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Molecular modeling software #2: Hypercube

Most of packages for Windows are without Python console. I need the feature and find avogadro I hope the developers will enable the console in the future. Click URL instructions: Please provide the ad click URL, if possible: Help Create Join Login. Resources Blog Articles Deals. Menu Help Create Join Login. Avogadro An intuitive molecular editor and visualization tool Brought to you by: Get project updates, sponsored content from our select partners, and more.

Get notifications on updates for this project. Get the SourceForge newsletter. You can contact me via: JavaScript is required for this form. No, thanks. Features Cross-Platform: Built to work easily for students and advanced researchers both.

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Supports multi-threaded rendering and computation. Plugin architecture for developers, including rendering, interactive tools, commands, and Python scripts Flexible: In the past active shutter glasses have been very expensive but prices have dropped significantly. Personally I found the Active 3D much superior, especially if you planning to use this mainly as a computer monitor rather than a TV that you view from the comfort of your sofa.

The compiled PYMOL binaries are available for paid download with different options for academic, industrial and non-profit. In addition the source code is available for free download. Not all new features make it to the source code right away, but eventually all features will, usually within a few months. The Schrodinger Small Molecule Drug Discovery Suite was updated over the weekend, this is a major update that brings in a host of new features and improvements.

Improved flexible ligand superposition Additional graphics settings Real-time antialiasing Real-time ambient occlusion, outlines, and cartoon shading effects Multivariate ranking in the Project Table Simultaneously maximize or minimize up to four property values, and rank entries based on the optimization Date Created and Date Modified fields automatically generated in the Project Table Workspace responsiveness of atom labels is up to 2. AlogP, Hbond acceptors, HBond donors, rotatable bonds, polar surface area, molar refractivity, and polarizability. Performance improvements to Phase database operations, including faster deletion and insertion of ligands Automatic restart of Phase database subjobs.

New interface to compute thermodynamic properties for reactions New faster TDDFT algorithm and graphical interface Compute Raman intensities Several improvements to the results script Jaguar pKa displays the computed pKa as an atom label by default Heat of formation graphical interface now supports bromine and iodine Improved numerical stability of the 1st and 2nd derivatives of the D3 correction Increased utility of canonical. MolSoft have announced that a new version of ICM is now available for download from the support site.

A description of the key new features can be found on the news page and release notes. In the tutorial Scripting Vortex 15 I showed how it is possible to create a contextual script for Vortex that downloaded a specific PDB file, then a FlexAlign Vortex script first identifies the structure column and then get the SMILES string of the selected molecule generates a 3D structure and uses Flex Align to do a one-shot flexalign between the ligand in the system in MOE, and the incoming ligand.

While this is useful if you have similar structures perhaps analogues in a series there will certainly be situations where it may be preferable to dock the new ligand into the binding site. The Scripting Vortex 17 tutorial describes how to achieve this. A patch update is now available for MOE This patch contains a series of important updates for better performance, s.

I recently came across this brilliant collection of software from Michel Petitjean. I was just reading the end of year newsletter from [Molsoft] and I came across this interesting snippet. Anaglyph stereo mode is added. I think this is the first app to enable this sort of stereo viewing and it just underlines the strides that mobile platforms are making in scientific computing.

For science apps for iOS have a look at the mobile science page. The following packages are also available. Whilst there are a number of desktop applications that allow for the creation or editing of 3-dimensional chemical structures there are not as far as I am aware any tools for editing the 3D structure within a web page. The details are described in a recent publication Journal of Cheminformatics , 5: Full installation instructions are available on the website together with the user manual and examples.

The examples can run effectively on an Intel Core i5 2. Estimates of the execution time and memory requirements will be given based on this more performant setup. Similarity computations and similarity searches UNITY 2D fingerprints are now accessible via Python to support various workflows, such as lead expansion, lead hopping, and cluster analysis. The current release also includes bit versions for each architecture. The Dock Menu also contains menu items in order for users to view the About panel bundled in MOE, as well as access the Preferences panel.

Users continue to be able to drag and drop compatible MOE documents i. New Preferences Menu. These parameters include the defaults key and path to MOE, the current configuration of MOE or bit, or Auto-select , as well as a selection of common command line tags, with a custom section for inputting other command line options. Output Continuity. Anyone involved in a drug discovery programme will be aware of the challenge presented by trying to visualise and explore structure-activity relationships SAR , in particular visualising questions like: Activity Miner is intended to help identify key elements of the SAR by starting from a set of aligned molecules and then automatically comparing them to each other.

