Molecular Science Software


  • More...

Category Category

    • More...

License License

Translations Translations

Programming Language Programming Language

  • More...

Status Status

Audience Audience

User Interface User Interface

Freshness Freshness

Molecular Science Software

  • Take Our Survey. We Plant a Tree. Take Our Survey. We Plant a Tree. Icon
    Take Our Survey. We Plant a Tree. Icon

    In honor of Earth Day, HPCC Systems is committed to planting 10,000 new trees across our national forests.

    HPCC Systems is dedicated to the environment and is giving you the opportunity to take action and be a small part of a big impact. In partnership with the National Forest Foundation, HPCC Systems is growing and promoting awareness of environmental sustainability with their 10K Trees Challenge. The best time to plan a tree was 20 years ago. The second best time is now! Take our survey and take part in helping the environment.
  • Microsoft Office 365 monitoring simplified Microsoft Office 365 monitoring simplified Icon
    Microsoft Office 365 monitoring simplified Icon

    Monitor your Office 365® (O365) Exchange™ mailboxes and system applications with the SolarWinds® Server & Application Monitor unified platform.

    SolarWinds Server & Application Monitor allows you to monitor your hybrid IT applications and systems. Monitor Microsoft® Office 365 Exchange side by side on your on-premises Exchange server and other applications. Check, track, and report on O365 user/shared mailbox growth, users over quota, archived mailboxes, inactive mailboxes, mobile device, mailbox groups, and more. You can also monitor Microsoft portal access to help ensure you’re meeting your SLAs.
  • relax Icon


    Molecular dynamics by NMR data analysis

    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 NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using anisotropic NMR parameters such as RDCs and PCSs, the investigation of stereochemistry in dynamic ensembles, and the analysis of relaxation dispersion data.

    Downloads: 970 This Week Last Update: See Project
  • APBS Icon


    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. <>. Please register at before downloading!

  • Gabedit

    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.

  • Subread

    High-performance read alignment, quantification and mutation discovery

    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 detection of exon-exon junction. For the mapping of RNA-seq reads, Subread performs local alignments and Subjunc performs global alignments. Subread and Subjunc were published in the following paper: Yang Liao, Gordon K Smyth and Wei Shi. "The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote", Nucleic Acids Research, 2013, 41(10):e108

    Downloads: 446 This Week Last Update: See Project

    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.

  • Get your Apps to customers 5x faster with RAD Studio. Get your Apps to customers 5x faster with RAD Studio. Icon
    Get your Apps to customers 5x faster with RAD Studio. Icon

    The easiest and most powerful cross platform development tool available on the market. Start a free trial today (no credit card needed).

    RAD StudioTM: Build cross-platform apps ridiculously FAST!
    • Delivering fast and powerful native applications for Windows, Linux, macOS, iOS, Android, cloud and IoT.
    • Rapidly design, build, and run applications optimized for native performance, from a single code base across all platforms.
    • Securely connect and embed any data, on any tier, in the Enterprise, or cloud.
  • BioXTAS RAW Icon


    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. It also allows easy processing of inline SEC-SAXS data and data deconvolution using the evolving factor analysis (EFA) method. To install: Check the instructions available at: and in the Files tab. User guides: RAW guides are available at: and in the Files tab. For requests, comments, and bug reports try our google group: If that doesn't work, contact: soren (dot) skou (at) saxslab (dot) com and hopkins (dot) jesse (at) gmail (dot) com.

    Downloads: 174 This Week Last Update: See Project
  • Ocean Optics Sample Pack Icon

    Ocean Optics Sample Pack

    Sample code for Ocean Optics OmniDriver spectrometer device driver

    Sample code demonstrating how to use OmniDriver to drive Ocean Optics full range of spectrometers from C, C++, C#, Java, LabVIEW, Delphi, MATLAB and more.

    Downloads: 81 This Week Last Update: See Project
  • SASfit Icon


    A program for fitting structural models to small angle scattering data

    SASfit has been written for analyzing and plotting small angle scattering data. It can calculate integral structural parameters like radius of gyration, scattering invariant, Porod constant. Furthermore it can fit size distributions together with several form factors including different structure factors. Additionally an algorithm has been implemented, which allows to simultaneously fit several scattering curves with a common set of (global) parameters. This last option is especially important in contrast variation experiments or measurements with polarised neutrons. The global fit helps to determine fit parameters unambiguously which by analysing a single curve would be otherwise strongly correlated. SASfit user guides: releases: code:

    Downloads: 66 This Week Last Update: See Project
  • SeaBreeze Icon


    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).

    Downloads: 54 This Week Last Update: See Project
  • Molecular Dynamics Studio

    Molecular Dynamics Cell Construction

    This is a collection of software modifications created to integrate NanoEngineer-1, PACKMOL and MSI2LMP for the purpose of easily creating molecular dynamics cells. NanoEngineer-1 is a molecular CAD software written by Nanorex and provides the user an easy way to create molecules, while the software modifications allow the user to type atoms using multiple force fields. PACKMOL can generate a random collection of molecules using the molecule templates from NanoEngineer-1 thus providing the initial MD cell. Modifications to PACKMOL allow the atom type data to be passed through to the MSI2LMP software. MSI2LMP creates a LAMMPS input file based on class I or class II force fields. MSI2LMP was modified to use numerically coded force field data generated by NanoEngineer-1. The MMP file format was extended and integrated into all three software applications.

