Svl file

File problems can be divided into the following:. Operating systems 1 0 0 0 0 0. The file is empty or incomplete. The SVL file may be unusually small compared to the original file. This is most often caused by a problem while downloading the SVL file.

The only repair option is to download the file again. The SVL file is infected with malware. The most common cause here is computer viruses. A virus scan using an up-to-date antivirus program should fix the problem.

If this is not possible, you can use the online scanner. For the best results, we will scan the entire operating system, not just our SVL file. Sometimes virus-infected SVL files cannot be recovered, so make a backup in advance. The file is an older version. A typical compatibility error - the program does not support the older version of the SVL file. On their websites, developers usually offer free solutions to such problems, e.

The file is invalid. There can be many reasons for this. Repairing is very dependent on the file type. Sometimes the program itself has options to repair the most popular SVL file corruption. The easiest way to restore the file is from a backup or by contacting SecurStar, but this one can be expensive. Not all damage can be reversed. The SVL file has been encrypted. Consensus Logo.

This SVL code allows to create a sequence consensus logo. It implements the approach published in: T. Schneider and R. Stephens Nucl. Acids Res. To generate an image of the logo press the button Export. Author Yoshirou Kimura. The models supervised-learned by the compound library can be further adjusted by reinforcement learning that incorporates scoring functions such as fingerprint similarity and activity prediction models. Executing and monitoring of reinforcement learning: Various parameters can be set from the GUI to execute reinforcement learning.

For more detail, Please see the attached PDF manual. Mcule Interface. Category ChemInfo. To install extract the zip file into your MOE installation folder. After loading the file you can enter a Mcule ID in the text widget of the builder e. A Authorization Token is required for searches. The availability will be displayed in the Ligand Properties. If you have questions, please let us know. Images from Docking Database Script. This script will allow a user to generate customized.

PNG images of every ligand-receptor complex contained in a database. Category Graphics. This script allows a user to generate. PNG images of every ligand-receptor complex contained in a database, ideally to maintain a sense of continuity when generating images of multiple docked poses for use in publications. Optionally, users can also display specific residues based on UID number and customize residue atom color.

Visualization of each docked pose contained in a database will be written to a numbered DPI. PNG file named after the database. When the first ligand-receptor complex is brought into the system, the user is prompted to select their desired point-of-view and visualization settings background color, ribbon quality, etc.

GridMarkets Plugin. We provide the tokens on a pay-per-use basis. Author GridMarkets. Category Cloud. Author Kinya Toda. Downloading this submission will create a new directory on your desktop.

In this directory you will find a folder with files for each exercise in the documentation. Installation: Copy the titledview.

Use the button in the button bar to start the tool. It also contains version 2. Click the "Add" button. Click on "archive" and browse to the zip file from this download. Click OK and follow the instructions on the screen. For any questions contact support chemcomp. Author Hooman Shadnia. Notes: The directory must be created if it does not already exist. SVL Node Package with more than nodes for a wide variety of life science modeling applications.

Reverse Fingerprint Modeling. Use reverse fingerprinting to highlight active motifs, color atoms by activity contribution and develop pharmacophore queries. Author Chris Williams. Category Obsolete. The legacy APIs will be unavailable between Nov , , and permanently discontinued on Dec 9, Create snapshots of the system in MOE and browse them with ease for presentation purpose. Please see pdf for installation directions and a tutorial. Enhanced Protein Properties and Patches.

Generates protein patches, descriptors and text reports on a database of structures at one or more pHs. Here is an overview of what this tool can do: Processes either a single structure in MOE or on a series of structures in a MOE database Generates protein patches and a translucent vdw surface over the protein Generates protein descriptors at various pHs Allows one to browse through a database of structures with the protein patches shown along with the corresponding 2D patch map Creates protein patch report s in either ASCII or XML format The titration algorithm uses Henderson-Hasselbalch kinetics and PropKa to estimate average amino acid charges at a given pH and local 3D environment that would be normally be present in an ensemble.

This is done using a single static structure. This tool may be called from the command line for batch processing. Please see pdf for installation directions and a description of the application. Dynamic Property Sampling.

