This list of protein structure prediction software summarizes commonly used software tools in protein structure prediction, including homology modeling, protein threading, ab initio methods, secondary structure prediction, and transmembrane helix and signal peptide prediction.
AUTOCAD – Leading 3D Modeling Software. The AUTOCAD for Mac is the best 3d modeling software that money can buy for you. The industry leading software is the first choice for every user who want the best user experience. Blender – Free Open 3D Modeler. The blender is a free open 3D modeler software which is free for use. Oct 03, 2018 Compare the best free open source Mac 3D Modeling Software at SourceForge. Free, secure and fast Mac 3D Modeling Software downloads from the largest Open Source applications and software directory. 358 This Week Last Update: 2014-06-21 See Project.
Jul 14, 2020 MAXON is a l eading developer of 3D software for the creative industries, best known for Its flagship 3D modeling, painting, rendering, and animation software. OpenSCAD is the free 3D Modeling software you can have when you don’t mind coding everything. The tool may not have much toolbars or in-built features, but you have to code everything, through lines of codes. OpenSCAD is the best 3D modeling software for Linux, Windows and Mac OS X devices present out there. Find and compare the top Architecture software on Capterra. Quickly browse through hundreds of options and narrow down your top choices with our free, interactive tool. Filter by popular features, pricing options, number of users and more. Read reviews from real users and find a tool that fits your needs. May 02, 2020 The best 3D modeling software will vary based on your needs, but there plenty of options available. Here are our favorite pieces of software.
Aug 21, 2018 The Ranking: 3D Modeling Software for Mac Users The two most used 3D modeling software programs for Macintosh devices are freeware program Blender (score: 80) and freemium software SketchUp (75). Blender is known for its enormous design freedom and its endless number of tools and functions – however, it’s also known for its steep learning.
Software list[edit]
Best 3d Modeling Software For Mac 2014 Update
Below is a list which separates programs according to the method used for structure prediction.
Homology modeling[edit]
| Name | Method | Description | Link |
|---|---|---|---|
| IntFOLD | A unified interface for: Tertiary structure prediction/3D modelling, 3D model quality assessment, Intrinsic disorder prediction, Domain prediction, Prediction of protein-ligand binding residues | Automated webserver and some downloadable programs | server and downloads |
| RaptorX | remote homology detection, protein 3D modeling, binding site prediction | Automated webserver and Downloadable program | server and download |
| Biskit | wraps external programs into automated workflow | BLAST search, T-Coffee alignment, and MODELLER construction | project site |
| CABS | Reduced modeling tool | Downloadable program | download |
| CPHModel | Fragment assembly | Automated webserver | server |
| ESyPred3D | Template detection, alignment, 3D modeling | Automated webserver | server |
| FoldX | Energy calculations and protein design | Downloadable program | download |
| GeneSilico | Consensus template search/fragment assembly | Webserver | server |
| Geno3D | Satisfaction of spatial restraints | Automated webserver | server |
| HHpred | Template detection, alignment, 3D modeling | Interactive webserver with help facility | |
| Homology Modeling Professional for HyperChem | Template detection, alignment, secondary structure prediction, 3D modeling, ab initio loop modeling, energy-based side-chain rotamer prediction | Standalone windows executable | Home page |
| LOMETS | Local Meta threading server | Meta-server combining 9 different programs | Server |
| MODELLER | Satisfaction of spatial restraints | Standalone program mainly in Fortran and Python | |
| MOE (Molecular Operating Environment) | Template identification, use of multiple templates and accounting for other environments (e.g. excluded ligand volumes), loop modelling, rotamer libraries for sidechain conformations, relaxation using MM forcefields. | Proprietary platform, supported on Windows, Linux and Mac | site |
| Phyre and Phyre2 | Remote template detection, alignment, 3D modeling, multi-templates, ab initio | Webserver with job manager, automatically updated fold library, genome searching and other facilities | server |
| Prime | Physics-based energy function | Graphical interface, sequence alignment, secondary structure prediction, homology modeling, protein refinement, loop-prediction, and side-chain prediction | site |
| ROBETTA | Rosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction | Webserver | server |
