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MOLSOFT L.L.C.: ICM-BROWSER ICM-Browser provides a biologist or a chemist with direct access to the treasures of structural biology and protein families.It reads a variety of file formats directly from the database web-sites including: PDB, chemical, electron density maps, sequence and alignment files. ICM-Browser provides a rich professional moleculargraphics
MOLSOFT L.L.C.: WELCOME TO THE INTERACTIVE PDB FAST VIEWER Welcome to the Interactive PDB Fast Viewer at Molsoft, LLC. The Protein Data Bank (PDB) is an archive of experimentally determined 3-dimensional structures of biological macromolecules, serving a global community of researchers, educators, and students. The archives contain atomic coordinates, bibliographic citations, primary andsecondary
ICM USER'S GUIDE: FIND BIOISOSTERE Step 4: Results Table In this example we find tetrazole which is a classic isostere of carboxylic acid. The data in the columns represent: Mol is the query chemical with the bioisostere attached.; R1 is the bioisostere.; biosterDist Bioisoster ‘distance' is calculated on the basis of five terms, two are knowledge-based and three are physicochemical. They are also reflected by the ICM USER'S GUIDE: 2D LIGAND INTERACTION DIAGRAM To create a 2D interaction diagram between a ligand and receptor: Read into ICM a PDB file containing the ligand and receptor. For correct hydrogen bond assignment you will need to convert to an ICM object. Right click on the ligand and choose Tools/Ligand 2D Diagram. A dialog box will be displayed. Select the receptor object from the drop down ICM USER'S GUIDE: CALCULATE PROPERTIES Select the properties you wish to calculate using the 'tick' check boxes. Click OK and the properties will be added as new columns in the chemical table. Actions Button Helps with Selections. If you click on the drop down button labeled Actions you will see 3 selection options: Select All properties. ICM USER'S GUIDE: CONVERT TO ICM OBJECT To convert a PDB structure into an ICM object follow the steps shown below: Right click on the name of the protein you wish to convert in the ICM Workspace.; A dialog box will be displayed as shown below. ICM USER'S GUIDE: IDENTFY LIGAND POCKETS Selections can also be made from the plot by clicking and dragging around a point in the graph. To identify ligand binding pockets which are completely enclosed in the receptor: Click on the menu Tools/Analysis/Closed Cavities and a window as shown below will be displayed. A similar output to that generated by ICMPocketFinder willbe displayed.
MOLSOFT L.L.C.ABOUTPRODUCTSDOWNLOADSTECHNOLOGYSERVICESNEWS High quality molecular graphics. 3D molecules in Powerpoint and web. Sequence analysis and bioinformatics tools. Structure prediction and mutation analysis. Molecular modeling and simulations. Homology and loop modeling. Protein interaction and binding site analysis. Protein-protein docking. Small molecule docking. MOLSOFT L.L.C.: DRUG-LIKENESS AND MOLECULAR PROPERTY Drug-Likeness and molecular property prediction. High speed Molecular properties calculator can be licensed. from Molsoft for the local use in the batch mode. For more information mail us at info@molsoft.com. Draw the structure and click the button below. C. MOLSOFT L.L.C.: WELCOME TO THE INTERACTIVE 2D TO 3D ICM 2D to 3D converter convertion functionality allows construction of icm molecular objects from 2D drawing and creates optimized 3D structures using MMFF atom type assignment and force-field optimization. You can use this page to test convert your chemical structure and view it using our ActiveIcm viewer or iMolview app formobile devices. C.
MOLSOFT L.L.C.: ICM-BROWSER ICM-Browser provides a biologist or a chemist with direct access to the treasures of structural biology and protein families.It reads a variety of file formats directly from the database web-sites including: PDB, chemical, electron density maps, sequence and alignment files. ICM-Browser provides a rich professional moleculargraphics
MOLSOFT L.L.C.: WELCOME TO THE INTERACTIVE PDB FAST VIEWER Welcome to the Interactive PDB Fast Viewer at Molsoft, LLC. The Protein Data Bank (PDB) is an archive of experimentally determined 3-dimensional structures of biological macromolecules, serving a global community of researchers, educators, and students. The archives contain atomic coordinates, bibliographic citations, primary andsecondary
ICM USER'S GUIDE: FIND BIOISOSTERE Step 4: Results Table In this example we find tetrazole which is a classic isostere of carboxylic acid. The data in the columns represent: Mol is the query chemical with the bioisostere attached.; R1 is the bioisostere.; biosterDist Bioisoster ‘distance' is calculated on the basis of five terms, two are knowledge-based and three are physicochemical. They are also reflected by the ICM USER'S GUIDE: 2D LIGAND INTERACTION DIAGRAM To create a 2D interaction diagram between a ligand and receptor: Read into ICM a PDB file containing the ligand and receptor. For correct hydrogen bond assignment you will need to convert to an ICM object. Right click on the ligand and choose Tools/Ligand 2D Diagram. A dialog box will be displayed. Select the receptor object from the drop down ICM USER'S GUIDE: CALCULATE PROPERTIES Select the properties you wish to calculate using the 'tick' check boxes. Click OK and the properties will be added as new columns in the chemical table. Actions Button Helps with Selections. If you click on the drop down button labeled Actions you will see 3 selection options: Select All properties. ICM USER'S GUIDE: CONVERT TO ICM OBJECT To convert a PDB structure into an ICM object follow the steps shown below: Right click on the name of the protein you wish to convert in the ICM Workspace.; A dialog box will be displayed as shown below. ICM USER'S GUIDE: IDENTFY LIGAND POCKETS Selections can also be made from the plot by clicking and dragging around a point in the graph. To identify ligand binding pockets which are completely enclosed in the receptor: Click on the menu Tools/Analysis/Closed Cavities and a window as shown below will be displayed. A similar output to that generated by ICMPocketFinder willbe displayed.