Samples protein conformers with Low Mode Conformational Search and computes ensemble averages of a variety of protein descriptors. Here is an overview of what this tool can do: Generates a series of protein conformations with control over the amount of movement in the backbone atoms and CDR loops if present For each conformer, a series of pre-defined protein patch, hydrophobic index and hydrophobic interaction chromatography HIC descriptors are computed and averaged Options exist to save the individual conformations and their associated descriptors.

Note that the conformations generated are minimized and are not subjected to Protonate 3D as the sampling option in the current Protein Properties application does. Membrane Builder. Use this script to multiply a previously loaded and pre-oriented molecule and to distribute it randomly rotated onto a 2D plane.

Author Andrew Henry. You can define the number of lipids along the X and Z side of the plane and the spacing in between for the X and Z coordinates. The distance does not take the shape of the lipid in account, it is the distance from the center of one lipid to the next one.

A green arrow is displayed in the MOE window. You can do this by selecting the atoms and rotating them by holding the Alt key and dragging the middle mouse button. Import your molecule as a lipid into the Local Database of the MembraneEditor. Add the molecule to the membrane. Drag and Drop the lipid from the Overview to the membrane in the Membrane View.

Change the settings for the Origin of Coordinates for the XZ plane and Y axis to the physical center. Now just export the project to a PDB file. Exploring the conformational space of Vpu from HIV a versatile adaptable protein. J Comput Chem. J Chem Inf Model. Adjust the lipid so that it is aligned along the axis shown in the green arrow.

Author Olivier Gagnon. Category MOEsaic. The y-axis WlogP of the model was substituted for the SlogP descriptor. A Monte Carlo MC method was used for computing the model, similar to the methodology described by Daina et al. To obtain optimal ellipses, 10 9 independent MC runs were performed. True and false positives TP, FP as well as true and false negatives FP, FN were used for the binning statistics of each ellipse and evaluated using Matthews correlation coefficient MCC ranges from -1, total disagreement between observation and prediction, to 1, perfect agreement.

The model achieve an MCC of 0. The original model reported similar MCC 0. The model should now be available in any MOEsaic session. Version MOE ProjectDock.

This utility takes a ligand selected atoms in MOE window and searches a MOE project for the entries with the most similar ligands. Optionally it prepares the target and docks the ligand to the target well. Category MedChem. Installation: Copy projectdock. Database String Manipulator. This submission contains a string aware version of the database calculator.

It can be used to concatenate multiple char fields or to work on a single char fields. The panel also allows to use numerical or molecular fields. If a molecule field is included the molecule name will used inside the formula. The return type can be char or numeric.

For numeric return types the function atoi or atof will be used respectively. Field can be added to the formula by clicking on available fields on the right. For comments, requests and feedback, please contact support at chemcomp. It allows you to easily perform operations related to QSAR modeling molecular standardization, descriptor calculation, independent variable selection, cross validation, outlier exclusion. It optimizes QSAR models by selecting independent variables based on genetic algorithm.

An automated method for generating pharmacophore models from protein binding pockets. Calculate Pharmacophore Model Feature Distances. This script uses the SiteFinder function in an automated manner to elucidate probable binding site residues. Once residue selection is completed, a dummy atom is placed at the mean position of all atoms comprising the SiteFinder selected residues and distances between pharmacophore features and from each pharmacophore feature to binding pocket centroid represented by the placed dummy atom are calculated.

Follow the instructions below to install the extracted files. Extract the archives named dock. If folders shown below do not exist, please create them. Usage: Browse to the main page of the MOEWeb server, locate the icon for the newly added application 'QuickDock' and click on it to start the application. Press MOE-Dock to start the docking.

Once docking is finished, use the links from the results page to download individual files. Open the target structure from any source and prepare it as desired.

Configure the docking as desired. Once ready to run, press the 'Batch Ensure to use a descriptive name. This file includes the structure of the target, cocrystallized ligand for comparison , and all the required settings. Browse to QuickDock application page.

The new target name must appear under the list. SDF files to perform conformational search. Installation: Extract confsearch. CYP Predictor. Author Michael Drummond. Principal Component Analysis for MD trajectory.

