SiteBinder User Manual
Contents
1. INTERFACE 4 Structures are grouped into five categories Added Structures that were added and no changes were made to them Modified Structures that were changed changed selection or chain Superimposed Structures that are currently superimposed along with the current aver age structures Previously Superimposed Structures that used to belong to the Superimposed group Wrong Selection Structures that could not be superimposed because their selections were not compatible If any modification is made to the structures in the Superimposed group the average struc ture is removed 6 2 2 RMSD Panel This panel contains the RMSD value of all currently superimposed and selected structures The value is calculated as ti 97 V RMSD S 9 i 1 j i 1 RMSD S where 5 is the set of the selected structures and m is the number of structures The RMSD of two structures is defined as RMSD A B 1 n 4 Bill 4 1 where n is the number of selected atoms Finally the error is calculated as the distance from the theoretically optimal solution i e the solution where each pair of structures in the ensemble has the minimal distance when superimposed Nevertheless this number should be taken with reserve as the optimal solution does not exist in general 01 1 Select This Ix Remove This Select All Select Group Clear Selection Remove Selected 882. PNG image and saved to a file Five resolutions are supported 640x480 800x600 1024x768 1280x1024 and 1600x1200 6 USER INTERFACE 10 6 3 6 Bond Lengths The values of bond lengths are stored in the file BondLengths xml and can be adjusted by the user All values are in Angstroms Three types of lengths can be adjusted Default Length Specifies bond lengths for unknown atoms Can be adjusted by changing the line lt default value x y gt in BondLengths xml Atom Radius Specifies the radius of a given atom Can be adjusted by chang ing adding the line lt radius element ElSymbol value x y gt BondLengths xml Bond Length Specifies the maximum distance between two atoms for which there is still a bond Can be adjusted by changing adding the line bond element1 ElSymbol element2 ElSymbol value x y gt BondLengths xml Bibliography 1 Wikipedia Mono software Wikipedia the free encyclopedia 2009 Online accessed 25 December 2009 Available from http en wikipedia org wiki Mono_ software 2 David Sehnal Multiple Structure Alignment and Exploring Protein Binding Sites Master s thesis Masaryk University Brno 2010 Available from http is muni cz th 140435 fi m 11
3. 0 00006 1 000003 Close FIGURE 1 7 Log Furthermore the information about structures can be exported to a CSV file to allow for further processing for example in Microsoft Excel This feature can be accessed from the statistics list s context menu 6 2 10 Rendering Toolbar The rendering toolbar provides these features Resolution selection allows the user to select the resolution of the image to be exported Save Image Brings up the save image dialog Settings Allows the user to select various colors and set up Direct3D Reset Camera Resets the rotation and zoom to its original value Display options Allows the user to change the current display type as discussed above 1024x768 H Save Image 9 fii Reset Camera Display B All Sticks FIGURE 1 8 Rendering toolbar 6 2 11 Direct3D Settings Direct3D Settings dialog shown in figure 1 9 allows the user to change the following settings Back Buffer Format Represents the data format individual pixels are stored as Depth Stencil Format Data format for z buffer and stencil buffer unused Multisample Type The quality of anti aliasing The higher the better the rendered im ages look like 6 2 12 Rendering and Highlighting SiteBinder supports rendering of molecules using Mi crosoft Direct3D 9 6 3 Rendering Window Structures in the rendering window can be rotated by pressing the left mouse button and moving the mouse accordingly P
