Reverse Dependencies of mdtraj
The following projects have a declared dependency on mdtraj:
- alphafold2-pytorch — AlphaFold2 - Pytorch
- anncolvar — Coding collective variables by artificial neural networks
- BICePs — BICePs
- bubblebuster — A Python Library for detecting water box bubbles in structural files used in molecular simulations.
- chemtrain — Training molecular dynamics potentials.
- clynmut — ClynMut: Predicting the Clynical Relevance of Genome Mutations (wip)
- contact-map — Contact maps based on MDTraj
- dask-traj — Parallel MDTraj, using Dask
- dylightful — Package to uncover hidden interaction patterns in supramolecular complexes
- dynAMMo — dynAMMo – dynamic Augmented Markov Models
- easytrajh5 — MD trajectory library
- frag-pele — FragPELE, a new tool for in silico hit-to-lead drug design, capable of growing a frag_pelement into a core while exploring the protein-ligand conformational space
- FRETpredict — A package for FRET Efficiency prediction of protein structures and trajectories, based on the Rotamer Library Approach (RLA). Can be installed with pip.
- fretraj — Predicting FRET with accessible-contact volumes
- Martinoid — This module was inspired by martinize (http://cgmartini.nl/index.php/tools2/proteins-and-bilayers/204-martinize) and has been created to perform automatic topology building of peptoids within the MARTINI forcefield (v2.1) in the GROMACS program.
- md-davis — A tool for comparative analysis of molecular dynamics simulations of proteins.
- MD2NMR — Tools for calculating NMR relaxation observables (R1/R2/NOE/T1/T2/Tau_c) directly from MD trajectories. Initially written for calculations regarding nucleosome simulations but can be extended for other proteins/complexes. version 0.0.5: 1.Updated with downloading testing MD traj on zenodo: https://zenodo.org/record/7806382 and a new readme file for testing different MD traj. 2. Updated a new function allowing user to select residues with use_chain_id option in config.py file.
- mdciao — mdciao: Analysis of Molecular Dynamics Simulations Using Residue Neighborhoods
- mdigest — Best practices made easy for analysis of correlated motions from molecular dynamics simulations.
- mdinteract — A Pandas interface to the analysis of biomolecular structures with MD trajectory support
- mdpertool — A Software Tool for Investigation of Allosteric Communication within Protein Structures via Energy Dissipation in Molecular Dynamics Simulations
- mdscan — RMSD-Based HDBSCAN Clustering of Long Molecular Dynamics
- mdsimseval — Collective analysis on a set of Molecular Dynamics simulations.
- MDsrv — Server for coordinate trajectories from molecular dynamics simulations.
- MSM-PELE — Monte Carlo Protein Energy Landscape Exploration (PELE) coupled with Markov State Model (MSM) analysis with the aim to calculate absolute free energies
- MultiSpecX — A package for calculating vibrational spectra of condensed-phase systems
- open3SPN2 — no summary
- OpenABC — no summary
- opennucleome — no summary
- openpathsampling — A Python package for path sampling simulations
- pharmd — PharMD: MD pharmacophores and virtual screening
- prolintpy — Automated analyis and visualization of lipid-protein interactions.
- pycgtool — Generate coarse-grained molecular dynamics models from atomistic trajectories.
- pylipid — PyLipID - A Python Library For Lipid Interaction Analysis
- pyPcazip — PCA-based molecular dynamics trajectory file compression and analysis.
- qaa — Quasi-Anharmonic Analysis
- radonpy-pypi — RadonPy is a Python library to automate physical property calculations for polymer informatics.
- rcdpeaks — Memory-Efficient Density Peaks Clustering for Long Molecular Dynamics
- rid-kit — RiD package for enhanced sampling
- roodmus — Synthetic SP micrograph creation and analysis
- SiMBols — A package containing similarity measures for life science purposes. The package contains or uses Fréchet Distance, Dynamic Time Warping, Hausdorff Distance, Longest Common Subsequence, Difference Distance Matrix, Wasserstein Distance and the Kullback-Leiber Divergence (Jenssen-Shannon Distance)
- taurenmd — A command-line interface for analysis routines in Molecular Dynamics data.
- tltsne — Time-lagged t-SNE of molecular trajectories
- trajcontacts — A package to caculate residue-residue contacts from MD trajectories
- transport-tools — a library for massive analyses of internal voids in biomolecules and ligand transport through them
- vermouth — no summary
- wepy — Weighted Ensemble Framework
- WESTPA — no summary
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