Description: The tool performs principal component analysis of atomic coordinates on trajectory data obtained by molecular dynamics and show the motion of molecules along each pricipal component axis in MOE window. This submission is an implementation of: J. Dunbar, A. Fuchs, J. Shi, C. See the Dunbar paper for definition of these descriptors. The SVL code also implements a graphical mode that renders the vectors. This only works if exactly one Fv is present in MOE.

New substructure filters for removal of pan assay interference compounds PAINS from screening libraries and for their exclusion in bioassays. J Med Chem. The new descriptors will be added to the list. Select the descriptor that you want to calculate and click the OK button.

Remarks: The rules were defined as SLN in the original publication. Due to different aromaticity perception slight differences are expected. If you find any problem with this implementation please contact CCG Support. Rebuild peptide sequence information.

Peptide and peptide-containing polymer structures are often stored in SMILES strings or other formats which do not retain information about amino-acid monomer identities and their relative positions in the polymeric structure. The amino acids are detected and named using the currently loaded rotamer library in MOE, and additional optional libraries of non-amino acid functionalities can also be provided for detection and naming of residue units.

This script will detect and encode the sequence information. Last Update: February Author David Thompson. Assisted Batch Dock Setup. This script is meant to automate the generation of multiple batch docking jobs where a single ligand is being docked into a database of proteins.

This script outputs multiple. This script requires user input during the generation of the batch files but greatly automates the process. Two Grid Surface. You can adjust the surface isolevel with a slider. Then you can use another grid file for the coloring of the surface. A typical application is creating a surface based on an electron density grid and using an electrostatic potential grid for the coloring.

Detect hot-spots for protein binding using the intersection consensus of individual property fields. Locating 'hot-spot' for binding to a protein structure is the goal of many computational chemistry applications.

Hot-spot analysis can help validate the importance of known interactions in holo complexes and suggest regions to target when designing ligands for apo structures. In the context of formulating biological-based medicines such as antibodies, hot-spots can be used to determine locations where excipients and other formulation molecules may aggregate on the protein surface and affect bulk properties of the medicine.

Allows for calculation of Ligand RMSD to crystallized ligand poses for each ligand conformation within a database. Enter this command: ligandRMSD ['reference structure', 'database', 'mol', 'receptor'] where "reference structure" is a. Ligand RMSD values will be written to a new column in the docking results database.

Specifically, these tools have been designed to tackle two fundamental challenges in PROTAC modeling: The prediction of the conformational ensemble accessible for a constructed ternary complex. The makeup of this conformational ensemble depends not only on the conformational flexibility of the PROTAC primarily imparted via its linker , but also on direct protein-protein interactions.

Conceptually, this challenge is similar to pose generation in traditional small molecule docking. The identification of ternary complex poses generated by the conformational sampling above that are deemed biologically relevant, i. Conceptually, this challenge is similar to pose scoring in traditional small molecule docking. This challenge is not addressed by these tools, i.

Multiple protein chains can be colored with different HDX input files, so that changes in the HDX signal during complexation can be visualized for multimeric proteins. An automated alignment procedure ensures that differences in the numbering schemes between the HDX data and the residue numbers within MOE can be handled. Information for the individual peptides in included, as is the ability to color by difference or in side-by-side mode.

Finally, the poses in a protein-protein docking database can be colored and scored by how well they correlate with the experimental HDX results. It also includes three videos showing the different steps for on-, offline installation and activation of SVL based nodes. Quick Federated Structure Search. A novel ultra-fast structure search program for huge molecular database stored in multiple mdb files.

Category Coding. SVL files are recognized using their file extension. Sequence Based Molecular Descriptors. Downloads 2. Warning: This version does NOT work on moe-type database fields. These protein descriptors are calculated on sequence only. Glu,Asp are deprotonated, Lys,Arg are protonated, His and all other amino acids are neutral. One pair of free termini is added per amino acid chain. Ref: A. Ref: J.

Kyte, R. Please note that polarizabity varies with conformation! Ref: K. Guruprasad, B. Reddy, M. Bjellqvist et al. PBSA solvation energy calculator. Downloads 7. A GUI will appear. The PBSA solvation energy will be written the text field in the panel.

