Easy-to-Use Graphical Interface Active Site Detection and Analysis Molecular Surfaces and Electron Density Visualize Non-bonded Interactions Publication-Quality Images and Movies GPU Accelerated 3D Stereo Graphics Mixed Virtual Reality and 3D Printing
Streamlined Interface for Ligand Design Active Site Detection and Analysis Interactive Ligand Design in the Pocket Protein-Ligand Interaction Diagrams Predict Water Sites and Energetics Induced-Fit Docking Link, Grow and Replace Fragments
Structure-Based Protein Engineering Assess Liabilities and Developability Optimize Affinity, Stability and Solubility High-Throughput Antibody Modeling Generate Virtual Libraries Protein Docking and Epitope Mapping Model ADCs and Fusion Proteins
SAR and SPR Visualization Free-Wilson Compound Suggestions Matched Molecular Pairs R-Group Analysis and Profiling Substructure and Similarity Search Design Novel Virtual Compounds Document Ideas and Share Sessions
- IMol is a free molecular visualization application for Mac OS X operating system. The program is an indispensable tool for chemists and molecular biologists. IMol allows loading molecules using several file formats: PDB, XYZ, MOL2, HIN, CAR, ALC, BIO.
- The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. TINKER has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98 and ff99), CHARMM (19 and 27), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA.
Conformation Generation and Clustering Align and Superpose Small Molecules MOEsaic for SAR Exploration Pharmacophore Elucidation and Screening Generate QSAR Models – MOE Descriptors Torsion Profiles for Conformation Analysis Combinatorial Library Enumeration
Visualize Proteins, Patches, and Interfaces Predict 3D Protein Structure from Sequence Build DNA/RNA Models Explore Mutations and Rotamers Molecular Dynamics Simulations Loop/Linker Searching and Sampling Protein-Protein Docking
MolView is an intuitive, Open-Source web-application to make science and education more awesome!
3D Pharmacophore Screening Shape and Feature Constraints Small Molecule Docking 2D and 3D Fingerprint Screening Scaffold and Fragment Replacement Conformation Databases Reaction-Based Library Design
Scaffold Hopping Fragment Linking and Growing Medicinal Chemistry Transformations Combinatorial Library Enumeration Multi-Fragment Search Ligand Hybridization (BREED) Custom Fragment Libraries
Multiple Sequence and Structure Alignment Annotate 3D Properties onto Sequences Create and Search Protein Family Databases Mine Structural Data Analyze Conserved Residues Generate Clustered Phylogenetic Trees Antibody and TCR Structural Databases
3d Molecule Program
Molecular Mechanics and Dynamics Automated Structure Preparation Free Energy Calculations Flexible Alignment of Multiple Molecules Conformational Analysis – LowModeMD Torsion Scan and Analysis QM-Based NMR, IR and VCD Spectra
Macrocyclic and Linear Peptides Identify Peptide-Protein Contacts Conformational Searching Enumerate Non–Natural Peptide Libraries Structure-Based Peptide Design Optimize Peptide Properties Peptide Docking
Molecular Simulation Software
Plot Electron Densities and Difference Maps Display Crystal Lattices and Contacts Prediction of Water Positions Electron Density-Guided Docking Create Aligned Protein Family Databases Homology Modeling for Molecular Replacement Health-Check of Protein Structures
400+ 2D and 3D Molecular Descriptors pKa Prediction and Protomer Generation Linear QSAR/QSPR Bayesian Classification / Machine Learning MOEsaic – Matched Molecular Pairs Focused Combinatorial Library Design Chemical Similarity, Diversity and Clustering
Laptop – Cluster – Cloud – Pipeline Windows – Linux – macOS Integrated Programming Environment (SVL) 3rd Party Software Integration Custom Applications and User Profiles Web Integration, Web Services, API HTTP Listener for Remote Control
RCSB Compliant Repository Browser Interface – 3D Visualization Automated Project Database Curation 3D Interaction Search and Statistics Pocket Similarity Search Protein Structure Alignment Standard IT Infrastructure
BrennerMD is a public domain Fortran moleculardynamics program by Donald Brenner and other people. This project is to maintain the original source code and to build a Python interface on top of. ...