MOLSOFT L.L.C.: ICMJS IcmJS is not just a molecule viewer you can: * Display chemical 3D interactive spreadsheets for viewing docking results * Interactive plots and histograms * Sequence alignments linked to 3D structure * 2D ligand diagrams (just added for version 1.2.4) This makes it a ICM USER'S GUIDE: FIND BIOISOSTERE Step 4: Results Table In this example we find tetrazole which is a classic isostere of carboxylic acid. The data in the columns represent: Mol is the query chemical with the bioisostere attached.; R1 is the bioisostere.; biosterDist Bioisoster ‘distance' is calculated on the basis of five terms, two are knowledge-based and three are physicochemical. They are also reflected by the ICM USER'S GUIDE: HOMOLOGY MODELING The items you need to begin making an Homology Model are: A template structure from the PDB converted into an ICM object.; Extract the sequence of the template structure from the PDB file.; The sequence of your query molecule (e.g. from UniProt or FASTA).; An alignment (see alignment section) of your query sequence against the template sequence from the PDB. ICM USER'S GUIDE: VIRTUAL LIGAND SCREENING 13.1.1 Virtual Ligand Screening. Virtual Ligand Screening (VLS) in ICM is performed by docking a database of ligands to a receptor structure followed by an evaluation of the docked conformation with a binding-score function. Best-scoring ligands are then stored in the multiple icm-object file. The set-up of the VLS process is largelyidentical
MOLSOFT L.L.C.: INSTALLATION OF FLEXLM SERVER FOR WINDOWS Go to run 3. enter cmd.exe. 4. enter cd C:\flexlm and then enter the following syntax: debug_log_path is the full path to the debug log file Prepending debug_log_path with the + character appends logging entries. Configure (or ask your system manager to do this) your localflexlm server to
ICM USER'S GUIDE: PROTEIN STRUCTURE TUTORIALS Background When preparing a PDB for analysis (eg docking or modeling) it is important to check the reported occupancies and b-factors. The occupancy is a fraction of atimic density at a given center. If there are two eqally occupied conformers both will have an occupancy of 0.5-
ICM USER'S GUIDE: SMALL MOLECULE DOCKING ICM ligand docking procedure performs docking of the fully flexible small-molecule ligand to a known receptor 3D structure. The goal of the flexible docking calculation is prediction of correct binding geometry for each binder. ICM stochastic global optimization algorithm attempts to find the global minimum of the energy function thatincludes
ICM USER'S GUIDE: EVALUATE LIGAND SCORE AND STRAIN Video | . After you have edited a ligand and re-docked or minimized it you can evaluate the Score and Strain for the ligand. Ideally a good modification to your ligand will lower the score. About the Score. VlsScore = the ICM-VLS score used for ligand screening. ICM USER'S GUIDE: INDUCED FIT (FLEXIBILITY) DOCKING TUTORIALS Background. Here we will demonstrate multiple receptor conformation docking in ICM using Aldose Reductase as an example. Aldose Reductase has a flexible loop in the ligand binding pocket vicinity which enables a variety of inhibitors to bind therefore in order to identify these ligands via docking it is necessary to sample the conformations of this loop and dock to an ensemble of structures. ICM USER'S GUIDE: DOCK OR MINIMIZE LIGAND Setup the ligand and receptor. Click on the dock or minimize button (see image above). Check the Score and Strain in the top right panel. If you dock a chemical spreadsheet will be displayed with the docking results. Use the check box in column 'L' to display the docked ligand or double click to load the ligand into the ligand editor. MOLSOFT L.L.C.ABOUTPRODUCTSDOWNLOADSTECHNOLOGYSERVICESNEWS High quality molecular graphics. 3D molecules in Powerpoint and web. Sequence analysis and bioinformatics tools. Structure prediction and mutation analysis. Molecular modeling and simulations. Homology and loop modeling. Protein interaction and binding site analysis. Protein-protein docking. Small molecule docking. MOLSOFT L.L.C.: DRUG-LIKENESS AND MOLECULAR PROPERTY Drug-Likeness and molecular property prediction. High speed Molecular properties calculator can be licensed. from Molsoft for the local use in the batch mode. For more information mail us at info@molsoft.com. Draw the structure and click the button below. C. ICM USER'S GUIDE: CALCULATE PROPERTIES Select the properties you wish to calculate using the 'tick' check boxes. Click OK and the properties will be added as new columns