| BHAGEERATH-H | Combination of ab initio folding and homology methods | Protein tertiary structure predictions | server |
| Selvita Protein Modeling Platform | Package of tools for protein modeling | Free demo, interactive webserver and standalone program including: BLAST search, CABS modeling, 3D threading, Psi-Pred secondary structure prediction | Home page |
| STRUCTUROPEDIA | WebInterface to MODELLER | Homology modeling of proteins in monomeric or multimeric forms alone and in complex with peptides and DNA as well as introduction of mutations and post-translational modifications (PTMs) into protein structures | server |
| SWISS-MODEL | Local similarity/fragment assembly | Automated webserver (based on ProModII) | server |
| TIP-STRUCTFAST | Automated Comparative Modeling | Webserver | site |
| WHAT IF | Position specific rotamers | Standalone program and webinterface | |
| Yasara | Detection of templates, alignment, modeling incl. ligands and oligomers, hybridization of model fragments | Graphical interface or text mode (clusters) |
Threading/fold recognition[edit]
| Name | Method | Description | Link |
|---|---|---|---|
| IntFOLD | A unified interface for: Tertiary structure prediction/3D modelling, 3D model quality assessment, Intrinsic disorder prediction, Domain prediction, Prediction of protein-ligand binding residues | Automated webserver and some downloadable programs | server and downloads |
| RaptorX | Remote template detection, single-template and multi-template threading, totally different from and much better than the old program RAPTOR designed by the same group | Webserver with job manager, automatically updated fold library | download server |
| FALCON@home | Single-template and multi-template threading, a high-throughput server based on volunteer computing | Webserver with job manager | |
| HHpred | Template detection, alignment, 3D modeling | Interactive webserver with help facility | |
| NovaFold | Combination of threading and ab initio folding | Commercial protein structure prediction application | Home page |
| I-TASSER | Combination of ab initio folding and threading methods | Structural and function predictions | server |
| mGenTHREADER/GenTHREADER | Sequence profile and predicted secondary structure | Webserver | main page |
| MUSTER | profile-profile alignment | Webserver | server |
| Phyre and Phyre2 | Remote template detection, alignment, 3D modeling, multi-templates, ab initio | Webserver with job manager, automatically updated fold library, genome searching and other facilities | server |
| Selvita Protein Modeling Platform | Package of tools for protein modeling | Free demo, interactive webserver and standalone program including: 3D threading and flexible 3d threading | Home page |
| SUPERFAMILY | Hidden Markov modeling | Webserver/standalone | main page |
| SPARKS-X | 3D structure modeling by Fold recognition according to Sequence profiles and structural profiles | Webserver | Server |
| BBSP - Building Blocks Structure Predictor | Hybrid template-based | Free application plus database | main page |
| DeepFR | Remote template selection, 3D modeling | Improving protein fold recognition by extracting fold-specific features from predicted residue-residue contacts | server |
Ab initio structure prediction[edit]
| Name | Method | Description | Link |
|---|---|---|---|
| trRosetta | trRosetta is an algortihm for fast and accurate de novo protein structure prediction. It builds the structure by deep learning restraints-guided energy mimization in Rosetta. | Webserver and standalone package | |
| EVfold | Evolutionary couplings calculated from correlated mutations in a protein family, used to predict 3D structure from sequences alone and to predict functional residues from coupling strengths. Predicts both globular and transmembrane proteins. | Webserver | Server |
| FALCON | A position-specific hidden Markov model to predict protein structure by iteratively refining the distributions of dihedral angles | Webserver | |
| QUARK | Monte Carlo fragment assembly | On-line server for protein modeling (best for ab initio folding in CASP9) | Server |
| NovaFold | Combination of threading and ab initio folding | Commercial protein structure prediction application | Home page |
| I-TASSER | Threading fragment structure reassembly | On-line server for protein modeling | Server |
| Selvita Protein Modeling Platform | Package of tools for protein modeling | Interactive webserver and standalone program including: CABS ab initio modeling | Home page |
| ROBETTA | Rosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction | Webserver | server |
| Rosetta@home | Distributed-computing implementation of Rosetta algorithm | Downloadable program | main page |
