I'm currently doing a research about alpha-conotoxin CVIA which is a recent type of conotoxin that can be utilized for a possible drug design. I already used UCSF Chimera but unfortunately, an error always appears saying that there are too many heavy atoms in the ligand (conotoxin). Is there any molecular docking softwares that I can use for this certain ligand?
As conotoxin is a disulfide-constrained peptide ligand, you go for peptide/protein docking programs rather than for small molecule docking programs. Hex ia an option, other are:
FlexPepDock
http://flexpepdock.furmanlab.cs.huji.ac.il
FlexPepDock is a high-resolution peptide-protein docking (refinement) protocol for the modeling of peptide-protein complexes, implemented in the Rosetta framework.
CABS-Dock
http://biocomp.chem.uw.edu.pl/CABSdock
Given a protein receptor structure and a peptide sequence, CABS-dock performs docking search for the binding site allowing for full flexibility of the peptide and small fluctuations of the receptor backbone.
HPepDock
http://huanglab.phys.hust.edu.cn/hpepdock/
MDockPep
http://zougrouptoolkit.missouri.edu/mdockpep/
SwissDock
http://www.swissdock.ch
SwissDock, a web service to predict the molecular interactions that may occur between a target protein and a small molecule.
HADDOCK
https://haddock.science.uu.nl
HADDOCK (High Ambiguity Driven protein-protein DOCKing) is an information-driven flexible docking approach for the modeling of biomolecular complexes. HADDOCK distinguishes itself from ab-initio docking methods in the fact that it encodes information from identified or predicted protein interfaces in ambiguous interaction restraints (AIRs) to drive the docking process. HADDOCK can deal with a large class of modelling problems including protein-protein, protein-nucleic acids and protein-ligand complexes
DockThor
https://www.dockthor.lncc.br/v2/
AMMOS2
http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.php
AMMOS2 (Automatic Molecular Mechanics Optimization for in silico Screening) employs an automatic procedure for energy minimization of protein-ligands complexes.
Clus-Pro
https://cluspro.bu.edu/login.php
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