CrystalMaker 10.4.7 CrystalMaker is a program for generating, displaying, and manipulating all kinds of crystal and molecular structures, in stunning photo-realistic colour. CrystalMaker is a very powerful crystallographic tool - but is designed to be used by everyone, not just professional crystallographers. SnapGene is a versatile molecular biology software that enables you to documents DNA constructs without having to deal with complicated tools or workflows. The data can then by exported to file formats compatible with other popular software solutions designed to work with DNA sequences.
- Best Molecular Biology Software Machines
- Molecular Biology Software Mac
- Best Molecular Biology Software Mac Os
- Best Molecular Biology Software Machine
This is a list of computer programs that are predominantly used for molecular mechanics calculations.
Best Molecular Biology Software Machines
- GPU – GPU accelerated
- I – Has interface
- Imp – Implicit water
- MC – Monte Carlo
- MD – Molecular dynamics
- Min – Optimization
- QM – Quantum mechanics
- REM – Replica exchange method
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| Name | View 3D | Model builder | Min | MD | MC | REM | QM | Imp | GPU | Comments | License | Website |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Abalone | Yes | Yes | Yes | Yes | Yes | Yes | I | Yes | Yes | Biomolecular simulations, protein folding. | Proprietary, gratis, commercial | Agile Molecule |
| ADF | Yes | Yes | Yes | Yes | No | No | Yes | Yes | Yes | Modeling suite: ReaxFF, UFF, QM-MM with Amber and Tripos force fields, DFT and semi-empirical methods, conformational analysis with RDKit; partly GPU-accelerated | Proprietary, commercial, gratis trial | SCM |
| Ascalaph Designer | Yes | Yes | Yes | Yes | Yes | Yes | I | Yes | Yes | Molecular building (DNA, proteins, hydrocarbons, nanotubes), molecular dynamics, GPU acceleration | Mixed: free open source (GNU GPL) & commercial | Ascalaph Project |
| Avogadro | Yes | Yes | Yes | No | No | No | I | No | No | Molecule building, editing (peptides, small molecules, crystals), conformational analysis, 2D/3D conversion; extensible interfaces to other tools | Free open sourceGNU GPL | Avogadro |
| BOSS | No | No | Yes | No | Yes | No | Yes | No | No | OPLS | Proprietary | Yale University |
| CHARMM | No | Yes | Yes | Yes | Yes | I | I | Yes | Yes | Commercial version with multiple graphical front ends is sold by Accelrys (as CHARMm) | Proprietary, commercial | charmm.org |
| CHEMKIN | No | No | No | No | No | No | No | No | No | Chemical reaction kinetics. | Proprietary | CHEMKIN |
| CP2K | No | No | Yes | Yes | Yes | No | Yes | Yes | Yes | CP2K can perform atomistic and molecular simulations of solid state, liquid and biological systems. | Free open sourceGNU GPLv2 or later | CP2K |
| Desmond | Yes | Yes | Yes | Yes | No | Yes | No | No | Yes | High performance MD; has comprehensive GUI to build, visualize, and review results and calculation setup up and launch | Proprietary, commercial or gratis | |
| Discovery Studio | Yes | Yes | Yes | Yes | Yes | No | Yes | Yes | No | Comprehensive life science modeling and simulation suite of applications focused on optimizing drug discovery process: small molecule simulations, QM-MM, pharmacophore modeling, QSAR, protein-ligand docking, protein homology modeling, sequence analysis, protein-protein docking, antibody modeling, etc. | Proprietary, trial available | Dassault Systèmes BIOVIA (formerly Accelrys) |
| fold.it | Y / I | Yes | Yes | Yes | Yes | Yes | I | No | No | University of Washington and The Baker Labs; structure prediction, protein folding | Proprietary, commercial or gratis | fold.it download page |
| FoldX | I | Yes | Yes | No | No | No | No | No | No | Energy calculations, protein design | Proprietary, commercial or gratis | CRG |
| GROMACS | No | No | Yes | Yes | No[1] | Yes | I | Yes[2] | Yes | High performance MD | Free open sourceGNU GPL | gromacs.org |
| GROMOS | No | No | Yes | Yes | Yes | Yes | No | Yes | Yes | Intended for biomolecules | Proprietary, commercial | GROMOS website |
| LAMMPS | Yes | Yes | Yes | Yes | Yes | Yes | I | Yes | Yes | Has potentials for soft and solid-state materials and coarse-grain systems | Free open source, GNU GPLv2 | Sandia |
| MacroModel | Yes | Yes | Yes | Yes | Yes | No | I | Yes | No | OPLS-AA, MMFF, GBSA solvent model, conformational sampling, minimizing, MD. Includes the Maestro GUI which provides visualizing, molecule building, calculation setup, job launch and monitoring, project-level organizing of results, access to a suite of other modelling programs. | Proprietary | Schrödinger |
| MAPS[3] | Yes | Yes | Yes | Yes | Yes | Yes | Yes | No | Yes | Building, visualizing, and analysis tools in one user interface, with access to multiple simulation engines | Proprietary, trial available | Scienomics |
| Materials Studio | Yes | Yes | Yes | Yes | Yes | No | Yes | Yes | Yes | Environment that brings materials simulation technology to desktop computing, solving key problems in R&D processes | Proprietary, trial available | Dassault Systèmes BIOVIA (formerly Accelrys) |
