Open Source Mac Molecular Science Software
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Molecular Science Software for Mac
View 22 business solutionsBrowse free open source Molecular Science software and projects for Mac below. Use the toggles on the left to filter open source Molecular Science software by OS, license, language, programming language, and project status.
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Avogadro
An intuitive molecular editor and visualization tool
Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. It offers a flexible rendering framework and a powerful plugin architecture. -
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Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
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PyRx - Virtual Screening Tool
Virtual Screening software for Computational Drug Discovery
PyRx is a Virtual Screening software for Computational Drug Discovery that can be used to screen libraries of compounds against potential drug targets. PyRx enables Medicinal Chemists to run Virtual Screening from any platform and helps users in every step of this process - from data preparation to job submission and analysis of the results. While it is true that there is no magic button in the drug discovery process, PyRx includes docking wizard with easy-to-use user interface which makes it a valuable tool for Computer-Aided Drug Design. PyRx also includes chemical spreadsheet-like functionality and powerful visualization engine that are essential for Rational Drug Design. Please visits PyRx home page to learn more about PyRx and watch videos on how to use it. -
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Gabedit is a Graphical User Interface for FireFly (PC-Gamess), Gamess-US, Gaussian, Molcas, Molpro, MPQC, NWChem, OpenMopac, Orca, PSI4 and Q-Chem computational chemistry packages.
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Toxtree: Toxic Hazard Estimation
Toxicity prediction for chemical compounds
A GUI application which estimates toxic hazard of chemical compounds. The latest version includes the following toxicity prediction modules: -Cramer rules (oral toxicity) -Toxicity mode of action via Verhaar scheme -Skin irritation and Eye irritation prediction -Benigni / Bossa rulebase for mutagenicity and carcinogenicity prediction -START biodegradation and persistence prediction -Skin sensitisation reactivity domain -Kroes TTC Decision tree -SMARTCyp - Cytochrome P450-Mediated Drug Metabolism and metabolites prediction -Structure Alerts for the in vivo micronucleus assay in rodents (ISSMIC) -Structural Alerts for Functional Group Identification (ISSFUNC) -Structural alerts associated with covalent protein binding and DNA binding. - Ames mutagenicity Toxtree provides a plugin framework to incorporate different approaches to the estimation. Platform independent (written in Java), with the use of The Chemistry Development Kit. -
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FDMNES powered by sparse solvers
The sources and builds history of FDMNES project
The sources and builds history of FDMNES project (http://neel.cnrs.fr/spip.php?rubrique1007&lang=en ) with parallel sparse solvers moved to github: https://github.com/gudasergey/fdmnes -
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BioXTAS RAW
Processing and analysis of Small Angle X-ray Scattering (SAXS) data.
BioXTAS RAW is a program for analysis of Small-Angle X-ray Scattering (SAXS) data. The software enables: creation of 1D scattering profiles from 2D detector images, standard data operations such as averaging and subtraction, analysis of radius of gyration (Rg) and molecular weight, and advanced analysis using GNOM and DAMMIF as well as electron density reconstructions using DENSS. It also allows easy processing of inline SEC-SAXS data and data deconvolution using the evolving factor analysis (EFA) or the regularized alternating least squares (REGALS) methods. Active source code is now maintained on github: https://github.com/jbhopkins/bioxtasraw To install: Check the instructions available at: http://bioxtas-raw.readthedocs.io/en/latest/install.html and in the Files tab. User guides: RAW guides are available at: http://bioxtas-raw.readthedocs.io/ and in the Files tab. To contact us, see: https://bioxtas-raw.readthedocs.io/en/latest/help.html -
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Molsketch
2D molecule editor
Molsketch is a 2D molecular editing tool. Its goal is to help you draw molecules quick and easily. Of course you're creation can be exported afterwards in high quality in a number of vector and bitmap formats. -
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luscus
molecular editor and viewer
Luscus is the program for graphical display and editing of molecular systems. The program allows fast and easy building and/or editing different molecular structures, up to several thousands of atoms large. Luscus can also visualize dipole moments, normal modes, molecular orbitals, electron densities and electrostatic potentials. In addition, simple geometrical objects can be rendered in order to point out a geometrical feature or a physical quantity. The program is developed as a graphical interface for MOLCAS program package, however it's adaptive nature makes possible using luscus with other computational program packages and chemical formats. If you use this program, please cite: G. Kovačević, V. Veryazov, J. Cheminformatics, 7 (2015) 1-10; DOI: 10.1186/s13321-015-0060-z -
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The MolTools Java library provides tools for building applications that handle nucleotide sequence data. Features include sequence I/O, handling of lists/databases of sequences, calculation of Tm, and other utilities for sequence design.
