Alternatives and similar repositories for biosimspace_tutorials

Users that are interested in biosimspace_tutorials are comparing it to the libraries listed below

• UCL-CCS / TIES_MD
  Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.
  ☆32Updated last year
• emleddin / research-scripts
  Different run and analysis scripts as described in the research guides.
  ☆13Updated 2 years ago
• forlilab / waterkit
  Tool to predict water molecules placement and energy in ligand binding sites
  ☆28Updated last month
• pfizer-opensource / TorsionNet
  A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM
  ☆39Updated 2 years ago
• openforcefield / ccpbiosim-2023
  Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week
  ☆30Updated last year
• drazen-petrov / SMArt
  ☆27Updated last week
• rinikerlab / reeds
  This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…
  ☆31Updated last month
• michellab / BioSimSpaceTutorials
  ☆25Updated last year
• bioexcel / cp2K_qmmm_tutorials_for_biological_simulations
  Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.
  ☆22Updated 5 years ago
• dspoel / remd-temperature-generator
  Temperature generator for Replica Exchange MD simulations
  ☆28Updated 2 years ago
• bigginlab / ABFE_workflow
  This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.
  ☆49Updated last month
• Shualdon / QupKake
  ☆27Updated 11 months ago
• hutchisonlab / QupKake
  Machine Learning model for molecular micro-pKa prediction
  ☆41Updated 7 months ago
• limresgrp / FMAP_v1
  Codes to use funnel-metadynamics and funnel metadynamics automated protocol
  ☆27Updated 3 years ago
• arwalkerlab / AutoParams
  ☆26Updated last year
• Gallicchio-Lab / openmm-atmmetaforce-plugin
  An OpenMM plugin that implements the Alchemical Transfer Potential
  ☆40Updated 2 years ago
• MauriceKarrenbrock / HPC_Drug
  A middleware python tool for computational drug discovery on HPC architectures
  ☆9Updated last year
• ykhdrew / qMSM_tutorial
  A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison
  ☆15Updated last year
• NNairIITK / Enhanced_Sampling_Methods_Tutorials
  Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..
  ☆45Updated 4 years ago
• WIMNZhao / AIR
  AI-augmented R-group exploration in medicinal chemistry
  ☆16Updated 7 months ago
• cbc-univie / transformato
  Set up relative free energy calculations using a common scaffold
  ☆22Updated 3 weeks ago
• OpenFreeEnergy / IndustryBenchmarks2024
  Repository for the 2024 OpenFE industry benchmark efforts
  ☆17Updated last month
• JecaTosovic / WaterNetworkAnalysis
  Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis
  ☆17Updated 6 months ago
• federico-fogolari / pdb2entropy
  Entropy from PDB conformational ensembles
  ☆7Updated last year
• litfsindt / LIT-SpaceDock
  ☆16Updated 10 months ago
• GHeinzelmann / GHOAT.py
  The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.
  ☆18Updated last week
• sbhakat / AF-cryptic-pocket
  Cryptic pocket prediction using AlphaFold 2
  ☆22Updated 2 years ago
• MottaStefano / PathDetect-SOM
  A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)
  ☆10Updated 3 years ago
• IAlibay / MDRestraintsGenerator
  Python code for generating Boresch restraints from MD simulations
  ☆20Updated 2 years ago
• otayfuroglu / deepQM
  ☆28Updated last week