The conditions are recorded in the database field names Excel Interface. The Excel interface is based on the Apache POI library which has to be downloaded and installed separately. We also recommend having Oracle Java installed.

The second number is for selected fields only. Generate Conformations from SD Files. Downloads 1. Protein Pocket Volumes. A panel that creates difference, intersection and union maps from a a set of aligned protein pockets. Used maps to highlight differeneces between pockets of similar proteins. Download and unpack the zip file. The pocket will be defined around the ligand atoms. To compare proteins with no ligands, first use the Site Finder to create dummy atoms in the binding site.

These will then be used to identify the pockets. The pocket volume comparison will proceed and a new graphics object rendering the volume difference will be create and listed in the panel. The volume enclosed by each surface is shown in name of the graphic object. MolPort Interface.

Enter the username and password you got from MolPort there. Click OK. Now you can enter a MolPort ID in the text widget of the builder e. Databases for imported structures contain links to the MolPort website which can be opened from the database browser by clicking Open in Browser. Based on a given alignment of a set of small molecules with activities, a grid potential analysis is applied using the principles of CoMFA. Hereby, steric and electrostatic interaction energies of a positively charged carbon probe atom placed on grid points around the aligned molecules are determined and grid potentials are calculated.

Then a partial least square model is created by fitting the activities to the grid point potential values. This process starts with a principal component analysis of the descriptors to reduce the number of components in the model to a value set by the user. The model coefficients for the principal components are then mapped back to the descriptors. These contributions can be visualized to identify areas with positive or negative contribution to the model spatially pre-condition: numerically higher activity values mean higher biological activities.

Benchmark Tests for MOE. Downloads 5. Basic Descriptor Collection Small Molecules. Author CCG Support. Most of these molecular descriptors are suitable for statistical modelling of molecular properties or activities e. All descriptors use the descriptor plug-in system in MOE.

The are divided 3 classes: 2D - conformation-independent i3D - conformation-dependent x3D - dependent on conformation and the structure currently in your MOE window Note: each of the descriptor files contains a number of related descriptors.

There are redundant descriptors in case they make sense in more than one file. Author Markus Kossner.

Rogers et al. NOTE: This latest version last change: feb ma of the script generates fingerprints that are incompatible to earlier versions!!! Please note that there are multiple XYZ format descriptions. The one used here is: 5 C 0. Author Maximilian Ebert. After restarting Sublime 3 you will have at the bottom right a new language from the drop-down list: Scientific Vector Language Sublime should also be able to autodetect SVL files by their extension.

Batch FlexAlign. Author Dimitri Bondarev. Automatic flexible alignment for all molecules in a database against reference molecules from the main MOE window. This function uses the FlexAlign [] function. If an output database filename is not supplied then it will be based on the input filename.

For instance if the input database was in. Save this file into that directory. Ferguson D. ACS Chem Neurosci. Downloads 6. The ZINC database is an excellent resource for structural information on small molecules.

Linker Design for Bivalent Ligands. A tool that links ligands via the shortest pathway along the receptor van der Waals interaction surface. The linker poses are scored to help the design of new bivalent ligands. This script builds models for the linker between two ligands, bound in two binding sites. Editor of molecule type fields. Extract or merge molecular objects of molecule type fields and store them in a new field.

For more information, please see the bubblehelps. This program may be useful if you want to extract ligand, receptor, or contacting solvent from molecule type field in MDB of molecular dynamics output. Compound Library Management Workflow. Remove duplicate conformations Update for MOE Description: Application to detect duplicate conformations in a MOE database. Use cabn set RMSD theshold for unique conformations.

Option of eithe selecting of deleting duplicate conformations Note: ALL entries must not be empty! Use the Browse button to select the input database.

Specify the molecule and optional mseq fields in the case of databases with multiple conformations. Molecular symmetry will be taken into account. Choose the actions for the duplicates - either select in the database viewer or delete. Press OK to perform teh operation. The formation of a covalent bond with a target protein is essential for a number of successful drugs but computational tools for covalent docking without significant restrictions regarding warhead or receptor classes are rare. DOCKTITE is a highly versatile workflow for covalent docking combining automated warhead screening, nucleophilic side chain attachment, pharmacophore-based docking and a novel consensus scoring approach.