| CABS | Reduced modeling tool | Downloadable program | download |
| CABS-FOLD | Server for de novo modeling, can also use alternative templates (consensus modeling). | Webserver | server |
| Bhageerath | A computational protocol for modeling and predicting protein structures at the atomic level. | Webserver | Server |
| Abalone | Molecular Dynamics folding | Program | Example |
| PEP-FOLD | De novo approach, based on a HMM structural alphabet | On-line server for peptide structure prediction | Server |
Secondary structure prediction[edit]
Detailed list of programs can be found at List of protein secondary structure prediction programs
Transmembrane helix prediction[edit]
| Name | Method | Description | Link |
|---|---|---|---|
| HMMTOP | Hidden Markov Model | Webserver/standalone | main page |
| MEMSAT | Neural networks and SVMs | Webserver/standalone | main page |
| PHDhtm in PredictProtein | Multiple alignment-based neural network system | Webserver/standalone | server |
| Phobius | Homology supported predictions | Webserver/standalone | main page |
| TMHMM | Hidden Markov Model | Webserver/standalone | main page |
| CCTOP | Consensus/Hidden Markov Model | Webserver/standalone | main page |
| SVMTop2 | Support Vector Machines | Webserver | main page |
Signal peptide prediction[edit]
| Name | Method | Description | Link |
|---|---|---|---|
| SignalP | artificial neural networks and hidden Markov models | Webserver/standalone | server |
| Phobius | Webserver | server |
See also[edit]
References[edit]
Best 3D Modeling Software for Mac: 3D Printing with Mac OS
Best 3d Software For Mac
Not all 3D modeling software is available for every operating system. That’s why we compiled a list of the most popular 3D design programs for Mac users. Read on to discover the top 20!
The list of the most used 3D design software for Mac (see below) is based upon our list of the 25 most popular 3D modeling programs. However, we excluded software that is not available or not suitable for the Mac OS. This leaves us with the ultimate 3D modeling list for Macintosh users.
The Ranking: 3D Modeling Software for Mac Users
The two most used 3D modeling software programs for Macintosh devices are freeware program Blender (score: 80) and freemium software SketchUp (75). Blender is known for its enormous design freedom and its endless number of tools and functions – however, it’s also known for its steep learning curve. SketchUp, on the other hand, is said to be rather beginner-friendly and great for architectural and geometric objects. However, it’s not suited for creating organic structures.
Next come three programs from the Autodesk family: its professional high-end programs AutoCAD (59) and Maya (59) as well as its beginner-friendly free-to-use online app Tinkercad (51) all score well with Mac users. ZBrush (49), a professional 3D sculpting software, comes in 6th. Its free light version, named Sculptris (19), made it to rank 15.
After ZBrush, Cinema 4D (43), 123D Design (42), OpenSCAD (38), and Rhinoceros (36) complete the list of the top 10.
Screenshot of SketchUp, a popular 3D modeling software with Mac users.
The Popularity Score for 3D Modeling Programs
We calculated the popularity of a 3D modeling software for Mac based on their ‘popularity score’ in the 3D printing community. The popularity score consists of mentions and fans on social media, page authority, forum mentions, video mentions, 3D printing database mentions, and Google results. This score is especially helpful if you’re looking for a modeling software for Mac that is widely used for 3D printing, so you can be assured of an online community to brainstorm with and help you out if you get stuck.
3D Design Programs that Won’t Run on Apple’s Mac
Most 3D design programs are available for Windows and Mac users alike. However, some 3D design software that is not available for Mac OS includes Solidworks (62), 3DS Max (55), and Inventor (55). While these are not many, they still represent quite popular 3D modeling software packages. In our original list which includes all platforms, these programs ranked 3rd, 6th, and 7th among the most popular.
Some good news to end with: there are more and more options for Mac users. For example, Rhino 5 is available for Mac. Since many 3D design apps run online now (browser-based), programs like Tinkercad and 3DTin are also accessible from any device. With Cheetah3D there’s also a 3D design software which is exclusively available for Mac OS.
Are you new to the world of 3D modeling and 3D printing? Make sure to avoid these 5 common mistakes in order to create stunning designs. Do you already know how to create printable 3D files? Then simply upload them to our website, choose from more than 100 materials and finishes, and let us take care of printing your object.