in the chemical table. Actions Button Helps with Selections. If you click on the drop down button labeled Actions you will see 3 selection options: Select All properties. ICM USER'S GUIDE: FIND BIOISOSTERE Step 4: Results Table In this example we find tetrazole which is a classic isostere of carboxylic acid. The data in the columns represent: Mol is the query chemical with the bioisostere attached.; R1 is the bioisostere.; biosterDist Bioisoster ‘distance' is calculated on the basis of five terms, two are knowledge-based and three are physicochemical. They are also reflected by the ICM USER'S GUIDE: DISPLAY OPTIONS 15.3.3 Display Hydrogen Atoms. To display hydrogen atoms: Single click on the hydrogen atom display button will toggle the display between: no hydrogens, polar hydrogens, all hydrogens, all hydrogens in ligand and polar hydrgens in receptor. Click and hold on the button and you can choose the option rather than using the toggle. ICM USER'S GUIDE: 2D LIGAND INTERACTION DIAGRAM To create a 2D interaction diagram between a ligand and receptor: Read into ICM a PDB file containing the ligand and receptor. For correct hydrogen bond assignment you will need to convert to an ICM object. Right click on the ligand and choose Tools/Ligand 2D Diagram. A dialog box will be displayed. Select the receptor object from the drop down ICM USER'S GUIDE: CONVERT TO ICM OBJECT To convert a PDB structure into an ICM object follow the steps shown below: Right click on the name of the protein you wish to convert in the ICM Workspace.; A dialog box will be displayed as shown below. ICM USER'S GUIDE: SMALL MOLECULE DOCKING ICM ligand docking procedure performs docking of the fully flexible small-molecule ligand to a known receptor 3D structure. The goal of the flexible docking calculation is prediction of correct binding geometry for each binder. ICM stochastic global optimization algorithm attempts to find the global minimum of the energy function thatincludes
ICM USER'S GUIDE: VIRTUAL LIGAND SCREENING 13.1.1 Virtual Ligand Screening. Virtual Ligand Screening (VLS) in ICM is performed by docking a database of ligands to a receptor structure followed by an evaluation of the docked conformation with a binding-score function. Best-scoring ligands are then stored in the multiple icm-object file. The set-up of the VLS process is largelyidentical
ICM USER'S GUIDE: IDENTFY LIGAND POCKETS Selections can also be made from the plot by clicking and dragging around a point in the graph. To identify ligand binding pockets which are completely enclosed in the receptor: Click on the menu Tools/Analysis/Closed Cavities and a window as shown below will be displayed. A similar output to that generated by ICMPocketFinder willbe displayed.
MOLSOFT L.L.C.ABOUTPRODUCTSDOWNLOADSTECHNOLOGYSERVICESNEWS High quality molecular graphics. 3D molecules in Powerpoint and web. Sequence analysis and bioinformatics tools. Structure prediction and mutation analysis. Molecular modeling and simulations. Homology and loop modeling. Protein interaction and binding site analysis. Protein-protein docking. Small molecule docking. MOLSOFT L.L.C.: DRUG-LIKENESS AND MOLECULAR PROPERTY Drug-Likeness and molecular property prediction. High speed Molecular properties calculator can be licensed. from Molsoft for the local use in the batch mode. For more information mail us at info@molsoft.com. Draw the structure and click the button below. C. ICM USER'S GUIDE: CALCULATE PROPERTIES Select the properties you wish to calculate using the 'tick' check boxes. Click OK and the properties will be added as new columns in the chemical table. Actions Button Helps with Selections. If you click on the drop down button labeled Actions you will see 3 selection options: Select All properties. ICM USER'S GUIDE: FIND BIOISOSTERE Step 4: Results Table In this example we find tetrazole which is a classic isostere of carboxylic acid. The data in the columns represent: Mol is the query chemical with the bioisostere attached.; R1 is the bioisostere.; biosterDist Bioisoster ‘distance' is calculated on the basis of five terms, two are knowledge-based and three are physicochemical. They are also reflected by the ICM USER'S GUIDE: DISPLAY OPTIONS 15.3.3 Display Hydrogen Atoms. To display hydrogen atoms: Single click on the hydrogen atom display button will toggle the display between: no hydrogens, polar hydrogens, all hydrogens, all hydrogens in ligand and polar hydrgens in receptor. Click and hold on the button and you can choose the option rather than using the