Top Most Downloaded Molecular Science Apps

3D molecular structure editorAvogadro is an application purely for scientists and students that have to draw three-dimensional molecular compositions that showing a molecule from every conceivable angle and perspective.It works across platforms and is used in computational chemistry, molecular modeling, bio informatics...

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....

Periodic Table of Elements a quick reference toolPeriodic Table of Elements is a quick reference tool that allows you a quick glance to get general information about an element. The program is for educational purposes. Paper charts are the most common way that people find the names, groups, atomic weights, and other i...

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 a...

The Subread software package is a tool kit for processing next-gen sequencing data. It includes Subread aligner, Subjunc exon-exon junction detector and featureCounts read summarization program. Subread aligner can be used to align both gDNA-seq and RNA-seq reads. Subjunc aligner was specified designed for the detecti...

APBS is a software package for the numerical solution of the Poisson-Boltzmann equation, a popular continuum model for describing electrostatic interactions between molecular solutes over a wide range of length scales. <http://www.poissonboltzmann.org/>. Please register at http://eepurl.com/by4eQr before downloa...

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 carcinogen...

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. Gabedit makes using Computational Chemistry Packages (CCP) simple and straightforward .Sketch in molecules using its advanced 3D Structu...

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. open, save and import in all formats supported by the OpenBabel(tm) libraryexport to Scalable Vector Graphics...

OpenCFU is a completely open source lightweight application designed to enumerate clustered circular objects such as bacterial colonies. It can handle digital pictures as well as live stream from a video device/webcam. OpenCFU is cross-platform, fast, reliable and allows the user to implement intuitive filters. Addit...

GSim - free software tool for visualisation and processing of experimental and simulated nuclear magnetic resonance (NMR) spectra....

The SourceForge OpenRasMol project is an adjunct to the RasMol and OpenrasMol project at http://rasmol.org. It is hoped that the SourceForge OpenRasMol project will provide a convenient focal point for active collaborative contributions....

RasTop is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules based on the popular Rasmol software. The program is aimed at the rapid visualization and analysis of molecules....

kSNP 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 kSNP can take 100's of microbial genomes as input. A SNP locus is def...

The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of...

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....

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...

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 ...

LAMMPS is a classical molecular dynamics simulator designed for parallel machines. It can model atomic, polymeric, biological, metallic, or mesoscale systems using a variety of force fields and boundary conditions and is easy to modify or extend....

Mac upgraded to OSX, Lepard which do not support os9 anymore. This project is build to help DNA Strider user to get their data out and perform some basic DNA analyze function....