I regularly seem to get questions about how to install various bioinformatics packages under Mac OS X and whilst I try to help this is not really my area of expertise so when I see detailed instructions on another site I tend to make a note.
The Trans-Proteomic Pipeline (TPP), is a suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to an open mzXML format. Unfortunately Mac OS X does not appear to be a supported platform, fortunately Bosco Ho has written very detailed instructions on how to install under Mac OS X here
UCSF Chimera Version 1.7 has been released. UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles.
- APBS (Surface/Binding Analysis) — interface to Poisson-Boltzmann electrostatics calculations with APBS, using either a web service provided by the National Biomedical Computation Resource (NBCR) or a locally installed copy
- AutoDock Vina (Surface/Binding Analysis) — interface to single-ligand docking with AutoDock Vina, using either a web service provided by the National Biomedical Computation Resource (NBCR) or a locally installed copy
- Model/Refine Loops (Structure Editing) — interface to Modeller for building missing parts or refining existing parts (the former Model Loops tool only performed the latter and did not facilitate combining the refined and unchanged parts)
- Notepad (Utilities) — allows entering descriptive text that can be saved along with sessions
- PDB2PQR (Structure Editing) — interface to structure cleanup and charge/radius assignment with PDB2PQR, using either a web service provided by the National Biomedical Computation Resource (NBCR) or a locally installed copy
OpenEye has announced the release of OEDocking v3.0.1. This is a bug fix release to the FRED, HYBRID, and POSIT programs. Of note, the report generated by both FRED and HYBRID has been significantly improved with this release
- The program dockreport has been renamed to DOCKINGREPORT
NEW FEATURES AND IMPROVEMENTS
- The formatting of the DOCKING_REPORT has been significantly improved and now includes:
- Added a protein interaction fingerprint
- Polar Surface Area (PSA)
- Improved the geometry detection for hydrogen bond protein constraints in FRED and HYBRID. These constraints should now be tighter.
- Stereo isomer detection in POSIT was not handling bridgeheads properly, this caused some non-stereo molecules to be identified as such.
- Fixed a bug in FRED and HYBRID where clash detection between hydrogen bonding groups was occasionally too strict.
I’ve previously highlighted the use of ChemDoodle web components to display molecular structures within a web page, and a recent publication DOI by Henry Rzepa lead me to explore some of the newer additions to the means to render molecules within a web page without the use of applets or plugins.
A recent publication describes the development of a software tool GPU-FS-kNN (GPU-based Fast and Scalable k-Nearest Neighbour) for CUDA enabled GPUs. The basic approach is simple and adaptable to other available GPU architectures. They observed speed-ups of 50–60 times compared with CPU implementation on a well-known breast microarray study and its associated data sets.
The source code of the proposed GPU-based fast and scalable k nearest neighbor search technique (GPU-FS-kNN) is available at https://sourceforge.net/p/gpufsknn/ under GNU Public License (GPL).
There is a listing of GPU accelerated scientific applications here.
DOCK is a suite of programs for molecular docking. In version 6.6 two new scoring functions are available: 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 6.6
MacVector Inc have released a free version of MacVector.
If you used a temporary trial license, then when the 21 days were up, MacVector would simply refuse to start unless you entered a new valid license code. With the release of MacVector 12.7 we have changed that behavior. Now, when the trial license (or any annual license) expires, MacVector will give you the option of continuing to work, but with reduced functionality. All of the functions in the Analyze menu become disabled, but you can still open, edit, save and print MacVector documents, or save MacVector files in other formats.
ichemlabs have announced the release of ChemDoodle Web Components 5.
ChemDoodle Web Components 5 is a massive update. The most notable addition is a Full Sketcher, for drawing multiple molecules, shapes and figures, in addition to the Single Molecule Sketcher already provided. iChemLabs Cloud services and the ChemDoodle JSON format have been updated and drastically improved. The entire codebase has been reoptimized and cleaned, doubling the performance in desktop browsers and more than quadrupling the performance in mobile browsers. All Canvases now handle managing multiple molecules and shapes. Many new additions have been added and dozens of bug fixes have been implemented. We will be unrolling our new proprietary options over the next month, but of course, everything is available for free today under the GPL license!
There is a tutorial for using ChemDoodle web components here.
