Alternatives and similar repositories for AlphaTraj

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

• durrantlab / deepfrag
  DeepFrag is a deep convolutional neural network that guides ligand optimization by extending a ligand with a molecular fragment, such tha…
  ☆28Updated 3 months ago
• forlilab / cosolvkit
  CosolvKit is a versatile tool for cosolvent MD preparation and analysis
  ☆26Updated this week
• giaguaro / PROTACable
  PROTACable is an end-to-end in-silico design toolkit for novel PROTACs
  ☆29Updated last year
• keisuke-yanagisawa / exprorer
  EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation
  ☆11Updated 3 years ago
• THGLab / HiQBind
  Workflow to clean up and fix structural problems in protein-ligand binding datasets
  ☆56Updated 5 months ago
• huifengzhao / CPSet
  ☆12Updated last year
• quantaosun / Dock-MD-FEP
  Open Source, Automated free binding free energy calculation between protein and small molecule. An all-in-one workflow, free energy pertu…
  ☆59Updated 6 months ago
• freeenergylab / FEP-SPell-ABFE
  FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery
  ☆73Updated 9 months ago
• sbhakat / AF-cryptic-pocket
  Cryptic pocket prediction using AlphaFold 2
  ☆24Updated 2 years ago
• molML / RUSH
  ☆19Updated 8 months ago
• monterosatx / molecular-surface-mining
  Code used to mine surfaces.
  ☆23Updated 8 months ago
• GilbertoPPereira / PROTACability
  ☆12Updated 2 years ago
• oxpig / MolSnapper
  ☆51Updated 5 months ago
• Zhang-Runze / PackDock
  PackDock: a Diffusion Based Side Chain Packing Model for Flexible Protein-Ligand Docking
  ☆34Updated last week
• darrenjhsu / tiny_IFD
  Lightweight induced fit docking
  ☆21Updated 2 years ago
• zchwang / OnionNet-2
  OnionNet-2 is constructed based on convolutional neural network (CNN) to predict the protein-ligand binding affinity.
  ☆22Updated last year
• lingcon01 / LumiNet
  A distance distribution-based visualization method for atomic pair energy and precise prediction of absolute binding free energy.
  ☆13Updated 8 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.
  ☆20Updated 5 months ago
• DrugBud-Suite / CADD_Vault
  ☆58Updated 7 months ago
• karanicolaslab / PROTAC_ternary
  ☆19Updated 3 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.
  ☆54Updated 6 months ago
• Exscientia / plif_validity
  Code and notebook for our paper "Assessing interaction recovery of predicted protein-ligand poses"
  ☆19Updated last year
• briandasantini / cPEPmatch
  Tool to design cyclic peptides that mimic proteins and target their binding partners.
  ☆16Updated last year
• Hoecker-Lab / pocketoptimizer
  Binding pocket optimization based on force fields and docking scoring functions
  ☆34Updated 7 months ago
• VicFisher / DiffPhore
  Knowledge-Guided Diffusion Model for 3D Ligand-Pharmacophore Mapping
  ☆42Updated 4 months ago
• UCL-CCS / TIES_MD
  Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.
  ☆33Updated last year
• OdinZhang / FragGen
  This Code is for Fragment-wise 3D Structure-based Molecular Generation with Reliable Geometry
  ☆28Updated 7 months ago
• brueckna2020 / MDFit
  Automated molecular dynamics simulations workflow for high-throughput assessment of protein-ligand dynamics
  ☆19Updated last year
• yydiao1025 / MacFrag
  ☆27Updated 2 years ago
• Gervasiolab / OpenBPMD
  ☆67Updated 2 years ago