toggle. ICM USER'S GUIDE: 2D LIGAND INTERACTION DIAGRAM To create a 2D interaction diagram between a ligand and receptor: Read into ICM a PDB file containing the ligand and receptor. For correct hydrogen bond assignment you will need to convert to an ICM object. Right click on the ligand and choose Tools/Ligand 2D Diagram. A dialog box will be displayed. Select the receptor object from the drop down ICM USER'S GUIDE: CONVERT TO ICM OBJECT To convert a PDB structure into an ICM object follow the steps shown below: Right click on the name of the protein you wish to convert in the ICM Workspace.; A dialog box will be displayed as shown below. ICM USER'S GUIDE: SMALL MOLECULE DOCKING ICM ligand docking procedure performs docking of the fully flexible small-molecule ligand to a known receptor 3D structure. The goal of the flexible docking calculation is prediction of correct binding geometry for each binder. ICM stochastic global optimization algorithm attempts to find the global minimum of the energy function thatincludes
ICM USER'S GUIDE: VIRTUAL LIGAND SCREENING 13.1.1 Virtual Ligand Screening. Virtual Ligand Screening (VLS) in ICM is performed by docking a database of ligands to a receptor structure followed by an evaluation of the docked conformation with a binding-score function. Best-scoring ligands are then stored in the multiple icm-object file. The set-up of the VLS process is largelyidentical
ICM USER'S GUIDE: IDENTFY LIGAND POCKETS Selections can also be made from the plot by clicking and dragging around a point in the graph. To identify ligand binding pockets which are completely enclosed in the receptor: Click on the menu Tools/Analysis/Closed Cavities and a window as shown below will be displayed. A similar output to that generated by ICMPocketFinder willbe displayed.
ICM USER'S GUIDE: FIND BIOISOSTERE Step 4: Results Table In this example we find tetrazole which is a classic isostere of carboxylic acid. The data in the columns represent: Mol is the query chemical with the bioisostere attached.; R1 is the bioisostere.; biosterDist Bioisoster ‘distance' is calculated on the basis of five terms, two are knowledge-based and three are physicochemical. They are also reflected by the MOLSOFT L.L.C.: WELCOME TO THE INTERACTIVE 2D TO 3D ICM 2D to 3D converter convertion functionality allows construction of icm molecular objects from 2D drawing and creates optimized 3D structures using MMFF atom type assignment and force-field optimization. You can use this page to test convert your chemical structure and view it using our ActiveIcm viewer or iMolview app formobile devices. C.
MOLSOFT L.L.C.: WELCOME TO THE INTERACTIVE PDB FAST VIEWER Welcome to the Interactive PDB Fast Viewer at Molsoft, LLC. The Protein Data Bank (PDB) is an archive of experimentally determined 3-dimensional structures of biological macromolecules, serving a global community of researchers, educators, and students. The archives contain atomic coordinates, bibliographic citations, primary andsecondary
ICM USER'S GUIDE: HOMOLOGY MODELING The items you need to begin making an Homology Model are: A template structure from the PDB converted into an ICM object.; Extract the sequence of the template structure from the PDB file.; The sequence of your query molecule (e.g. from UniProt or FASTA).; An alignment (see alignment section) of your query sequence against the template sequence from the PDB. ICM USER'S GUIDE: DISPLAY OPTIONS If you are docking to Atomic Property Fields (APF - 3D Pharmacophore) as described here you can visualize the APF fields. Click on the button shown below and choose Visualize APF. The fields will be displayed and they can be toggled on and off in the ICM workspace - right click in the display box in the ICM workspace to change the surface display (e.g from mesh to transparent surface). MOLSOFT L.L.C.: ICMJS IcmJS is not just a molecule viewer you can: * Display chemical 3D interactive spreadsheets for viewing docking results * Interactive plots and histograms * Sequence alignments linked to 3D structure * 2D ligand diagrams (just added for version 1.2.4) This makes it a ICM USER'S GUIDE: SMALL MOLECULE DOCKING ICM ligand docking procedure performs docking of the fully flexible small-molecule ligand to a known receptor 3D structure. The goal of the flexible docking calculation is prediction of correct binding geometry for each binder. ICM stochastic global optimization algorithm attempts to find the global minimum of the energy function thatincludes