4. GURE 1 5 Atom selection for single left and multiple right structures Multiple selection An aggregate of all atoms in all structures is computed based on the number and type of residues and on atom names This allows for the selection of the same atoms over multiple structures The structures are grouped by the types of residues they contain 6 2 7 Progress Dialog During the superimposition of structures a progress dialog shown in figure 1 6 is displayed The dialog provides the following information e Number of the current iteration and the error of the last iteration e Progress of the current iteration e Progress of the current superimposition of pairs of structures e Time elapsed since the operation has started Working teration 2 Last iteration Error 0 063 Target 0 0005 Current Progress 07 20 Superimposing 3gv4 807 to average Current Progress 301 78 345650 Time Elapsed Im21s FIGURE 1 6 Progress dialog Furthermore the dialog gives the user the option to abort the process 6 2 8 Logs The logging dialog is used to display two types of information One refers to error reports on exceptions which occurred during program runtime plus possible suggestions of solutions The other reports on the alignment operations and their summary The log is reset each time Superimpose is called 6 2 9 Statistics Panel The list in this panel contains structures from the Superimposed group of t
5. HISx2 ZN Superimposed RMSD 0 627 H m lt average gt 0 387 CYSx2 HISx2 ZN v Vl 1455 0 910 CYSx2 HISx2 ZN v 1 V 1496 B 0 910 CYSx2 HISx2 ZN ND1 Vlieh6 1274 0 627 CYSx2 HISx2 2N ae V 1eh7 1234 A 0 651 CYSx2 HISx2 2N zA 1269 0 650 CYSx2 HISx2 ZN Mc V 1 21 5011 0 495 CYSx2 HISx2 ZN V 1 21 5012 0 443 CYSx2 HISx2 ZN Kc V 1 21 5013 H 0 443 CYSx2 HISx2 ZN 7 m V 1 2i_5014 0 476 CYSx2 HISx2 ZN F w 1 2i_5015 I 0 429 CYSx2 HISx2 ZN F ca V 1 2i_5016 I 0 465 CYSx2 HISx2 ZN M V 1 2i 5017 2 0 494 CYSx2 HISx2 ZN o 1 21 5018 J 0 413 CYSx2 HISx2 ZN E CB 1 21 5019 0 509 CYSx2 HISx2 ZN zn 1924 2774 0 474 CYSx2 HISx2 ZN V lung 4530 0 487 CYSx2 HISx2 ZN 4 pp ned n RMSD selected superimposed 0 627 N A 16 structure s selected FIGURE 1 1 SiteBinder Furthermore SiteBinder contains a log window allowing the user to see exceptions during the program runtime and detailed information about each superimposition Each of the individual components is described in detail bellow 6 2 1 Structure List The structure list is shown on figure 1 2 Information provided by the structure list Id Identifier of the structure extracted from the filename of the structure Chain Identifier Currently displayed chain Average RMSD RMSD Arithmetic average RMSD of the last s
6. Highlight lear Highlightis Bond Color Select Chain b 220 Export Selected FIGURE 1 3 Structure list pop up menu 6 2 3 Structure List Pop up Menu The structure list pop up menu shown on figure 1 3 be invoked by right clicking inside the Structure List The following features are available Select This Selects only the clicked structure and deselects all other structures Remove This Removes the clicked structure Select Group Selects all structures in the clicked structure s group The average struc ture is excluded from this selection and has to be selected manually Select All Selects all structures The average structure is excluded from this selection and has to be selected manually Clear Selection Deselects all structures Remove Selected Removes all selected structures 6 USER INTERFACE 5 Highlight Puts highlight on the clicked structure This visually distinguishes the structure in the list Clear Highlight s Removes all active highlights Bond Color Allows the user to change the color of the clicked structure Select Chain Allows user to select a different chain on the clicked structure Export Selected Exports all selected structures Add DX Superimpose Settings Log T FIGURE 1 4 Structure manipulation toolbar 6 2 4 Structure Manipulation Toolbar The toolbar shown in figure 1 4 has the following fea tures Add Ope