  • Locate Sensitive Data across Networks and Workstations Locate Sensitive Data across Networks and Workstations Icon
    Locate Sensitive Data across Networks and Workstations Icon

    Build the Business Case for Effective Security Investments

    Your customers recognize the importance of security, but often don’t realize the urgency until they see something tangible. SolarWinds® Risk Intelligence assigns value to your data vulnerability, helping you build a strong business case for data protection and triage the most important problems to tackle. Some powerful features include data risk communicated as financial impact, at-risk data discovery and PCI DSS, PAN & PII scans.
  • Open3DQSAR Icon


    Open3DQSAR is a free, open-source tool written in C aimed at pharmacophore exploration by high-throughput chemometric analysis of molecular interaction fields (MIFs).

  • luscus Icon


    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

    Downloads: 29 This Week Last Update: See Project
  • EMC: Enhanced Monte Carlo

    EMC: Enhanced Monte Carlo; A multi-purpose modular and easy extendable solution to molecular and mesoscale simulations

    Downloads: 27 This Week Last Update: See Project

    MELTING is a software to compute, for a nucleic acid duplex, the enthalpy and the entropy of the helix coil transition and then the melting temperature. Four types of hybridization are possible : DNA/DNA, RNA/RNA, RNA/DNA and mRNA/RNA.

  • STochastic Engine for Pathway Simulation Icon

    STochastic Engine for Pathway Simulation

    Stochastic simulator for signaling pathways occuring in biological cells. Handles reaction-diffusion processes in 3D tetrahedral meshes.

  • Iphigenie Icon


    A fast and versatile molecular dynamics program

    The molecular mechanics (MM) program Iphigenie provides a broad range of molecular dynamics (MD) methods and technologies, including polarizable force fields (PMM), the HADES reaction field, and QM/(P)MM hybrid simulations.

    Downloads: 24 This Week Last Update: See Project
  • RMGDFT Icon


    Real Space Multigrid based electronic structure code.

    News: V2.2.2 released on 10/14/2017 with minor bug fixes. News: V2.2 with performance enhancements, bug fixes and new features released on 06/26/2017. Sources are available with binaries to follow soon. News: V2.1 with many improvements released on 07/15/2016. Sources and binaries are available. RMG is a density functional theory (DFT) based electronic structure code that uses real space grids to represent wavefunctions, charge densities and ionic potentials. Designed for scaleability it has been run successfully on systems with thousands of nodes and hundreds of thousands of CPU cores. It is currently under active development and contributions are gladly accepted.

    Downloads: 7 This Week Last Update: See Project
  • Open3DALIGN Icon


    An open-source software aimed at unsupervised molecular alignment

    Downloads: 6 This Week Last Update: See Project
  • Open3DGRID Icon


    An open-source software aimed at high-throughput generation of molecular interaction fields (MIFs)

  • PUPIL Icon


    PUPIL (Program for User Package Interface and Linking), is a software environment that allows developers to link quickly and efficiently together multiple pieces of software in a fully automated multi-scale simulation. More specifically, it supports QM/MM MD simulations where the user might choose among any of the different MD engines and QM engines, which are connected to PUPIL as external programs through a tiny specific interface. One of the main advantages here is that the user can use most of the functionalities that may have those external programs interfaced without the necessity to be reimplemented again on independent interfaces. In fact, this simulation interface concentrates all the common code involved in the coupling terms of the QM/MM approach.

    Downloads: 4 This Week Last Update: See Project
  • APBSmem

    APBSmem is a Java-based graphical user interface for Poisson-Boltzmann electrostatics calculations at the membrane. APBS version 1.2.0 or later is required.

    Downloads: 3 This Week Last Update: See Project
  • Tahoe

    Tahoe is a research-oriented platform for the development of numerical methods and models for the simulation of complex material behavior.

    Downloads: 2 This Week Last Update: See Project
  • genomecomb

    Genomecomb is a package for the analysis of complete genome data. It can be used to compare, annotate and especially filter the results of complete genome sequencing.

    Downloads: 2 This Week Last Update: See Project
  • HostDesigner

    General purpose de novo molecular design software

    Although many potential applications exist in chemistry and material science, software to allow the general application of de novo structure-based design methods in supramolecular chemistry was non-existent. To address this limitation we created HostDesigner, a code that builds and evaluates millions of molecules in minutes. This command line executable builds 3D molecular structures by covalently connecting user-defined input fragments with pre-computed hydrocarbon fragments from a library. The results are ranked with respect to desired geometric constraints defined by the user. See the User's Manual for further details including a list of literature citations for example applications. Download includes User's Manual, HostDesigner 4.0 source code (in Fortran), data files, example input, HDViewer executables for MacOS, Linux, and Windows, and mengine source code (in C). HostDesigner was developed and posted by author Dr. Benjamin P Hay

    Downloads: 1 This Week Last Update: See Project
  • Collaborative Computing Project for NMR

    Collaborative Computing Project for NMR (CCPN)

    The Collaborative Computational Project for NMR (CCPN) provides tools and knowledge to maximise the impact of the biological NMR studies. The CCPN software facilitates data analysis and software integration. The project actively promotes the exchange of knowledge and provides training and best practices for the NMR community. CCPN also has a leading role in the development of a NMR data-sharing standard and coordination of NMR instrumentation proposals for RCUK and BIS. The 28 partners of CCPN jointly cover all aspects of biomolecular NMR and together they promote excellence in science in their respective fields.

    Downloads: 0 This Week Last Update: See Project
  • Previous
  • You're on page 1
  • 2
  • Next

Get latest updates about Open Source Projects, Conferences and News.

No, Thank you