ICM USER'S GUIDE: PROTEIN STRUCTURE TUTORIALS Background When preparing a PDB for analysis (eg docking or modeling) it is important to check the reported occupancies and b-factors. The occupancy is a fraction of atimic density at a given center. If there are two eqally occupied conformers both will have an occupancy of 0.5-
ICM USER'S GUIDE: EVALUATE LIGAND SCORE AND STRAIN Video | . After you have edited a ligand and re-docked or minimized it you can evaluate the Score and Strain for the ligand. Ideally a good modification to your ligand will lower the score. About the Score. VlsScore = the ICM-VLS score used for ligand screening. ICM USER'S GUIDE: FAQ INSTALLATION AND TROUBLESHOOTING 21.1.17 Set ICM to remember the server name on startup in Windows. In Windows sometimes the license server name is not remembered and you have to enter the server name each time you open ICM. To fix this: Right click on the ICM-Pro icon and choose "Run as Administrator". Enter the server name. MOLSOFT L.L.C.ABOUTPRODUCTSDOWNLOADSTECHNOLOGYSERVICESNEWS High quality molecular graphics. 3D molecules in Powerpoint and web. Sequence analysis and bioinformatics tools. Structure prediction and mutation analysis. Molecular modeling and simulations. Homology and loop modeling. Protein interaction and binding site analysis. Protein-protein docking. Small molecule docking. MOLSOFT L.L.C.: DRUG-LIKENESS AND MOLECULAR PROPERTY Drug-Likeness and molecular property prediction. High speed Molecular properties calculator can be licensed. from Molsoft for the local use in the batch mode. For more information mail us at info@molsoft.com. Draw the structure and click the button below. C. ICM USER'S GUIDE: FIND BIOISOSTERE Step 4: Results Table In this example we find tetrazole which is a classic isostere of carboxylic acid. The data in the columns represent: Mol is the query chemical with the bioisostere attached.; R1 is the bioisostere.; biosterDist Bioisoster ‘distance' is calculated on the basis of five terms, two are knowledge-based and three are physicochemical. They are also reflected by the ICM USER'S GUIDE: CALCULATE PROPERTIES Select the properties you wish to calculate using the 'tick' check boxes. Click OK and the properties will be added as new columns in the chemical table. Actions Button Helps with Selections. If you click on the drop down button labeled Actions you will see 3 selection options: Select All properties. ICM USER'S GUIDE: DISPLAY OPTIONS 15.3.3 Display Hydrogen Atoms. To display hydrogen atoms: Single click on the hydrogen atom display button will toggle the display between: no hydrogens, polar hydrogens, all hydrogens, all hydrogens in ligand and polar hydrgens in receptor. Click and hold on the button and you can choose the option rather than using the toggle. ICM USER'S GUIDE: CONVERT TO ICM OBJECT To convert a PDB structure into an ICM object follow the steps shown below: Right click on the name of the protein you wish to convert in the ICM Workspace.; A dialog box will be displayed as shown below. ICM USER'S GUIDE: 2D LIGAND INTERACTION DIAGRAM To create a 2D interaction diagram between a ligand and receptor: Read into ICM a PDB file containing the ligand and receptor. For correct hydrogen bond assignment you will need to convert to an ICM object. Right click on the ligand and choose Tools/Ligand 2D Diagram. A dialog box will be displayed. Select the receptor object from the drop down ICM USER'S GUIDE: SMALL MOLECULE DOCKING ICM ligand docking procedure performs docking of the fully flexible small-molecule ligand to a known receptor 3D structure. The goal of the flexible docking calculation is prediction of correct binding geometry for each binder. ICM stochastic global optimization algorithm attempts to find the global minimum of the energy function thatincludes
ICM USER'S GUIDE: VIRTUAL LIGAND SCREENING 13.1.1 Virtual Ligand Screening. Virtual Ligand Screening (VLS) in ICM is performed by docking a database of ligands to a receptor structure followed by an evaluation of the docked conformation with a binding-score function. Best-scoring ligands are then stored in the multiple icm-object file. The set-up of the VLS process is largelyidentical
ICM USER'S GUIDE: IDENTFY LIGAND POCKETS Selections can also be made from the plot by clicking and dragging around a point in the graph. To identify ligand binding pockets which are completely enclosed in the receptor: Click on the menu Tools/Analysis/Closed Cavities and a window as shown below will be displayed. A similar output to that generated by ICMPocketFinder willbe displayed.