7. MASARYK UNIVERSITY NATIONAL CENTER FOR BIOMOLECULAR RESEARCH SiteBinder User Manual Version 1 1 1 Contents Chapter le OVervieuoL BR EEEE EEEE E ENER 1 I RUNDE E a 0 D eee Eee 1 1 1 1 Overview of SiteBinder 1 Running Environment SiteBinder is a software package for Microsoft NET Framework 3 5 and Microsoft DirectX more specifically its 3D part called Direct3D for displaying graphics The current version works under all 32 bit platforms supported by Framework including Windows Ser vice Pack 3 Windows Server 2003 Windows Vista Windows Server 2008 and Windows 7 In addtition a simple command line version of SiteBinder works on Linux and Mac using Mono 2 Hardware Requirements The hardware requirements are the same as of the operating system the software is running on Furthermore a graphic card that supports Direct3D is required Direct3D support is fairly common in today s computers 3 Features The features of SiteBinder include Loading PDB structures Structures in PDB format can be loaded Superimposing Superimposing an arbitrary number of structures limited by computer memory and time constraints Calculation of RMSD The RMSD of an arbitrary number of molecules can be com puted Modeling Binding Site Models of binding sites can be computed Statistics A simple statististical ana
8. ation about residue identifiers 3 Element Symbol Groups the atoms based on the information about element symbols If grouping of level n is not possible i e the selection of atoms does not allow Residue Name grouping grouping of level n 1 is automatically used However in some cases even if Residue Name Residue grouping is possible it may not provide the optimal fit In these cases the problem might be solved by forcing a higher level grouping which usually means a somewhat slower computation For details please refer to the author s Master s thesis SiteBinder 2 By default Residue Name grouping is used For the explanation of the individual settings please see author s master s thesis 2 6 2 6 Atom Selection Tree SiteBinder supports a comfortable selection of atoms shown in figure 1 5 for superimposing structures There are two modes of this function Single selection A tree of atoms grouped by residue name is provided and individual selection of atoms is possible 6 USER INTERFACE 6 zw 201 8 2 2 2 1161 107 nez E ca iP ile 485 i Eo LI ase ME ce PF ME 112 125 2 5 125 E zh lif ZN FI
9. e in the structure list Residues All structures with a given set of residues are highlighted by hovering over the names of the residues in the Atom Selection Tree multiple selection mode only Residue name All residues with a given name are highlighted by hovering over the residue name in the Atom Selection Tree multiple selection mode only Residue serial number The residue with a given serial number is highlighted by hov ering over the residue in the Atom Selection Tree single selection mode only Atom name All atoms with a given name are highlighted Only the atoms in the original atom s residue are considered by hovering over the atom name in the Atom Selection Tree multiple selection mode only Atom serial number The atom with a given serial number is highlighted by hovering over the atom in the Atom Selection Tree single selection mode only Mouse over highlight If the number of displayed structures is not too large hovering over atoms in the render window will give information about their element symbol name serial number residue residue identifier and the structure identifier 6 3 4 Coloring Atoms can be colored based on whether they are selected or not Both colors can be adjusted Also highlight color can be adjusted When a structure is loaded it is assigned a random bond color to help distinguish individ ual structures The bond color can also be adjusted 6 3 5 Saving Molecules can be rendered to a
10. he structure list The standard deviation of the RMSD values is computed and the structures are grouped in four groups based on the distance from the overall mean value less than c less than 20 less than 3c and greater than 30 Structures removed in the statistics tab will be removed from the structure list in the superimposing tab as well 6 USER INTERFACE 2 lali 1162 to lali 1161 1gug 11204 alignee lali it63 tn lalr 1161 to lele 4218 to lali 1161 1 1 1161 other lgug 11126 to lali 1161 lgug 11165 te lali 1161 original alianee sequence 140911204 to lali 1161 AN N S S nj liad 4526 to lali 1161 Original ather sequence Indk 5608 to lali 1161 ee ln8k 5667 to lali 1161 135 Irmd 913 to lali 1161 Shia lali 1161 to lt average gt II HEH lali 1162 to lt average gt Sorted alignee sequence lali 1163 to lt averager Tn SS NNI 1 4218 to lt average gt Sorted other sequence lguq 11126 to average ien 5 5 N Nj lgug 11165 to lt average gt Original Pairing lgug 11204 to lt average gt 119592 636 19214 673 18761 489 18736 5237 111204 1161 liad 4526 to lt average gt Pairing ing k 5 ENS to aver ager 118592 636 1971 4 57318751 433418738 523 11 1204 1 161 H rm ln8k 5667 to lt averager lrmd 913 to lt average gt Summary Predicted RMSD 0 15962 Computed RMSD 0 15962 Rotation type Proper Rotation matrix 111 00000 D 00123 0 000115 10 00123 7 00000 1 00006 0 00011
