for library compilation are provided together with the package 4 1 2 Compiling without the GUI In MolShaCS src folder there is a Makefile named Makefile nogui Follow the steps described below to compile MolShaCS without GUI 1 Edit the file src Makefile nogui It is important to check t
14. e charges and negative charges respectivelly The charge distribution is modeled as a Gaussian similar to equation 3 1 taking o as proportional to the atomic charge So the final objective function in MolShaCS is given by VAB wil drpi r p r wel dedi ME r w dedi r oF r gt gt J ee i J 3 4 MolShaCS optimizes this objective function shown in equation 3 4 by chang ing the molecular atomic coordinates using six parameters for rotation and translations i e the molecule is moved as a rigid body After a maximal over lap is found a similarity index SI is computed as a Hodgkin s index 5 2VaB SI Vaa VBB 3 5 MolShaCS uses NLOPT library for numerical optimization Different algo rithms provided by NLOPT are available for the user choose 1 Augmented Lagrangians 3 nlopt ln auglag 2 Method of Moving Asymptotes 8 nlopt_mma Improved Stochastic Ranking Evolution Strategy nlopt_isres Broyden Fletcher Goldfarb Shanno Algorithm nlopt_1bfgs2 o e O Nelder Mead Simplex method nlopt_simplex 11 6 A variant of Nelder Mead simplex that uses Nelder Mead on a sequence of subspaces nlopt_subplex 7 COBYLA nlopt_cobyla 12 CHAPTER 3 THEORY Chapter 4 Getting and Installing MolShaCS can be obtained free of charge in the web address http www ifsc usp br biotechmol Alternativelly the program can be obtained in the google code repository http molshacs googlecode
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17. he LDFLAGS and CFLAGS 2 Build MolShaCS with the command make 3 If compilation succeeds you will find the binary MolShaCS in the source folder The program is ready to use in the text mode 4 1 3 Compiling with GUI In order to build the Qt GUI it is necessary to have the program qmake and some QT libraries Again it can be done with OS repositories in many cases In ubuntu you can use the following command sudo apt get install qt4 qmake libqtcore4 libqtgui4 libgt4 dev Alternativelly Qt can be obtained from Nokia webpage and installed To compile MolShaCS with the GUI follow the stepd described below 1 Edit the file MolShaCS pro The important keys to look after are LIBS and INCLUDEPATH Make sure that the necessary libraries are listed there 2 Run qmake with the command qmake recursive MolShaCS pro 3 Compile the program with make 4 If everything works file the binary file named MolShaCS will be built 4 2 Building MolShaCS for Windows Systems MolShaCS can be built on MS Windows However the compilation process can be quite painful If MS Windows is your operational system of choice I would recomment to use the pre built binary provided in the dowload page This binary contains the GUI already so that the user can choose whether or not he wants to use the graphical interface However if you really want to build MolShaCS on MS Windows you can download and install Qt libraries from Nokia webpage The other l
18. ibraries GSL and nlopt can be built using MINGW Then you can build MolShaCS and link with the correct libraries Be careful to use the same compiler to compile the libraries and Qt some Qt distributions comes with GNU compilers that may have different versions of your MINGW compiler Chapter 5 Using MolShaCS MolShaCS can be compiled and used using a Qt graphical user interface or my preferred method using command line For command line type MolShaCS Molshacs inp Where Molshacs inp is a text file with the following syntax refmol_mol2 moli mol2 output_prefix MolShaCS minimizer nlopt_mma align_molecules yes timeout 60 write_coordinates yes mol2_aa no box_size 30 0 30 0 30 0 multimol molecules list step 1 0E 5 tol 1 0E 4 delta 1 0E 5 A file molecules list should also exist in the directory where MolShaCS is running This file must be a text file with the path for the comparing molecules only For example more molecules list mo12 mo11 mo12 mo12 mo12 mo12 mo12 mo13 mo12 mo12 mo14 mo12 5 1 Sample Run As an example on how to use MolShaCS we will compare aldosterone to a set of FDA approved molecules and take a look at the molecules in the top of the list First of all lets get the molecules 15 16 CHAPTER 5 USING MOLSHACS Lets go to ZINC and download the Drugbank list of approved drugs with 1761 representative molecules The molecules are provided as MOL2 files through script to dow
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21. l screening of actives compounds using a pharmacophore like model i e a 3 D model of another compound known to be active ii identification of off target interactions i e the sim ilarities among molecules supposed to have different pharmacological effects or mechanisms of actions We provide the software as it is hoping that it can be useful for the chemoin formatics medicinal chemistry community following the terms of the license shown below Any suggestions doubts problems on using the program can be directed to the address below Prof Alessandro S Nascimento Sao Carlos Physics Institute University of Sao Paulo Av Trabalhador saocarlense 400 Centro Sao Carlos SP Brazil 13560 970 Email asnascimento ifsc usp br CHAPTER 1 INTRODUCTION Chapter 2 License terms Copyright 92012 Alessandro Nascimento MolShaCS is a free software you can redistribute it and or modify it under the terms of the GNU General Public License as published by the Free Software Foundation either version 3 of the License or any later version This program is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY without even the implied warranty of MERCHANTABIL ITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU General Public License for more details CHAPTER 2 LICENSE TERMS Chapter 3 Theory MolShaCS uses the concept of overlap of Gaussians for molecular overlay and similarity computation
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24. nload in Linux or Windows Supposing you already have the mol2 files named fda80 1 mol2 fda80 2 mol2 fda80 3 mol2 etc in a separate folder named mol2 lets generate a molecules list file If you use Linux or Cygwin in Windows this should be easy see below These lines will look for the files in the folder mol2 and put them on the list if the file exists for i in seq 1 1761 do if e mol2 fda80 i mol2 1 then echo mol2 fda80 i mol2 gt gt molecules list fi done Lets get aldosterone from ZINC again using this link Now lets prepare an input file for MolShaCS This file should have the fol lowing instructions see below Save the file as input inp refmol_mol2 aldo mol2 output_prefix MolShaCS minimizer nlopt_mma_sog align_molecules yes timeout 60 write_coordinates yes write_coord_threshold 0 85 mol2_aa no box_size 30 0 multimol molecules list step 1 0E 5 tol 1 0E 4 delta 1 0E 5 Ok we are ready to start the computation with the command Mo1ShaCS input inp After a couple of minutes the calculation is done and two files are written MolShaCS log and MolShaCS cc dat The latter has the similarities computed for each of the provided molecules We can rank the results using a bash com mand again below and we will find the top scored molecules more MolShaCS cc dat sort n r k 5 more Bibliography 1 zer E E Hodgkin A C Good and W G Richards Similarity screening
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