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.vmd.d

VMD configuration files

ab-bind-database

Antibody Binding Mutational Database

ablang

AbLang: A language model for antibodies

add-to-beta-factor-column

adds 2nd column of input (eg. rmsf.xvg each line corresponding to residue) to beta factor column of pdb.

add_acyl_tails_martini_2.2

add_vsites

adding virtual sites to system

alphafold_non_docker

AlphaFold2 non-docker setup

amorprot

Code for "AmorProt: Amino Acid Molecular Fingerprints Repurposing-based Protein Fingerprint" (https://doi.org/10.1021/acs.biochem.3c00253)

atom_overlap_checker

checks for atom overlaps, and shifts any overlapping atoms

binding-ddg-predictor

open source repository

cg2at

Conversion of coarsegrain to atomistic (complete rewrite of the original CG2AT)

dacum

The Database of binding Affinity Change Upon Mutations in protein complexes

dynamics_protein

writes out rmsd and rmsf to protein bfac

enhanced_sampling_methods_tutorials

Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..

google-research

Google Research

martini3-small-molecules

Martini 3 small-molecule database

masterclass-21-4

Repository of the data for PLUMED Masterclass 21.4

metadynamics_analysis

A script for analysing well tempered metadynamics

metadynminer

Package for reading, analysis and visualization of metadynamics HILLS

neb

Nudged-Elastic Band implementation in python

oligomerization-state_and_contact-map

openfold

Trainable PyTorch reproduction of AlphaFold 2

propka

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.

pros-gnn

pylipid

A python toolkit for analysing membrane protein-lipid interactions.

self_assembly

automated setup of martini membranes using the self assembly method

show_deformation

writes the deformation of a membrane over time, using the z coordinate height

staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

stride_vmd

updating stride to work with lipoproteins

ticagg