11. inder CMD has a very simple command line interface working as following sitebinder cmd exe sl pdb s2 pdb si pdb atoms in each structure are implicitly selected the prefix conventions discussed above are ignored If the loaded structures can be superimposed the output is a number representing RMSD otherwise an error is reported 6 2 SiteBinder Graphical User Interface Figure 1 1 shows the SiteBinder GUI with sev eral structures loaded and selected The structure of the main window is split into four basic parts Rendering Window Shows the render of currently selected structures Advanced fea tures such as highlighting parts of a molecule are supported Superimposing Tab Structure List Contains a list of structures and basic information about them such as which residues they contain Atom Selection Tree A tree view allowing the user to select atoms in structures RMSD Panel Provides the value of the RMSD of the currently selected structures assuming they were superimposed and the error of the alignment if available located under the Structure List and Atom Selection Tree Statistics Tab Basic statistical analysis of the obtained values of RMSD 6 USER INTERFACE 3 SiteBinder 1 1 0 2 1 Soy 1024x768 M H Save Image ii Reset Camera Display Dx Sticks Superimposing Statistics A 7 5 o i Superimpose Settings Log eo ID RMSD Residues F evSx2
12. ino acid Residue sequence number A unique integer identifier of the residue the atom is in Chain identifier Usually represents the ternary structure of the protein Position 3D coordinates of the atom Moreover SiteBinder supports a special naming convention to make working with large a number of structures easier e If a given file has the m_ prefix all atoms in the structure get automatically selected upon load e If there are files m_x pdb and ma_x pdb in the same directory structure x will load from the ma_x pdb file and atoms from m_x pdb will be selected 5 Output Specification By default the only output SiteBinder provides is a floating point number representing the resulting RMSD or two numbers if we consider the error of multiple alignment Nevertheless aligned structures can be exported to PDB files with these properties e an m_z pdb file is created for each structure and contains its selected atoms e an ma_x pdb file is created for each structure and contains all of its atoms e The order of atoms in all exported and aligned structures is the following First the selected atoms are stored 1st atom in structure x corresponds to the 1st atom in structure Non selected atoms are appended at the end of the file and sorted by their element symbol e Only ATOM and HETATM records are exported e Only the currently selected chain is exported 6 User Interface 6 1 SiteBinder CMD SiteB
13. lysis can be performed on the obtained data The re sults can be exported to a CSV file for further processing for example using Microsoft Excel Rendering Structures are rendered using Microsoft Direct3D Highlighting Various types of highlighting are supported to enable the user a more friendly manipulation of structures Exporting Results Superimposed structures can be exported in PDB format Also structures can be rendered to a PNG image 3 1 Versions Two major versions of the software are available SiteBinder An application with rich graphical user interface SiteBinder CMD A simple command line interface to SiteBinder Core 4 Input Specification SiteBinder supports input from the PDB file format however some restrictions apply e There can be only one structure contained in one file e Alternate locations of atoms are not supported e If a file contains more chains only one chain can be displayed and operated with at any given time In order for SiteBinder to work properly these columns have to be filled Atom serial number A unique integer identifier of the atom Atom name String representing atom name 1 6 USER INTERFACE 2 Element symbol Element symbol of the atom for example 5 Ca etc If element symbol is not filled part of the atom name record is used instead the first two characters of the name Residue name String representing the name of the residue the atom is in usually the name of an am
