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aa-score-tool

a tool for protein-ligand binding affinity prediction

allzzw.github.io

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autodock-vina

AutoDock Vina

aww

bioicons

A library of free open source icons for science illustrations in biology and chemistry

distance-between-center-of-mass

This is a PyMol script to calculate distance between center of mass of two proteins from a set of selected residues.

duivy

some scripts for analysis of MD and CADD. And some tutorials.

fcc

Fraction of Common Contacts Clustering Algorithm for Protein Structures

geminimol

Incorporation of conformational space profile into molecular representation learning, and its application to drug discovery, including virtual screening, target identification, and QSAR.

gmx-dssp-analysis

Tool for visualizing protein secondary structure trajectories from gmx dssp's ss.dat files, inspired by a ResearchGate query.

gmx_mmpbsa

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.

gmxtool

tools for GROMACS

haddock-tools

localcolabfold

ColabFold on your local PC

mmgbsa

Thesis research for predicting binding of mutated peptide ligands

mmgbsa_analyser

This program is to analyse Per Residue Decomposition Resutls from MMPBSA.py program of AMBER MD package.

mmpbsa-output-file-parser

This Programme will help the scientific community using MMPBSA.py or MMPBSA.MPI scripts from AmberTools Package to extract energy values from output (*.dat) file.

molecular_dynamics

The scripts here describe the process of producing a 100 ns Molecular Dynamics Simulation, the trajectory analysis and the calculations with the MMGBSA and MMPBSA methods. The scripts are writen for the AMBER suit.

nju-clock-in

南京大学自动打卡

nju-thesis

南京大学学位论文XeLaTeX模板

pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.

pepfun2

PepFun 2.0: improved protocols for the analysis of natural and modified peptides

pepvis

Peptide Virtual Screening Pipeline

pythonmmgbsa

Program for running end point free energy calculations on protein-ligand complexes using AMBER and its associated MMPBSA.py program. Requires only a protein and ligand structure as input.

remd_analysis

A repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations

rfdiffusion

Code for running RFdiffusion

rosetta2go

Package Rosetta in Docker and Singularity with MPI supported.

uni-gbsa

An automatic workflow to perform MM/GB(PB)SA calculations from force field building, and structure optimization to free energy calculation.