More details are here. The script will download the associated PDB structures from the rcsb Protein Data Bank , put them into a database then start the browser. It may take a few seconds to download the structure; this does rely on MOE having the right proxy settings to access the internet use the Java console to set them. You can now transfer this to MOE and amend the display to highlight the ligand. It is probably easier to see this in action, if it appears rather small click on the YouTube icon in the bottom right corner of the video.

Full details are here. The application can be downloaded from here , the source code is also available. It seems that whilst Hydrogen bonds are clearly defined pi-stacking interactions are not and in my brief experiments bonding to halogens was not detected 3GT3. This release incorporates several improvements and some bug fixes. The chemistry of molecular interactions is a matter of shape and electrostatics, but doing electrostatics poorly is worse than doing none at all; accurate charges are required.

Even the best charge models are useless if protonation states are wrong. It includes pKa and tautomer enumeration in order to get correct protonation states, partial charges using multiple models that cover a range of speed and accuracy, and electrostatic potential map construction and storage.

I have written a brief overview here. Here is a list of the reviews available. It is written in java and can be downloaded from github here. I have not tested it extensivey but on my cursory look it seems to work fine under Mac OS X, provided you have installed java. Using a convenient graphical user interface, it allows one to check how ligand and binding site coordinates fit to the electron density map.

The user can specify threshold values for a series of properties related to the fit of coordinates to electron density Real Space R, Real Space Correlation Coefficient and average occupancy are used by default. The user is also able to visually check the quality of the fit of residues and ligands to the electron density map and reclassify them if needed. To start the application simply double-click on the icon, and then enter a PDB code or you can load a list from a file the analysis takes a few mins so if you are planning to examine a list of structures you may want to set it running overnight.

The results can then be examined in the viewer which is uses JMOL. It all seems pretty intuitive. In the view above the ligand atoms are purple and the associated electron density red, the protein atoms are white and a dubious area of associated electron density is shown in yellow. You can read more details here Journal of Cheminformatics , 5: In addition Python 2. To check simply type python in a Terminal window. The research group headed by Prof. Gerd B. Rocha at the Federal University of Paraiba, Brazil, has been successful in implementing a significant speedup.

Two modifications have been made: Details of the modifications can be found here. Times, in seconds, for a single-point calculation run on a 2 x 2. This means that proteins with free radical sites, excited state proteins, and proteins containing iron, chromium or other transition metal atoms should not be modeled using MOZYME. The free open-source molecular editor and visualization package IQmol has recently been updated to include. IQmol now has its own Youtube channel which contains some animations generated with IQmol.

ProDy is a free and open-source Python package for protein structural dynamics analysis. It is designed as a flexible and responsive API suitable for interactive usage and application development. ProDy has fast and flexible PDB and DCD file parsers, and powerful and customizable atom selections for contact identification, structure comparisons, and rapid implementation of new methods. An update to the Molegro Virtual Docker has been announced.

It includes new data analysis tools that are now available directly from within Molegro Virtual Docker. Some of the new features include:. OMEGA v2. Highlights from this release include: OpenMPI version 1. These new flags replace the oempirun script. PVM parallel virtual machine is no longer supported. An option has been added to allow hydrogen atoms in -OH, -SH, and amines to take part in conformational sampling. This new option can be enabled via the -sampleHydrogens parameter. By default, hydrogen atoms are not sampled. Now using -fixsmarts without -fixmol will rematch for every input structure.

Previously, this would only match the first input structure and reuse that match for the rest of the calculation. Using both -fixsmarts and -fixmol will continue to match against the fixmol and use that match for the entire calculation. EON v2. The default hitlist format has been changed from sdf to oeb for increased functionality and decreased filesize. The output format is adjustable with the -oformat parameter. The tags are optional with the -sdTags parameter. Added to the list of Hints and Tips.

There are a huge number of new features and improvements in the small molecule drug discovery suite as well as Materials Science. However a couple of features caught my eye, pKa prediction for both rule-based and QM-based methods has been improved. Covalent ligand docking has been added and includes a variety of common docking chemistries.