MOLSOFT L.L.C.ABOUTPRODUCTSDOWNLOADSTECHNOLOGYSERVICESNEWS High quality molecular graphics. 3D molecules in Powerpoint and web. Sequence analysis and bioinformatics tools. Structure prediction and mutation analysis. Molecular modeling and simulations. Homology and loop modeling. Protein interaction and binding site analysis. Protein-protein docking. Small molecule docking. MOLSOFT L.L.C.: DRUG-LIKENESS AND MOLECULAR PROPERTY Drug-Likeness and molecular property prediction. High speed Molecular properties calculator can be licensed. from Molsoft for the local use in the batch mode. For more information mail us at info@molsoft.com. Draw the structure and click the button below. C. ICM USER'S GUIDE: FIND BIOISOSTERE Step 4: Results Table In this example we find tetrazole which is a classic isostere of carboxylic acid. The data in the columns represent: Mol is the query chemical with the bioisostere attached.; R1 is the bioisostere.; biosterDist Bioisoster ‘distance' is calculated on the basis of five terms, two are knowledge-based and three are physicochemical. They are also reflected by the ICM USER'S GUIDE: CALCULATE PROPERTIES Select the properties you wish to calculate using the 'tick' check boxes. Click OK and the properties will be added as new columns in the chemical table. Actions Button Helps with Selections. If you click on the drop down button labeled Actions you will see 3 selection options: Select All properties. ICM USER'S GUIDE: DISPLAY OPTIONS 15.3.3 Display Hydrogen Atoms. To display hydrogen atoms: Single click on the hydrogen atom display button will toggle the display between: no hydrogens, polar hydrogens, all hydrogens, all hydrogens in ligand and polar hydrgens in receptor. Click and hold on the button and you can choose the option rather than using the toggle. ICM USER'S GUIDE: CONVERT TO ICM OBJECT To convert a PDB structure into an ICM object follow the steps shown below: Right click on the name of the protein you wish to convert in the ICM Workspace.; A dialog box will be displayed as shown below. ICM USER'S GUIDE: 2D LIGAND INTERACTION DIAGRAM To create a 2D interaction diagram between a ligand and receptor: Read into ICM a PDB file containing the ligand and receptor. For correct hydrogen bond assignment you will need to convert to an ICM object. Right click on the ligand and choose Tools/Ligand 2D Diagram. A dialog box will be displayed. Select the receptor object from the drop down ICM USER'S GUIDE: SMALL MOLECULE DOCKING ICM ligand docking procedure performs docking of the fully flexible small-molecule ligand to a known receptor 3D structure. The goal of the flexible docking calculation is prediction of correct binding geometry for each binder. ICM stochastic global optimization algorithm attempts to find the global minimum of the energy function thatincludes
ICM USER'S GUIDE: VIRTUAL LIGAND SCREENING 13.1.1 Virtual Ligand Screening. Virtual Ligand Screening (VLS) in ICM is performed by docking a database of ligands to a receptor structure followed by an evaluation of the docked conformation with a binding-score function. Best-scoring ligands are then stored in the multiple icm-object file. The set-up of the VLS process is largelyidentical
ICM USER'S GUIDE: IDENTFY LIGAND POCKETS Selections can also be made from the plot by clicking and dragging around a point in the graph. To identify ligand binding pockets which are completely enclosed in the receptor: Click on the menu Tools/Analysis/Closed Cavities and a window as shown below will be displayed. A similar output to that generated by ICMPocketFinder willbe displayed.
ICM USER'S GUIDE: FIND BIOISOSTERE Step 4: Results Table In this example we find tetrazole which is a classic isostere of carboxylic acid. The data in the columns represent: Mol is the query chemical with the bioisostere attached.; R1 is the bioisostere.; biosterDist Bioisoster ‘distance' is calculated on the basis of five terms, two are knowledge-based and three are physicochemical. They are also reflected by the MOLSOFT L.L.C.: WELCOME TO THE INTERACTIVE 2D TO 3D ICM 2D to 3D converter convertion functionality allows construction of icm molecular objects from 2D drawing and creates optimized 3D structures using MMFF atom type assignment and force-field optimization. You can use this page to test convert your chemical structure and view it using our ActiveIcm viewer or iMolview app formobile devices. C.
MOLSOFT L.L.C.: WELCOME TO THE INTERACTIVE PDB FAST VIEWER Welcome to the Interactive PDB Fast Viewer at Molsoft, LLC. The Protein Data Bank (PDB) is an archive of experimentally determined 3-dimensional structures of biological macromolecules, serving a global community of researchers, educators, and students. The archives contain atomic coordinates, bibliographic citations, primary andsecondary