- brennerc-in-fungimol-0.5.0.tar.gz
- brennermd
- Freeware (Free)
- 255 Kb
- BSD; Linux
Mdxvu is a C code program for Linux, Un*x and Win32/Cygwin. It analyses molecular structures and moleculardynamics (MD) trajectories from the AMBER, GROMACS, TINKER and DISCOVER (TM) programs. Simple graphics are provided by using the X11/XLIB. ...
- mdxvu_april2008_v2.tar.gz
- mdxvu
- Freeware (Free)
- 2.85 Mb
- N/A
PFMD performs a MolecularDynamics simulation of some polarizable fluids at the liquid state by means of a dissociable potential. Supported molecules are H2O (water) and MX3, where M is a metal among Al, Fe, or Ga and X is a halogen among Cl, Br, or. ...
- pfmd-1.0RC2.tar.gz
- pfmd
- Freeware (Free)
- 348 Kb
- Windows; Mac; Linux
ProtoMol is an object-oriented component based framework for moleculardynamics ProtoMol is an object-oriented component based framework for molecular dynamics simulations..
- ProtoMol-3.3.0-Windows-32bit.zip
- protomol
- Freeware (Free)
- 12.59 Mb
- Windows; BSD; Solaris; Linux
Fumody, is a program for work with XYZ file types, have two principal lines for xyz file types, one is for more general XYZ file options as a utility for rescaled, center, informations, etc. and other line more specifically for analysis configurations.
- File utilities for moleculardynamics
- Joaquin Peralta
- Freeware (Free)
- Windows
This project aims at providing a user package for the moleculardynamicssoftware LAMMPS, which allows the complete simulation to run on a GPU. Additional information and svn access to 'bleeding etch' code can be found on the project website. ...
- LAMMPS_CUDA
- code
- Freeware (Free)
- 52.68 Mb
- BSD; Linux
This project contains a custom version of the GROMACS moleculardynamicssoftware package that helps users to choose parameters for the PME electrostatics model which produce a known error in the PME approximation for minimal computational. ...
- pme-optimization-4.5.4.tar.gz
- pmeopt
- Freeware (Free)
- 14.76 Mb
- Linux
The Molecular Modeling Templates, MMT is a C++ class library for molecular simulation applications. MMT serves as a code basis that can be easily extended and modified to perform Monte Carlo and moleculardynamics simulations.
- Molecular Modeling Templates
- Masakatsu Ito
- Freeware (Free)
- Windows
Open3DALIGN is an open-source software aimed at unsupervised molecular alignment. Open3DALIGN is a command-line tool which is operated by means of a few commands which can be entered interactively from a command prompt, read from a batch script or. ...
- Open3DALIGN x64
- Paolo Tosco
- Freeware (Free)
- 5.2 Mb
- WinXP, Windows Vista, Windows 7 x64
Open3DALIGN is an open-source software aimed at unsupervised molecular alignment. Open3DALIGN is a command-line tool which is operated by means of a few commands which can be entered interactively from a command prompt, read from a batch script or. ...
- Open3DALIGN for Mac OS X
- Paolo Tosco
- Freeware (Free)
- 3.6 Mb
- Mac OS X
Open3DALIGN is an open-source software aimed at unsupervised molecular alignment. Open3DALIGN is a command-line tool which is operated by means of a few commands which can be entered interactively from a command prompt, read from a batch script or. ...
- Open3DALIGN
- Paolo Tosco
- Freeware (Free)
- 4.1 Mb
- WinXP, Windows Vista, Windows 7
Open3DALIGN is an open-source software aimed at unsupervised molecular alignment. Open3DALIGN is a command-line tool which is operated by means of a few commands which can be entered interactively from a command prompt, read from a batch script or. ...
- Open3DALIGN for Linux
- Paolo Tosco
- Freeware (Free)
- 3.3 Mb
- Linux