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EMC: Enhanced Monte Carlo; A multi-purpose modular and easy extendable solution to molecular and mesoscale simulations
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GSim - free software tool for visualisation and processing of experimental and simulated nuclear magnetic resonance (NMR) spectra.
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picard
A set of tools for working with high-throughput sequencing data
A set of tools (in Java) for working with next generation sequencing data in the SAM/BAM format. Note that development has moved to GitHub at https://github.com/broadinstitute/picard and support is available on the GATK forum at http://gatkforums.broadinstitute.org/categories/ask-the-team -
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The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
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Software and codes created in "Laboratorio de Química Computacional" of "Facultad de Ciencias y Tecnología" of "Universidad de Carabobo"
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Open3DQSAR is a free, open-source tool written in C aimed at pharmacophore exploration by high-throughput chemometric analysis of molecular interaction fields (MIFs).
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kSNP
kSNP4 does SNP discovery and SNP annotation from whole genomes
kSNP4 identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs. SNP discovery is based on k-mer analysis, and requires no multiple sequence alignment or the selection of a reference genome, so kSNP4 can take 100's of microbial genomes as input. A SNP locus is defined by an oligo of length k surrounding a central SNP allele. kSNP4 can analyze both complete (finished) genomes and unfinished genomes in assembled contigs or raw, unassembled reads. Finished and unfinished genomes can be analyzed together, and kSNP can automatically download Genbank files of the finished genomes and incorporate the information in those files into the SNP annotation. No programming skills are required to use kSNP4 Gardner, S.N. and Hall, B.G. 2013. . PLoS ONE, 8(12):e81760.doi:10.1371/journal.pone.0081760 Gardner, S.N., T. Slezak, and B.G. Hall. 2015 Bioinformatics 31: 2877-2878 doi: 10.1093/bioinformatics/btv271 -
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MZmine 2
A framework for differential analysis of mass spectrometry data
MZmine 2 is a framework written in Java for differential analysis of mass spectrometry data. -
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ShelXle
ShelXle is a Qt GUI for SHELXL
ShelXle combines an editor with syntax highlighting for the SHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (Fo) and difference density (Fo-Fc) maps. See J. Appl. Cryst. (2011). 44, 1281–1284. for details. -
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NanoCap
Carbon Fullerene and Capped Nanotube Generator
NanoCap is a generic application for the construction of low energy fullerene and capped nanotube structures. It provides an ideal tool to accompany the study of finite carbon molecules using computer simulation. The implementation involves a standalone application which includes a GUI and allows for dynamic visual inspection through 3D rendering. In addition, the NanoCap core libraries can be used in custom Python scripts that enabled the user to produce structures in bulk or to include the structure generation routines into pre-existing code. -
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QMForge reads output from various quantum mechanical calculations and provides tools for analyzing these results. Specifically, population (Mulliken and C-squared), fragment, and charge decomposition analyses are available. See https://qmforge.net for more info.
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GrowthRates
Calculate growth rates from microplate reader output
The Bellingham Research Institute (BRI) develops and distributes software that is free of charge to academic and other non-profit organizations. GrowthRates is our software tool that simplifies the analysis of microplate reader output from microbial growth experiments without having to program in Python, R, or MATLAB. It automates the calculation of growth rate parameters, including rates, lag times, maximum population density. Manual calculation of those parameters requires at least 5 minutes per well, or 32 hours for a 384 well plate. GrowthRates completely analyzes growth parameters in all 384 wells in under 5 minutes. CGR2 (Compare Growth Rates) is a statistical program specifically designed to assess the results of a growth rate experiment that has been analyzed using the program GrowthRates. The purpose of a statistical analysis is to establish our level of trust in both the data and in the conclusions we draw from that data. Both the GrowthRate and CGR2 packages are -
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RDML-Ninja is an editor for qPCR data. It is the reference implementation for the RDML data standard allowing to visualize, edit and reanalyze qPCR data.
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SeaBreeze
Open-source cross-platform spectrometer device driver
SeaBreeze is a device driver library that provides an interface to select Ocean Optics spectrometers. It is written in C/C++ and builds and runs on Windows (XP/7/8), MacOSX, and Linux (x86/x64/ARM). -
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