Improved pi-stacking interactions in docking. The molecular dynamics has been updated and now includes support for GPU-acceleration. The QM tools look to have been updated and the interface improved. ADME tools have been updated and in particular P site of metabolism has improved accuracy. Predictive capabilities that can be applied across a wide range of chemical systems, including ,Reaction thermochemistry and reaction path exploration ,Rate constants for reactions and transport from transition state theory ,Validated models for calculating oxidation and reduction potentials, Accurate heats of formation and atomization energies for larger systems, Reliable properties for systems containing transition metals,Efficient calculation of electric field dependent properties,Prediction of vibrational and electronic spectra for complex systems,Multiple pre-defined calculation modes representing tested simulation parameters balancing speed and accuracy.

An update to NWChem has been released with a host of new features. NWChem 6. This capability allows researchers to probe the ultrafast dynamical behavior of molecules and materials in response to an applied electric field. With this release, researchers will for the first time be able to perform large scale coupled cluster with perturbative triples calculations utilizing the NVIDIA GPU technology.

A highly scalable multi-reference coupled cluster capability will also be available in NWChem 6. In addition, NWChem 6.

Molecular Graphics Software Links

Binaries are not yet available but the source code and instructions for compilation on a Mac are available are available. You will need Xcode and gfortran 4. AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations using NAB or mdgx , with either explicit water or generalized Born solvent models. It includes. Antechamber and MCPB Create force fields for general organic molecules and metal centers, tleap a basic preparation program for Amber simulations.

AmberTools is distributed in source code format, and must be compiled in order to be used. The distribution contains a Reference Manual in pdf format. We continue to improve and expand our software suite with the aid of our academic and industrial ADF authors and other partners. Fully functional versions of all modules of our release are available free of charge for a day evaluation period. The programs may be run on any machine at your organization, with full support.

Just fill out our Free Trial Form. Other questions? When you compare the amount of resources and effort that goes into computer games with the amount that is available for scientific software it is clear that the games industry wind hands down. It is not surprising therefore that some enterprising scientists are looking at leveraging games technologies to build new applications.

The video games industry develops ever more advanced technologies to improve rendering, image quality, ergonomics and user experience of their creations providing very simple to use tools to design new games. In the molecular sciences, only a small number of experts with specialized know-how are able to design interactive visualization applications, typically static computer programs that cannot easily be modified.

Are there lessons to be learned from video games? Could their technology help us explore new molecular graphics ideas and render graphics developments accessible to non-specialists? UnityMol is a molecular editor, viewer and prototyping platform, coded in C with the Unity3D game engine. The SAR Table app has had the ability to match scaffolds to molecules for a while now, but as of the latest release 1. The actual process of performing the scaffold match is provided by a webservice molsync. More details here.

OpenMM is a toolkit for molecular simulation. It can be used either as a stand-alone application for running simulations, or as a library you call from your own code. It provides a combination of extreme flexibility through custom forces and integrators , openness, and high performance especially on recent GPUs that make it truly unique among simulation codes.

Smina is a fork of AutoDock Vina that is customized to better support scoring function development and high-performance energy minimization. Stanford University When: March , Registration: Free but required and spaces are limited. To register or for more information, visit http: OpenMM http: It has demonstrated speed ups for both implicit solvent[1] and explicit solvent simulations[2] on graphics processing units GPUs.

A well-designed framework provides an application layer and a library, so that non-programmers can easily and quickly run MD simulations and develop custom algorithms on GPUs, while programmers are simultaneously able to integrate OpenMM cleanly into their own programs. The workshop offers two tracks: The last two days of the workshop are devoted to having the OpenMM team assist participants with their individual projects. You can sign up for an instructional track, just the open working days, or both.

To learn more about Simbios and its research and software tools, visit http: MS Friedrichs, et al. There is a listing of GPU accelerated scientific applications here. This is a bug fix release that repairs one major bug and several minor ones. SZMAP uses semi-continuum Poisson-Boltzmann electrostatics to map variations in solvent properties in a protein binding site. It identifies key waters, shows their interactions, compares them to the corresponding ligand atoms, and determines whether neighboring waters aid or hinder binding, giving insights into the role of water molecules in ligand binding.

The included tool GAMEPLAN, suggests ways to modify ligand chemistry based on this understanding of water structure in the immediate environment of the ligand. The code of Fen Zi is now available in Google Code at http: Any help or feedback is welcome! Fen Zi currently includes: Switching or shifting - Long distance electrostatic interactions: Ewald summation method and Reaction field - Solvent: Features include a graphical molecule builder, GAMESS input generation, animation of output and visualization of molecules, normal modes, orbitals and other properties. DOCK is a suite of programs for molecular docking.

