92 packages found. Page 1 of 2.

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Name Version Votes Popularity? Description Maintainer Last Updated
gromacs 2023.2-1 24 0.00 A versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. hseara 2023-08-04 19:09 (UTC)
vmd 1.9.4a57-1 20 0.00 Visual Molecular Dynamics (official binary build) berquist 2023-06-10 01:50 (UTC)
emboss 6.6.0-3 20 0.00 A collection of molecular biology applications mschu 2020-05-11 20:54 (UTC)
ucsf-chimera 1.16-1 15 0.00 Extensible molecular modeling system Athemis 2022-03-14 11:11 (UTC)
lammps 20230802-1 12 0.01 Large-scale Atomic/Molecular Massively Parallel Simulator fromtheeast710 2023-08-13 17:50 (UTC)
seaview 5.0.5-8 11 0.00 GUI for multiple sequence alignment and molecular phylogeny. https://doi.org/10.1093/molbev/msp259 malacology 2022-09-03 01:59 (UTC)
molden 7.3-3 7 0.10 A program for molecular and electronic structure visualization banana-bred 2024-03-08 17:18 (UTC)
avogadroapp 1.99.0-2 7 0.28 An advanced molecular editor malacology 2024-02-12 17:24 (UTC)
xcrysden 1.6.2-2 6 0.00 crystalline and molecular structure visualisation program specter119 2020-06-03 08:59 (UTC)
libmsym-git 0.2.3.r190.c994703-1 6 0.00 A library for handling molecular point group symmetry, with a Python interface (git version) berquist 2018-04-06 18:34 (UTC)
autodock-vina 1.2.5-1 6 0.00 A tool for drug discovery, molecular docking and virtual screening mschu 2023-07-10 12:04 (UTC)
python-mdtraj 1.9.7-1 4 0.00 A modern, open library for the analysis of molecular dynamics trajectories hseara 2022-01-06 12:01 (UTC)
plumed 2.8.2-1 3 0.00 An open source plugin for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. hseara 2023-05-19 09:30 (UTC)
garlic 1.6-13 3 0.00 Molecular visualization program malacology 2023-04-04 19:03 (UTC)
gamess 2023R2-1 3 0.00 The General Atomic and Molecular Electronic Structure System a.kudelin 2024-01-27 10:08 (UTC)
apbs 3.4.1-2 3 0.00 Software for biomolecular electrostatics and solvation calculations willemsk 2022-12-01 08:45 (UTC)
vmd-src 1.9.4a57-3 2 0.00 Visual Molecular Dynamics a.kudelin 2023-06-01 08:51 (UTC)
rasmol-gtk 2.7.5.2-2 2 0.00 A program for molecular graphics visualisation (aka openrasmol) leepesjee 2015-12-03 00:48 (UTC)
openbabel-git 3.0.90.r5774.686ee22f2-1 2 0.00 A library designed to interconvert between many file formats used in molecular modeling and computational chemistry (git version, builds Python bindings) berquist 2020-03-22 18:02 (UTC)
namd 2.14-3 2 0.00 Scalable molecular dynamic engine orphan 2020-10-02 17:06 (UTC)
megax-bin 10.2.6-1 2 0.65 Molecular Evolutionary Genetics Analysis malacology 2021-06-12 01:37 (UTC)
kim-api 2.2.1-1 2 0.00 Online framework for reliable, reproducible and portable molecular simulations dschopf 2020-12-29 08:54 (UTC)
gromacs-plumed 2022.5-1 2 0.00 GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. (Plumed patched) hseara 2023-05-19 10:08 (UTC)
cp2k-bin 2024.1-1 2 0.00 A quantum chemistry and solid state physics software package for atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. (precompiled, OpenMP) petronny 2024-01-15 07:57 (UTC)
chimerax 1.7-2 2 1.33 UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. tzok 2024-03-22 10:27 (UTC)
blender-plugin-molecular 1.1.1_r249.e4ef6a2-2 2 0.00 Blender addon for advance particle physics, multithreaded. bartus 2021-01-12 18:44 (UTC)