14. ns the add structure dialog Export Exports all selected structures Reload Reloads all structures Clear Removes all structures Superimpose Superimposes the selected structures Settings This feature is discussed in a separate section bellow Log Shows log Help Shows help About Shows about dialog 6 2 5 Settings The following settings can be adjusted Load Hydrogen Atoms If not checked hydrogen atoms are ignored Enable Chain Selection If checked only one chain of a structure can be active How ever it is possible to select this active chain Allow Reflection Enables disables the feature to look for improper rotations as well Enabling this feature sometimes provides better fits by reflecting the structure Nev ertheless in some cases the reflection transformation is not desired By default this feature is disabled Method Allows the user to select the method for the multiple alignment algorithm One slower running in quadratic time providing information about the quality of the alignment and another one faster running in linear time presenting only the value of RMS By default the basic version of the algorithm is selected Grouping Level Allows the user to manually override the grouping level to sometimes achieve better results There are three grouping levels 1 Residue Name Groups the atoms based on the information about residue names 2 Residue Groups the atoms based on the inform
15. ressing the right button and moving up or down zooms the structures 6 3 1 Display Types Two display types are supported All Displays all the atoms of the structure figure 1 10h Selected Displays only selected atoms figure 1 10b Selected atoms are displayed us ing a different color 6 USER INTERFACE Direct3D Settings Beck Buffer Format Depth Stencil Format D2458 Mutisample Type Waming Changing these setting might result in application crash FIGURE 1 9 Direct3D settings Highlighting see below ignores display type Therefore it is possible to see highlighted atoms even if they are not selected 6 3 2 Display Modes Two display modes are supported Balls Atoms are displayed as balls figure 1 11h Sticks Only bonds are displayed figure 1 11p a All b Selected FIGURE 1 10 Display types a Balls b Sticks FIGURE 1 11 Display modes 6 USER INTERFACE 9 6 3 3 Highlights A variety of highlight types figure 1 12 are supported by SiteBinder we 4 Ny 17 sv 2 Whole structure b Residue name Atom name N d Residue serial number Atom serial number f Mouse over FIGURE 1 12 Highlight types Whole structure The whole structure is highlighted by hovering over its ID in the struc ture list Furthermore there is an option to select a persistent highlight of a structure that also distinguishes the given structur
16. uperimposition oper ation Residues Residue names of the residues contained in the given structure String CYSx2 HISx2 means there are 2 CYS and 2 HIS residues in the given structure Selected Atoms Alphabetically ordered element symbols of selected atoms ID EMSD Residues Selected atoms Wrong Selection leh8 1265 N A CYSzz HISzZ ZM AN 25 lan 13 1 2 5014 H ZN 10 28 lZn 15 Modified 1 2 5011 CYS5xz HISxz zN zN 25 lZn 11 1 21 5012 ZN ZN 25 lZn 111 1 2 5013 H CY5x2 HISx2z zN ec ZN 25 lZn 11 Added lalj 1162 CYSxZz HISxZz ZNH No atoms selected lalj 1163 CYSxz HISxz ZNH atoms selected Superimposed RMSD 0 819 average A 0 446 CYSx2 HISx2 ZN 25 12 13 lele 1495 0_502 CYSzz 2 ZN eC AN 25 lzn 13 lee 1456 H 0 502 CYSx HISx 2H 4N 25 lzn 13 leh6 1274 1 003 CYSx2 HISx2 ZN 28 12 13 Previously Superimposed 1eh7 1234 N A CYSx2 HISx2 ZN 4N 25 12 13 l 2i 5015 I N A CYSx2 HISx2z ZzN 4N 25 lan 413 E 1 21 5016 I CYSx HISxE 2H 4N 25 lzn 13 1 21 5019 N A 2 2 2 AN 25 17 13 192a 2774 N A CYSx2 HISx2 ZN 6C 4N 25 12 13 iune 4530 N A CYSx2 HISx2 Z2N 6 4N 25 12 13 FIGURE 1 2 Structure list 6 USER
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