DOCKTITE is a fast and user friendly method for covalent docking without restrictions upon warhead or receptor classes and is predestined to deal with large-scale virtual screening tasks. Furthermore, advanced users may modify the open source program to suit their demands.

Author Christoph Scholz and Sabine Knorr. QSAR Wizard. Author Simon Grimshaw. The process works like so: 1. Load and optionally back up an MDB of molecules with an activity field 2. Calculate descriptors and specify the name of the activity field 3. Split the database optional step into training and test sets. Various methods are available, including k means clustering and selection from binned activity values.

Select descriptors. The selection can be pruned by looking for low variance or highly correlated descriptors. In addition the training and test sets can be compared in PC space based on the current descriptor selection. Build the QSAR model. If a test set has been created, the model can now be applied to the test set.

Author Curt Breneman and N. RECON Descriptors RECON is an algorithm for the rapid reconstruction of molecular charge densities and charge density-based electronic properties of molecules, using atomic charge density fragments precomputed from ab initio wavefunctions.

The method is based on Bader's quantum theory of Atoms in Molecules. A library of atomic charge density fragments has been built in a form that allows for the rapid retrieval of the fragments and molecular assembly.

The RECON algorithm reads in a molecular database, determines atom types and environments, assigns the closest match from the library of atom types and combines the densities of the atomic fragments to compute a large set of new and traditional QSAR descriptors. Oloff, S. Zhang, N. Sukumar, C. Lavine, C. Davidson, W. Katt, C. Davidson, C. Katt, "Electronic van der Waals surface property descriptors and genetic algorithms for developing structure-activity correlations in olfactory databases" Journal of Chemical Information and Computer Sciences, 43 6 : , Nov-Dec Author Jens Laettig.

Epub Mar This scripts sends protein sequences to PFAM website and pareses the resulting hits, colors various detected domains and creates MOE 'sets' to access the domains as detected. Downloads 4. It allows to read and write ORCA coordinates. For ORCA options etc.

The output of ORCA calculations can be read by the script geometric data only! A collection of svl scripts for the purpose of creating MOPAC input files as well as interpreting and visualizing the results.

Author Richard Bartelt, Wolfgang Brandt. Define planes through sets of atoms. Then measure the distance between an atom and the plane, the angle between planes, and reflect atoms in the plane.

Type: svl. Extends the functionality of MOE's text editor. Revised 24th Oct Installation 1. Unpack the zip file in any directory. Please be aware that the menu will over-ride the default MOE text editor menu and any other modifications to those menu you might have made. Restart MOE. This allows a more fully featured search either in the current file or in MOE or User directories as defined in step 4 of the installation process.

Searches in file may fail if the file has been modified; please save then search if problems are encountered. Select a few lines of text and indent it further right or left to make your code easier to read. TED SVL Execute Command will execute any selected text, or if there is no selected text it will open a command line in the current text editor. This makes it fairly easy to step through a function executing one line at a time. Selected text is automatically expanded to complete lines.

If the first line starts with "local", "global", "static", or "const" then that word is removed this only affects the first line. Commands can be executed by selecting one or more of them and clicking "Execute", or can also be executed by double-clicking.

Selected commands can be sent to a MOE text editor by clicking on "Make script". Selectivity Pharmacophore Scheme. This application highlights pharmacophore features that can be used to maximize selectivity for a protein target vs a chosen set of off-targets. This application uses a collection of proteins aligned using a common ligand and will highlight pharmacophore features that can be used to maximize selectivity for each individual protein. An experimental scoring table provided in the dabatase file imatrix.

The resulting visuals can be used to modify the ligand to increase selectivity, i. Sample files provided for quick testing. MD snapshots to BMP files. The user needs to set up the visualization before hand.

Pretty Protein Ribbon Sidechains. The smooothed protein ribbon representations sometimes pass a short distance from the C alpha atoms. Remember, different programs may use SVL files for different purposes, so you may need to try out a few of them to be able to open your specific file. Try a universal file viewer like Free File Viewer. It can open over different types of files - and most likely yours too. Download Free File Viewer here. Not sure exactly what type of file you are trying to open?

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