sci-chemistry

• GromacsWrapper 0.9.1 ::gentoo 1 overlay Python framework for Gromacs
• MDAnalysis 2.10.0 ::gentoo 1 overlay A python library to analyze and manipulate molecular dynamics trajectories
• MotionCor2 1.4.0 1 overlay Correction of electron beam-induced sample motion
• ParmEd 4.3.1 ::gentoo 1 overlay Parameter and topology file editor and molecular mechanical simulator engine
• autodock 4.2.6-r1 ::gentoo 1 overlay A suite of automated docking tools
• autodock_vina 1.2.7 ::gentoo 1 overlay Program for drug discovery, molecular docking and virtual screening
• avogadro2 2.0.0 ::gentoo 1 overlay Advanced molecule editor and visualizer 2
• bodr 10 ::gentoo 1 overlay The Blue Obelisk Data Repository listing element and isotope properties
• browndye 9999 2 yr 1 overlay Brownian Dynamics of Biological Molecules
• cara-bin 1.8.4-r2 ::gentoo 1 overlay Analysis of NMR spectra and Computer Aided Resonance Assignment
• chemex 2026.6.1 ::gentoo 1 overlay Program to fit chemical exchange induced shift and relaxation data
• chemical-mime-data 0.1.95_pre20171122 ::gentoo 1 overlay A collection of data files to add support for chemical MIME types
• chemtool 1.6.14-r1 ::gentoo 1 overlay A GTK program for drawing organic molecules
• chimera 1.19 1 overlay Next generation molecular visualization program from RBVI
• clashlist 3.17-r1 ::gentoo 1 overlay Build lists of van der Waals clashes from an input PDB file
• cluster 1.3.081231-r2 ::gentoo 1 overlay Build lists of collections of interacting items
• concoord 2.1.2 1 overlay Protein conformations around a known structure based on geometric restrictions
• ctffind 4.1.14-r1 1 overlay CTF estimation (ctffind, ctftilt)
• dl_poly 5.0.0 1 overlay a general purpose molecular dynamics simulation package
• drawxtl 55 1 overlay Crystal structure drawings from structural data
• dssp 4.6.1 ::gentoo 1 overlay The protein secondary structure standard
• easychem 0.6-r2 ::gentoo 1 overlay Chemical structure drawing program - focused on presentation
• elem 1.0.3-r3 ::gentoo 1 overlay periodic table of the elements
• erkale 0_p20220106 1 overlay Quantum chemistry program for atoms and molecules
• gamess 20180930.3-r1 1 overlay A powerful quantum chemistry package
• gelemental 2.0.2-r1 ::gentoo 1 overlay Periodic table viewer with detailed information on the chemical elements
• gnome-chemistry-utils 0.14.17_p6-r4 ::gentoo 1 overlay Programs and library containing GTK widgets and C++ classes related to chemistry
• gperiodic 3.0.3-r1 ::gentoo 1 overlay Periodic table application for Linux
• gromacs 2026.3 ::gentoo 1 overlay The ultimate molecular dynamics simulation package
• ksdssp 040728-r1 ::gentoo 1 overlay An open source implementation of sci-chemistry/dssp
• mdtraj 1.11.1_p1 ::gentoo 1 overlay Read, write and analyze MD trajectories with only a few lines of Python code
• mics 1.00.2011.327.12.00-r1 1 overlay Prediction of Protein Structural Motifs from NMR Chemical Shifts
• moldy 2.16e-r2 ::gentoo 1 overlay Molecular dynamics simulations platform
• molmol 2k_p2-r11 ::gentoo 1 overlay Publication-quality molecular visualization package
• molsketch 0.8.4 ::gentoo 1 overlay Drawing tool for 2D molecular structures
• mpqc 2.3.1-r4 ::gentoo 1 overlay The Massively Parallel Quantum Chemistry Program
• msms-bin 2.6.1-r1 ::gentoo 1 overlay MSMS very efficiently computes triangulations of Solvent Excluded Surfaces
• mustang 3.2.2 ::gentoo 1 overlay MUltiple STructural AligNment AlGorithm
• nmrpipe 8.7.20230206 1 overlay Spectral visualisation, analysis and Fourier processing
• openbabel 3.2.0 ::gentoo 1 overlay Interconverts file formats used in molecular modeling
• ovito 3.7.12-r2 1 overlay Open Visualization Tool
• pales-bin 0_pre140717 1 overlay Prediction of alignment from structure
• panav 0.20130730 1 overlay Probabilistic approach for validating protein NMR chemical shift assignments
• pdbcat 1.3-r1 ::gentoo 1 overlay Manipulate and process PDB files using tools such as Perl, awk, etc
• pdbcns 2.0.010504 ::gentoo 1 overlay Convert atom names for amino acids/nucleic acid bases between PDB and CNS format
• pdbmat 3.89-r1 ::gentoo 1 overlay Calculate Tirion's model from pdb structures
• probe 2.13.110909 ::gentoo 1 overlay Evaluates atomic packing within or between molecules
• propka 3.5.1-r1 ::gentoo 1 overlay pKa-value prediction of ionizable groups in protein and protein-ligand complexes
• psi 3.4.0-r3 ::gentoo 1 overlay Suite for ab initio quantum chemistry computing various molecular properties
• pymol 3.1.0-r1 ::gentoo 1 overlay Python-extensible molecular graphics system
• raster3d 3.0.6-r1 ::gentoo 1 overlay Generation high quality raster images of proteins or other molecules
• relion 4.0.0 1 overlay Image-processing software for cryo-electron microscopy
• sage-jmol-bin 14.29.52 23 mo 1 overlay Jmol is a java molecular viever for 3-D chemical structures.
• ssp 09.11 1 overlay Secondary structure propensities
• suitename 0.3.070628 ::gentoo 1 overlay The ROC RNA Ontology nomenclature and conformer-list development
• surf 1.0 ::gentoo 1 overlay Solvent accesible Surface calculator
• theseus 3.3.0-r1 ::gentoo 1 overlay Maximum likelihood superpositioning and analysis of macromolecular structures
• threeV 1.2-r2 ::gentoo 1 overlay 3V: Voss Volume Voxelator
• tinker 8.2.1-r1 ::gentoo 1 overlay Molecular modeling package that includes force fields, such as AMBER and CHARMM
• tm-align 20150914-r1 ::gentoo 1 overlay Quick & Accurate Structural Alignment
• vesta 3.5.8 11 d 2 overlays Visualization for Electronic and STructural Analysis
• vesta-bin 3.5.8 1 overlay Visualisation for Electronic and STructural Analysis.
• vmd 1.9.4_alpha57-r4 ::gentoo 1 overlay Visual Molecular Dynamics
• wxmacmolplt 7.7.2-r1 ::gentoo 1 overlay Chemical 3D graphics program with GAMESS input builder
• xcrysden 1.6.2-r2 1 overlay For the visualisation of molecular and crystal structures.
• xds-bin 20240831 ::gentoo 1 overlay Software for processing single-crystal X-ray monochromatic diffraction data