| MBN Explorer[4] + MBN Studio | Yes | Yes | Yes | Yes | Yes | No | No | Yes | Yes | Standard and reactive CHARMM force fields; molecular modeler (carbon nanomaterials, biomolecules, nanocrystals); explicit library of examples | Proprietary, free trial available | MBN Research Center |
| MDynaMix | No | No | No | Yes | No | No | No | No | No | Parallel MD | Free open sourceGNU GPL | Stockholm University |
| MOE | Yes | Yes | Yes | Yes | No | No | I | Yes | No | Molecular Operating Environment (MOE) | Proprietary | Chemical Computing Group |
| Orac | No | No | Yes | Yes | No | Yes | No | Yes | No | Molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomic level | Free open source | Orac download page |
| NAMD + VMD | Yes | Yes | Yes | Yes | No | Yes | I | Yes | Yes | Fast, parallel MD, CUDA | Proprietary, free academic use, source code | Beckman Institute |
| NWChem | No | No | Yes | Yes | No | No | Yes | No | No | High-performance computational chemistry software, includes quantum mechanics, molecular dynamics and combined QM-MM methods | Free open source, Educational Community License version 2.0 | NWChem |
| Protein Local Optimization Program | No | Yes | Yes | Yes | Yes | No | No | No | No | Helix, loop, and side chain optimizing, fast energy minimizing | Proprietary | PLOP wiki |
| Q | No | No | No | Yes | No | No | No | No | No | (I) Free energy perturbation (FEP) simulations, (II) empirical valence bond (EVB), calculations of reaction free energies, (III) linear interaction energy (LIE) calculations of receptor-ligand binding affinities | Free open sourceGNU GPLv2 or later | Q |
| SAMSON | Yes | Yes | Yes | Yes | No | No | Yes | No | No | Computational nanoscience (life sciences, materials, etc.). Modular architecture, modules termed SAMSON Elements | Proprietary, gratis | SAMSON Connect |
| Scigress | Yes | Yes | Yes | Yes | No | No | Yes | Yes | No | MM, DFT, semiempirical methods, parallel MD, conformational analysis, Linear scaling SCF, docking protein-ligand, Batch processing, virtual screening, automated builders (molecular dynamics, proteins, crystals) | Proprietary | SCIGRESS.com |
| Spartan | Yes | Yes | Yes | No | Yes | No | Yes | Yes | No | Small molecule (< 2,000 a.m.u.) MM and QM tools to determine conformation, structure, property, spectra, reactivity, and selectivity. | Proprietary, free trial available | Wavefunction, Inc. |
| TeraChem | No | No | Yes | Yes | No | No | Yes | No | Yes | High performanceGPU-accelerated ab initiomolecular dynamics and TD/DFT software package for very large molecular or even nanoscale systems. Runs on NVIDIAGPUs and 64-bitLinux, has heavily optimized CUDA code. | Proprietary, trial licenses available | PetaChem LLC |
| TINKER | I | Yes | Yes | Yes | Yes | I | I | Yes | Yes | Software tools for molecular design-Tinker-OpenMM[5] Software tools for molecular design-Tinker-HP[6] | Proprietary, gratis | Washington University |
| Tremolo-X | I | No | Yes | Yes | No | No | No | No | No | Fast, parallel MD | Proprietary | Tremolo-X |
| UCSF Chimera | Yes | Yes | Yes | No | No | No | No | No | No | Visually appealing viewer, amino acid rotamers and other building, includes Antechamber and MMTK, Ambertools plugins in development. | Proprietary, free academic use | University of California |
| YASARA | Yes | Yes | Yes | Yes | No | No | Yes | No | Yes | Molecular graphics, modeling, simulation | Proprietary | YASARA.org |
Molecular Biology Software Mac
See also[edit]
Best Molecular Biology Software Mac Os
Notes and references[edit]
Best Molecular Biology Software Machine
- ^Harrison ET, Weidner T, Castner DG, Interlandi G (2017). 'Predicting the orientation of protein G B1 on hydrophobic surfaces using Monte Carlo simulations'. Biointerphases. 12 (2): 02D401. doi:10.1116/1.4971381. PMC5148762. PMID27923271.
- ^Implicit Solvent - GromacsArchived July 29, 2014, at the Wayback Machine
- ^'MAPS'. Archived from the original on 2019-11-28. Retrieved 2016-11-14.
- ^I.A. Solov'yov, A.V. Yakubovich, P.V. Nikolaev, I. Volkovets, A.V. Solov'yov (2012). 'MesoBioNano Explorer - A universal program for multiscale computer simulations of complex molecular structure and dynamics'. J. Comput. Chem. 33 (30): 2412–2439. doi:10.1002/jcc.23086. PMID22965786.CS1 maint: uses authors parameter (link)
- ^M. Harger, D. Li, Z. Wang, K. Dalby, L. Lagardère, J.-P. Piquemal, J. Ponder, P. Ren (2017). 'Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs'. Journal of Computational Chemistry. 38 (23): 2047–2055. doi:10.1002/jcc.24853. PMC5539969. PMID28600826.CS1 maint: multiple names: authors list (link)
- ^L. Lagardère,L.-H. Jolly, F. Lipparini, F. Aviat, B. Stamm, Z. F. Jing, M. Harger, H. Torabifard, G. A. Cisneros, M. J. Schnieders, N. Gresh, Y. Maday, P. Y. Ren, J. W. Ponder, J.-P. Piquemal (2018). 'Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields'. Chemical Science. 9 (4): 956–972. doi:10.1039/C7SC04531J. PMC5909332. PMID29732110.CS1 maint: multiple names: authors list (link)
External links[edit]
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