I’ve just finished a review of the latest version of MOE from the Chemical Computing Group.
There are a number of new features that will be of particular interest to Mac users and I’ve included a few tips for using Marvin as the external 2D chemical drawing package.
There is a collection of software reviews here.
The Chemical Computing Group have announced the release of PSILO version 2012.11. PSILO is a protein structure database and visualization system that provides an easily accessible, consolidated repository for macromolecular and protein-ligand information. Some key features in PSILO include:
- 3D Interaction Query
- Pocket Similarity Search
- Project Standard Orientation
New and enhanced features in PSILO 2012.11 include: domain motif search, nonredundant BLAST summary report, automatic GPCR annotation and Interactive protein:ligand interaction diagrams. PSILO offers research organizations a means to systematically track, register and search both experimental and computational macromolecular data. A web-browser interface facilitates searching and accessing public and private data
Integrated Protein Engineering Applications
- Residue scanning to identify critical residues for affinity
- Search for optimal mutations to modulate thermostability
- Predict hydrophobic and electrostatic hot spots with the protein Patch Analyzer
Domain Motif Searching
- Compare protein domains based on secondary structure elements
- Search proteins for secondary structure sub-geometries
- Identify similarities independent of sequence
Amber12:EHT: New Force Field for Biopolymers and Small Molecules
- Amber12 parameters for proteins and nucleic acids
- Extended Hückel Theory parameterization of small molecules
- More precise treatment of resonance and substituent effects
Reaction-based Library Enumeration and Screening
- New reaction engine combined with library enumeration or sampling
- Sketch reactions or core/R-group libraries
- Screen products with 2D or 3D filters (educts & products)
- Docked System Manager with control over surfaces
- Undo, redo, keyboard shortcuts, configurable mouse, drag & drop, etc.
- 2D sketcher integration with MOE Window
MacVector 12.7 is now available for download for all active users. Be sure to check out the new unique Cloning Clipboard window that simplifies creating new constructs
There is a new window available called the Cloning Clipboard that maintains a history of the DNA fragments created each time you use the Digest function. For example, if you select two restriction enzymes in a Map tab, then click on the Digest button, the fragment between the sites gets placed on the Cloning Clipboard. You can then join fragments together directly on the Cloning Clipboard by clicking on one end of a fragment and dragging to a different end
CLC bio is pleased to announce a new release of Molegro Virtual Docker , an integrated platform for computational drug design available for Windows, Linux, and Mac OS X. 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.
New features in version 5.5:
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: 'Run Docking in Multiple Processes'. 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.
This version of ChemBioDraw released in August 2012 is the first release since Cambridgesoft became part of Perkin-Elmer and there are a significant number of changes. This is the first version to be released since the introduction of Mac OS X 10.7 and 10.8 and both are now officially supported. In addition the ChemDraw plugin is now supported in 64 bit mode and Microsoft Office 2011 is supported. I’ve written a brief review here.
I recently wrote a review of ForgeV10 from Cresset in which I actually imported the results into Vortex to do the analysis. There were however two issues with doing this, firstly interpretation of the 3D structures is sometimes difficult, this can be resolved by creating a 2D rendering of the structure. The other issue is trying to interpret the docking pose whilst looking at the analysis of the results in say a Vortex scatter plot.
This is a review of ForgeV10 the latest offering from Cresset, whilst a new product those familiar with FieldAlign and FieldTemplater will recognise much of the functionality. ForgeV10 allows the scientist to use Cresset’s proprietary electrostatic and physicochemical fields to align, score and compare diverse molecules. It allows the user to build field based pharmacophores to understand structure activity and then use the template to undertake a virtual screen to identify novel scaffolds.
There is a compilation of software reviews here.
Schrodinger have just announced the release of PyMOL on the iPad. It is a free download from the App Store. With the app you can:-
- View 3D molecular structures, images, and PDFs
- Search and download data from the PDB, PubChem, Dropbox, or your own custom server.
- Intuitively interactive: rotate, pan, twist, zoom, center, and adjust clipping planes, with simple gestures
- Select atoms, residues, molecules, chains, objects, etc. – just by tapping the screen
- Easy-to-use visualization presets cover the majority of visualization needs such as bond representations and surfaces.