In version 6. Grid-based footprint scoring and SASA-based scoring. The MultiGrid Footprint Score calculates the pair-wise interaction energies over multiple grids. Important receptor residues are initially identified with a reference ligand, and individual grids are generated to model such residues. The SASA score calculates the percent exposure of a ligand, and the percentage of the hydrophobic portion of a ligand and the receptor that are buried in the pocket. In addition, a symmetry corrected RMSD Hungarian matching method was added to facilitate pose reproduction studies. Full information on what is new in DOCK 6.

I use Moe for molecular modeling work, this uses a license.

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The FlexLM license manager lmgrd must be configured and run. Usually this runs quietly in the background and needs little intervention, however I've found that on some occasions the server quits perhaps after updates and needs to be restarted. However since it is something I don't need to do regularly I always spend a while working out the exact syntax. So I created this short Applescript to restart the server. As I mentioned in my recent review of MOE there is now support for using Marvin as an external 2D chemical drawing package, but what happens if you want to use another drawing package?

Well that is where Applescript comes to the rescue, using Applescript support for shell scripts and one line of SVL scientific vector language we can use ChemBioDraw as the external editor. Full details of the script are here. The Applescript section contains more tutorials, scripts and resources.

There is a collection of software reviews here. Analytical calculation of van der Waals surfaces and volumes. Minimal radius enclosing cylinder. Minimal radius circumscribed cylinder. Selects by clustering major conformations of a molecule in a set of its conformers. Docking Geometrically two molecules. Computation of the Radius and Diameter of a molecular graph.

Optimal Partition classification: The number of classes is computed. Computes the RMSD between two ligand poses.

Free Molecular Modeling Software

No rotation translation is performed. Computation of the Radius and Diameter of a spatial set.

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Molegro Virtual Docker offers high-quality protein-ligand docking based on novel optimization techniques combined with a user interface experience focusing on usability and productivity. A new 'Energy Maps' tool provides volumetric visualization of protein force fields. This makes it possible to understand why a compound interacts with a given receptor, and may provide insights on how to improve the binding.

We also added a new execution mode in the Docking Wizard: This makes it possible to run medium sized jobs on a local machine, while utilizing multiple CPU cores and even multiple GPU graphics cards. For large jobs on multiple machines, Molegro Virtual Grid should still be used. The ray-tracer has been improved to more closely match the live 3D view output.

This makes it possible to create high resolution renderings of the 3D view. OpenEye is pleased to announce that the OpenEye Toolkits v Oct have been released. NET versions of the Toolkits. OEChem TK: Details of the changes to the individual libraries are here. Cresset have announced the formal release of sparkV10 the replacement for FieldStere. If FieldStere is currently installed then it is recommended to uninstall the binary to avoid confusion over which application should be used to open FieldStere project files.

Avogadro is a free, open source, cross-platform molecular editor designed for flexible use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. See the Release Notes: For more information: It is a free download from the App Store.

With the app you can: This significantly improves geometries and energies of proteins, crystals, co-crystals, metal clusters, inorganics and other condensed phase systems. New PM7 method significantly improves intermolecular energies, providing increased accuracy for condensed phase chemistry.

PM7 can be applied to modeling enzyme reactions and predicting co-crystals. It identifies key waters, shows their interactions, compares them to the corresponding ligand atoms, and determines whether neighboring waters aid or hinder binding. The newly released tool GAMEPLAN, suggests ways to modify ligand chemistry based on this understanding of water structure in the immediate environment of the ligand. Its robustness, comprehensiveness, speed and performance makes CORINA a perfect application to convert large chemical datasets or databases.

YASARA has seen several updates since I last mentioned it, most recently the ability to display pi-pi and cation-pi interactions. PVL allows you to visualize even the largest proteins and enables true interactive real-time simulations with highly accurate force fields on standard computers. You can push and pull molecules around and work with dynamic models instead of static pictures. I was wondering when someone would use an iPad as the front-end to a fully featured modelling package running on a remote server, looks like Wavefunction have done a pretty impressive job with taking their sophisticated Spartan computational chemistry package from the desktop to mobile devices.