MOLSOFT L.L.C.: ICMJS IcmJS is not just a molecule viewer you can: * Display chemical 3D interactive spreadsheets for viewing docking results * Interactive plots and histograms * Sequence alignments linked to 3D structure * 2D ligand diagrams (just added for version 1.2.4) This makes it a ICM USER'S GUIDE: HOMOLOGY MODELING The items you need to begin making an Homology Model are: A template structure from the PDB converted into an ICM object.; Extract the sequence of the template structure from the PDB file.; The sequence of your query molecule (e.g. from UniProt or FASTA).; An alignment (see alignment section) of your query sequence against the template sequence from the PDB. ICM USER'S GUIDE: INDUCED FIT (FLEXIBLE) DOCKING Before you can start multiple receptor docking all your structures need to be in a stack. Step 1: Read in the conformations of the receptor you would like to dock to. Convert the Main Object to an ICM Object. Step 2: Select MolMechanics/Impose Conformation. Step ICM USER'S GUIDE: SMALL MOLECULE DOCKING ICM ligand docking procedure performs docking of the fully flexible small-molecule ligand to a known receptor 3D structure. The goal of the flexible docking calculation is prediction of correct binding geometry for each binder. ICM stochastic global optimization algorithm attempts to find the global minimum of the energy function thatincludes
ICM USER'S GUIDE: VIRTUAL LIGAND SCREENING 13.1.1 Virtual Ligand Screening. Virtual Ligand Screening (VLS) in ICM is performed by docking a database of ligands to a receptor structure followed by an evaluation of the docked conformation with a binding-score function. Best-scoring ligands are then stored in the multiple icm-object file. The set-up of the VLS process is largelyidentical
ICM USER'S GUIDE: PROTEIN STRUCTURE TUTORIALS Background When preparing a PDB for analysis (eg docking or modeling) it is important to check the reported occupancies and b-factors. The occupancy is a fraction of atimic density at a given center. If there are two eqally occupied conformers both will have an occupancy of 0.5-
ICM USER'S GUIDE: EVALUATE LIGAND SCORE AND STRAIN Video | . After you have edited a ligand and re-docked or minimized it you can evaluate the Score and Strain for the ligand. Ideally a good modification to your ligand will lower the score. About the Score. VlsScore = the ICM-VLS score used for ligand screening. MOLSOFT L.L.C.ABOUTPRODUCTSDOWNLOADSTECHNOLOGYSERVICESNEWSMOLSOFT ICM BROWSERMOLSOFT BROWSERMOLSOFT ICM PROMOLSOFT LLCMOLSOFT CALCULATORDOWNLOAD COMPUTER SOFTWARE FOR FREE ICM-Browser-Pro. A high quality visualizer and annotator for three dimensional molecular structures, sequences, and biological data. MOLSOFT L.L.C.: DRUG-LIKENESS AND MOLECULAR PROPERTYMOLSOFT BROWSERMOLSOFT ICM BROWSERMOLSOFT CALCULATORMOLSOFT ICM PRO CRACK High speed Molecular properties calculator can be licensed from Molsoft for the local use in the batch mode. For more information mail us at info@molsoft.com MOLSOFT L.L.C.: WELCOME TO THE INTERACTIVE PDB FAST VIEWERHOW TO OPEN PDB FILEPDB VIEWER ONLINEPDB FILE READER FREE DOWNLOADWHAT ARE PDB FILESPROTEIN PDBPDB BANK The Protein Data Bank (PDB) is an archive of experimentally determined 3-dimensional structures of biological macromolecules, serving a global community of researchers, educators, and students. MOLSOFT L.L.C.: ICMJS ICM USER'S GUIDE: CALCULATE PROPERTIES The ToxScore gives a prediction for how reactive or toxic a chemical is.. How the ToxScore is Calculated Around 1000 SMARTS strings associated with toxicity/reactivity were collected from various sources. They were assigned demerit score based on their perceived toxicity and frequency of ICM USER'S GUIDE: CONVERT TO ICM OBJECT To convert a PDB structure into an ICM object follow the steps shown below: Right click on the name of the protein you wish to convert in the ICM Workspace.; A dialog box will be displayed as shown below. ICM USER'S GUIDE: LOOP MODELING Other resources: Tutorial Background Building an accurate model of a loop is very tough. However with small loops ICM has been very succesful. ICM was used to design two new 7 residue loops and in both cases the designs were successful. ICM USER'S GUIDE: 2D LIGAND INTERACTION DIAGRAM To create a 2D interaction diagram between a ligand and receptor: Read into ICM a PDB file containing the ligand and receptor. For correct hydrogen bond assignment you will need to convert to an ICM object.; Right click on the ligand and choose Tools/Ligand 2D Diagram. ICM USER'S GUIDE: DOCK OR MINIMIZE LIGAND How to change the size of the docking region: The purple box represents the region in which the energy maps are generated. If you want to change the size of this region you can do so by displaying the box (go to Advanced menu) and clicking and dragging on the corners ofthe puprle box.
ICM USER'S GUIDE: MEASURE DISTANCES NOTE: Distances can be displayed and undisplayed in the 3D labesl section of the ICM Worskapce (left hand side of graphical user interface). You can change the color of a distance label by right clicking on it in the ICM Workspace. You can alse export the distanceto a table.