- Distance calculations, structure alignments, anaglyph 3D, and much more
YASARA has seen several updates since I last mentioned it, most recently the ability to display pi-pi and cation-pi interactions.
YASARA is powered by PVL (Portable Vector Language), a new development framework that provides performance way above traditional software . 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 just got this request,
Hi there, I was wondering if you knew of a program that offers similar functionality as Applied Maths BioNumerics software, but runs on Mac OS X (pref 10.7).
Not really my area, anyone have suggestions?
I just noticed ChemDoodle web components have been updated
MacVector 12.6 is now available for download
MacVector is a comprehensive Macintosh application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, and a variety of other functions.
The release notes gives full details of the update
FITTED is a suite of programs to dock flexible ligands into flexible proteins. This software relies on a genetic algorithm to account for flexibility of the two molecules and location of water molecules, and on a novel application of a switching function to retain or displace water molecules and to form potential covalent bonds (covalent docking) with the protein side-chains.
The Suite includes many new features and implementations:
FITTED is a suite of programs (FITTED, PREPARE, ProCESS and SMART), JAVA GUI for easy keyword file editing and docking, Fully automated and flexible protein docking program, Automated covalent docking, Automatic protein preparation from pdb to mol2, Multi-mol2 support for docking and ligand processing, Uses an evolutionary algorithm, Semi-flexible protein docking with flexible waters, Has the ability to consider water molecules displaceable, Keyword files are simpler than ever, Support for Windows, Linux 32 and 64 bits, Mac OSX.
Added to alphabetical listing
ARP/wARP is a software project for automated protein model building and structure refinement. 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. (At the moment only CGMAT is active.) REFMAC also produces an MTZ output file containing weighted coefficients for SigmaA weighted mFo-DFcalc and 2mFo-DFcalc maps, where "missing data" have been restored.
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.
It has now been a couple of years since the human genome was first sequenced and we are now seeing companies offering personal genome sequencing. Illumina are now offering MyGenome an iPad app that allows you to explore a real human genome. In due course they hope to allow you to explore your own genome.
There is more information about the app here.
Now added to the mobile science page.
In systems biology it is becoming a routine task to build models of increasing complexity on a given biochemical network or pathway of interest. One of the main problems in building such models is the determination of the parameters underlying each modelled process. ByoDyn has been designed to provide an easily extendable computational framework to estimate and analyse parameters in highly uncharacterised models
Just added to the alphabetical listing
Graphite - LifeExplorer is a tool for modelling DNA, the tool generates DNA along a Bézier curve, open or closed, allows fine-tuning of atoms' position and, most importantly, exports to PDB. 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: - import PDB files - create isosurface of molecular object - highlight residues of interest - calculate distance between residues pairs - import and export in 3D formats - model DNA and export the result in PDB - visualize a 3D scene with Level of Detail - explore a scene with real-time ambient occlusion - import a file with x,y,z coordinates and convert it into a DNA representation.
You can see a it in action here
A new version of AMBER 12 and AMBER Tools 12 has been released, the main changes are:-
- Force fields: Amber has a new fixed-charge protein force field, ff12SB, enchanced support for polarizable potentials and a new modular lipid force field Lipid11 designed to be compatible with the other pairwise additive AMBER force fields.
- Expanded options for numerical Poisson-Boltzmann solvation calculations, including models for membrane systems and support for periodic systems.
- An enchanced 3D-RISM integral equation model, using the Kovalenko-Hirata (and other) closure approximations, with a better treatement of aqueous electrolytes.
- Improved ideas for self-guided Langevin dynamics and accelerated molecular dynamics, to enchance sampling along soft degrees of freedom.
- Simplified installation and automatic update support.
- Semi-empirical quantum calculations can use d-orbitals, allowing the use of Hamiltonian models such as AM1/d and PM6.
- QM/MM calculations can interface with a variety of external quantum chemistry programs, expanding the types of quantum models available.
- More features from sander have been added to the pmemd code for both CPU and GPU, including Temperature Replica Exchange, Isotropic Periodic Sum, Accelerated Molecular Dynamics and support for various harmonic restraints based on the use of NMRopt on GPUs.
- Expanded methods are available for free energy calculations that change Hamiltonian models, including better procedures for appearing and disappearing atoms, and tighter integration with replica-exchange simulations.