ambertools 23.00-1 2 0.00 Biomolecular simulation package (tools only) yitzi 2023-06-01 14:47 (UTC)
python-pdb2pqr 3.6.2-1 1 0.00 Automates many of the common tasks of preparing structures for continuum solvation calculations as well as many other types of biomolecular structure modeling, analysis, and simulation. willemsk 2024-01-10 16:03 (UTC)
python-mdanalysis 2.6.1-1 1 0.00 An object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, NAMD, LAMMPS, or Amber. hseara 2023-11-17 18:28 (UTC)
pymol-git r5639.ca185848f-1 1 0.00 Molecular visualization system on an Open Source foundation brisvag 2024-03-12 11:01 (UTC)
plumed-mpi 2.8.2-1 1 0.00 An open source plugin for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines (with MPI support) Tenshi65535 2023-05-23 01:24 (UTC)
packmol 1:20.3.5-1 1 0.00 Creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. IslandC0der 2022-04-17 00:48 (UTC)
namd-multicore-cuda-bin 2.14-1 1 0.00 Parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. willemsk 2021-02-10 09:03 (UTC)
molsketch 0.8.0-1 1 0.00 A 2D molecular editing tool a.kudelin 2023-10-21 21:08 (UTC)
mega 11.0.13-3 1 0.00 Molecular Evolutionary Genetics Analysis. https://doi.org/10.1093/molbev/msy096 malacology 2023-04-04 19:30 (UTC)
martinize-git v0.3.1.r8.2a50f80-1 1 0.00 Describe and apply transformation on molecular structures and topologies Ezmagon 2019-12-10 11:45 (UTC)
lammps-git 38442.b620c52-1 1 0.00 Large-scale Atomic/Molecular Massively Parallel Simulator yuhldr 2024-03-19 03:09 (UTC)
iqmol 2.14-1 1 0.00 A molecular editor and visualization package with Q-Chem integration berquist 2020-03-22 17:24 (UTC)
iboview 20150427-1 1 0.02 A program for analyzing molecular electronic structure, based on Intrinsic Atomic Orbitals (IAOs). orphan 2020-09-26 13:50 (UTC)
gromacs-4.6-complete 4.6.7-7 1 0.00 A versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. hseara 2019-01-27 19:20 (UTC)
dseams-git 1.0.0.r14.g333cc82-1 1 0.00 Deferred Structural Elucidation Analysis for Molecular Simulations orphan 2020-06-20 16:40 (UTC)
yaehmop 3.1.0b2-4 0 0.00 Yet Another extended Huckel Molecular Orbital Package (YAeHMOP) lantw44 2021-04-10 17:53 (UTC)
vmd-molfile-plugins 1.9.4a55-1 0 0.00 Visual Molecular Dynamics - molfile plugins orphan 2022-01-21 05:59 (UTC)
vmd-bin 1.9.4a57-1 0 0.00 VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting tzok 2023-04-17 07:12 (UTC)
tempest-bin 1.5.3-1 0 0.00 a tool for investigating the temporal signal and 'clocklikeness' of molecular phylogenies malacology 2021-05-27 05:31 (UTC)
tachyon-opengl 0.99b6-3 0 0.00 Parallel ray tracer (used as part of Visual Molecular Dynamics), OpenGL-enabled orphan 2016-02-17 21:30 (UTC)
smoldyn 2.71-1 0 0.00 particle-based biochemical simulator for modeling molecular diffusion, surface interactions, and chemical reactions orphan 2023-06-28 22:01 (UTC)
r-triplex 1.42.0-1 0 0.00 Search and visualize intramolecular triplex-forming sequences in DNA BioArchLinuxBot 2023-10-26 03:06 (UTC)
r-tnbc.cms 1.18.0-1 0 0.00 TNBC.CMS: Prediction of TNBC Consensus Molecular Subtypes BioArchLinuxBot 2023-10-30 18:33 (UTC)
r-tcgabiolinksgui 1.23.0-4 0 0.00 "TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data" BioArchLinuxBot 2023-04-29 07:09 (UTC)

92 packages found. Page 1 of 2.

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