MOLSOFT L.L.C.ABOUTPRODUCTSDOWNLOADSTECHNOLOGYSERVICESNEWSMOLSOFT ICM BROWSERMOLSOFT BROWSERMOLSOFT ICM PROMOLSOFT LLCMOLSOFT CALCULATORDOWNLOAD COMPUTER SOFTWARE FOR FREE ICM-Browser-Pro. A high quality visualizer and annotator for three dimensional molecular structures, sequences, and biological data. MOLSOFT L.L.C.: DRUG-LIKENESS AND MOLECULAR PROPERTYMOLSOFT BROWSERMOLSOFT ICM BROWSERMOLSOFT CALCULATORMOLSOFT ICM PRO CRACK High speed Molecular properties calculator can be licensed from Molsoft for the local use in the batch mode. For more information mail us at info@molsoft.com MOLSOFT L.L.C.: WELCOME TO THE INTERACTIVE PDB FAST VIEWERHOW TO OPEN PDB FILEPDB VIEWER ONLINEPDB FILE READER FREE DOWNLOADWHAT ARE PDB FILESPROTEIN PDBPDB BANK The Protein Data Bank (PDB) is an archive of experimentally determined 3-dimensional structures of biological macromolecules, serving a global community of researchers, educators, and students. MOLSOFT L.L.C.: ICMJS ICM USER'S GUIDE: CALCULATE PROPERTIES The ToxScore gives a prediction for how reactive or toxic a chemical is.. How the ToxScore is Calculated Around 1000 SMARTS strings associated with toxicity/reactivity were collected from various sources. They were assigned demerit score based on their perceived toxicity and frequency of ICM USER'S GUIDE: CONVERT TO ICM OBJECT To convert a PDB structure into an ICM object follow the steps shown below: Right click on the name of the protein you wish to convert in the ICM Workspace.; A dialog box will be displayed as shown below. ICM USER'S GUIDE: LOOP MODELING Other resources: Tutorial Background Building an accurate model of a loop is very tough. However with small loops ICM has been very succesful. ICM was used to design two new 7 residue loops and in both cases the designs were successful. ICM USER'S GUIDE: 2D LIGAND INTERACTION DIAGRAM To create a 2D interaction diagram between a ligand and receptor: Read into ICM a PDB file containing the ligand and receptor. For correct hydrogen bond assignment you will need to convert to an ICM object.; Right click on the ligand and choose Tools/Ligand 2D Diagram. ICM USER'S GUIDE: DOCK OR MINIMIZE LIGAND How to change the size of the docking region: The purple box represents the region in which the energy maps are generated. If you want to change the size of this region you can do so by displaying the box (go to Advanced menu) and clicking and dragging on the corners ofthe puprle box.
ICM USER'S GUIDE: MEASURE DISTANCES NOTE: Distances can be displayed and undisplayed in the 3D labesl section of the ICM Worskapce (left hand side of graphical user interface). You can change the color of a distance label by right clicking on it in the ICM Workspace. You can alse export the distanceto a table.
MOLSOFT L.L.C.: WELCOME TO THE INTERACTIVE 2D TO 3D ICM 2D to 3D converter convertion functionality allows construction of icm molecular objects from 2D drawing and creates optimized 3D structures using MMFF atom ICM USER'S GUIDE: FIND BIOISOSTERE Step 4: Results Table In this example we find tetrazole which is a classic isostere of carboxylic acid. The data in the columns represent: Mol is the query chemical with the bioisostere attached.; R1 is the bioisostere.; biosterDist Bioisoster ‘distance' is calculated on the basis of five terms, two are knowledge-based and three are physicochemical. They are also reflected by the ICM USER'S GUIDE: HOMOLOGY MODELING The items you need to begin making an Homology Model are: A template structure from the PDB converted into an ICM object.; Extract the sequence of the template structure from the PDB file.; The sequence of your query molecule (e.g. from UniProt or FASTA).; An alignment (see alignment section) of your query sequence against the template sequence from the PDB. ICM USER'S GUIDE: DISPLAY OPTIONS If you are docking to Atomic Property Fields (APF - 3D Pharmacophore) as described here you can visualize the APF fields. Click on the button shown below and choose Visualize APF. The fields will be displayed and they can be toggled on and off in the ICM workspace - right click in the display box in the ICM workspace to change the surface display (e.g from mesh to transparent surface). MOLSOFT L.L.C.: ICM-REBEL ELECTROSTATICS Use ICM-REBEL to calculate the accurate electrostatic potential of a molecule using boundary element algorithm, and generate a 3D surface skin model colored by potential.. ICM-REBEL: The ICM-REBEL module allows to solve the Poisson equation for a molecule without a grid and with exact positions of electric charges. REBEL is a new powerful implementation of the boundary element method with ICM USER'S GUIDE: VIRTUAL LIGAND SCREENING Before VLS jobs can be run make sure you follow the instructions in the manual entitled Small Molecule Docking from docking project setup menu to the calculate maps menu.Select the "From indexed database", "From MolCart" or "From File: SDF/Mol2" option in the Setup Batch Ligand.Docking setup can be scripted see the terminal output from the GUI options to view the commands. MOLSOFT L.L.C.: PROTEIN-PROTEIN DOCKING Click to enlarge image. ICM-Pro contains a well validated and successful protein-protein docking algorithm. ICM-Pro also contains an algorithm to predict protein-protein docking interaction sites. MOLSOFT L.L.C.: CRYSTALLOGRAPHIC ANALYSIS TOOLS Click to enlarge image. Display crystallographic cell .The crystal structure of a protein is often discussed in terms of its unit cell. The unit cell is a box containing one or more motifs, a MOLSOFT L.L.C.: DEVELOPMENT OF SUCCESSFUL METHODS FOR In the last few years there have been a number of success stories published describing methods for incorporating induced fit in ligand docking using ICM-Pro. ICM USER'S GUIDE: MAKE A MOVIE FROM A SET OF SLIDES Please see the movie chapter on how to make a movie from a set ofslides.
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