- New facilities are present for using electron density maps (e.g. from cryo EM/ET experiments) as constraints, and to support rigid (or partially flexible) groups in simulations.
There are detailed instructions for installing AMBER 12 under MacOSX and building CUDA enabled AMBER 12.
MolSoft have announced the release of ICM version 3.7-2c.
New features include Atomic Property Fields APF is a 3D pharmacophoric potential implemented on a grid. APF can be generated from one or multiple ligands and seven properties are assigned from empiric physico-chemical components (hydrogen bond donors, acceptors, Sp2 hybridization, lipophilicity, size, electropositive/negative and charge).
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.
Use AQUASITES to design chemicals based on their ability to displace or keep water molecules inside the ligand binding site of proteins. 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).
Protein Modelling Inside ICM there are many features for homology modelling and loop modelling. 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.
"Pipe-able" Scripting in ICM. New options to pipe icm commands and scripts. Easy way to write pipe-able scripts (see $ICMHOME/molpipe/*.icm). Easy way to add parallelism to unix/mac ICM scripts: fork with pipe option ($ICMHOME\molpipe*.icm)
There have been a few comments about an older blog posting concerning EBioTools so I thought I’d bump it to the top of the list.
EBioTools is a compilation of bioinformatics software that has been packaged for easy installation on Mac OS X. It covers many areas, from simple sequence analysis to RNA folding and sequence assembly.
The included software is:
- Name Version
- Clustal W1.83.UNIX
- NCBI Tools2.2.16
As mentioned in the comments added to the older post “EBioTools works under Snow Leopard and Lion but Staden is broken because Apple changed several Libraries to make the MacOSX core "smaller". Most issues are due to Apple changing graphic libraries.”
Users might also be interested in eBioX which brings easy-to-use sequence analysis to Mac-using biologists. It features an editor for sequences and multiple alignments, and graphical viewers for trace files and molecule structures. Many popular file formats are supported. Databases can be created locally or queried over the network, both for metadata and homology (BLAST). Analysis functions include searching for patterns, primers, restriction sites and repeats, translation and back translation, calculating DNA melting temperature, dot plots, as well as aligning sequences (multiple, local and global). Multiple alignments can be created by several of the most popular algorithms
I was just catching up with some reading and I came across an article in Algorithms for molecular biology describing ViennaRNA 2.0 consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. With the new release of version 2.0, they introduce the most recent nearest neighbour energy model for all free energy calculations. Additionally, most of the stand-alone programs included are now able to read FASTA formatted input data. The distribution includes:-
- RNAfold -- predict minimum energy secondary structures and pair probabilities
- RNAeval -- evaluate energy of RNA secondary structures
- RNAheat -- calculate the specific heat (melting curve) of an RNA sequence
- RNAinverse -- inverse fold (design) sequences with predefined structure
- RNAdistance -- compare secondary structures
- RNApdist -- compare base pair probabilities
- RNAsubopt -- complete suboptimal folding
- RNAplot -- RNA structure drawings in PostScript, SVG, or GML
- RNAcofold -- predict hybrid structure of two sequences
- RNAduplex -- predict possible hybridization sites between two sequences
- RNAup -- predict RNA-RNA interaction sites using accessibilities
- RNAalifold -- predict the consensus structure of several aligned sequences
- RNAaliduplex -- comparative (multiple alignment) version of RNAduplex
- RNALfold -- predict locally stable structure of long sequences
- RNAplfold -- compute average pair probabilities for local base pairs in long sequences
- RNApaln -- fast structural alignment of RNA sequences using string alignments
- Several small but helpful Perl Utilities
According to the authors both 1.8.x and 2.0 versions of the Vienna package compile and run on Mac OS X. Currently there's a small compile problem with the included Perl module and the latest gcc versions on Intel based Macs. The defaults for gcc recently changed to compile only Intel code, while the installed Perl is a fat binary containing both PPC and Intel code. The download page contains instruction how to work around this by simply setting an environment variable.
I just got a note that MacVector has been updated to version 12.5 MacVector is a comprehensive Macintosh application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, and a variety of other functions. MacVector is widely regarded as the most intuitive, easy to use program available for sequence analysis.