Atomic and molecular properties, NMR and infrared spectra, molecular orbitals and electrostatic potential maps are available from a 5, molecule subset of the Spartan Spectra and Properties Database SSPD. The database may also be searched by substructure. Properties, spectra and graphical models of molecules in the SSPD subset are available for examination. For molecules not included in the database, connection to iSpartan Server supports calculation of structures, properties, and spectra for all user generated molecules from iSpartan running on the iPad, iPhone, and iPodTouch.

There is a listing of science apps for iOS here. Using a combination of OpenEye approaches, including structure generation, shape alignment and flexible fitting, it produces a predicted pose whose accuracy depends on similarity measures to known ligand poses. As such, it produces a reliability estimate for each predicted pose. A memory leak in the optimizer was fixed, POSIT should now properly handle large streams of molecules. The -mcs flag is now turned off by default. In some cases, the mcs was taking far too long for no real benefit in pose prediction.

I was at the Cresset Science Meeting last week and heard about the plans to update their comprehensive suit of drug discovery and design computational tools. The renaming will not be complete until September so in the interim the links on some of the download pages still point to the originally named application. TorchV10lite is a free 3D molecule viewing, editing and drawing application that shows your molecules in 3D overlaid with field patterns generated using their proprietary field technology together with 2D structure and physicochemical properties.

It is the replacement of FieldView. It is used to take leaps in structural design by identifying compounds with similar fields but different 2D chemical structures while maintaining or improving biological activity. It is the replacement for FieldAlign and due for release very soon. You can then use calculated physiochemical properties to filter and select the best designs. The three applications above look to be intended for use by Medicinal Chemists whilst the remaining two applications are perhaps better suited to those more experienced in computational chemistry.

BlazeV10 uses the shape and electrostatic character of known ligands to rapidly search large chemical collections for molecules with similar shape and electrostatic properties. It is installed and runs on a Linux cluster but is operated through a web-browser, enabling access from any platform and multiple locations.

Cresset has pioneered the use of field point descriptors to give a more accurate description of the charge around an atom and to enable better comparisons and visualisation. This has been shown to be particularly important when trying to understand some molecular interactions such as Aryl-Aryl interactions or creating bioisosteric replacements. Cresset now have an impressive suite of tools for drug discovery and I hope to review them in due course. It is based on a unified approach to the structure solution process. It combines electron density interpretation using the concept of the hybrid model, pattern recognition in an electron density map and maximum likelihood model parameter refinement with REFMAC.

The REFMAC program can carry out rigid body, tls, restrained or unrestrained refinement against Xray data, or idealisation of a macromolecular structure. It minimises the coordinate parameters to satisfy either a Maximum Likelihood or Least Squares residual. There are options to use different minimization methods. Toxtree is a full-featured and flexible user-friendly open source application, which is able to estimate toxic hazard by applying a decision tree approach. Toxtree could be applied to datasets from various compatible file types.

User-defined molecular structures are also supported - they could be entered by SMILES, or by using the built-in 2D structure diagram editor. IQmol is a free open-source molecular editor and visualization package. It offers a range of features including a molecular editor, surface generation orbitals and densities and animations vibrational modes and reaction pathways.

This software allows to model in 3D assemblies of proteins and DNA. Its main feature is the capability to create 3D models of DNA in a highly intuitive manner. To date, the modeling and visualization tool allows to: The Molecular Data Explorer is a multi-component tool for molecular data analysis and visualization, and early testers tell us they obtain insights into their dataset in minutes that previously would have taken days.

Open3DALIGN is a command-line molecular alignment tool which is operated by means of a few commands which can be entered interactively from a command prompt, read from a batch script or piped through standard input. The 3D ligand Editor is a powerful new tool for the interactive design of new lead compounds in 3D.

It allows you to make modifications to the ligand and see the affect of the modification on the ligand binding energy and interaction with the receptor. The first step is to identify water binding sites and then the second step is to estimate the free energy of water displacement for a particular ligand s. This new option can be used if you have a gap in your protein and you want to find loops in the PDB which fit the gap. New options to pipe icm commands and scripts.

Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics. This is a major update and whilst some of the new features and tools are described below full details can be found at http: This page is a review of some programs for molecule viewing and modeling, I found to be useful. If you are searching for one of these things, follow the URL listed below. In addition, it is pretty outdated by now the last more or less serious update is from or so. For something more recent, go here.

Very simple, it is a visual editor which can manipulate sets of coordinate-data of molecules. These datasets are normally derived from experimental output like X-ray-diffraction or NMR.

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