Alexandre Bonvin bio photo

Computational Structural Biology group focusing on dissecting, understanding and predicting biomolecular interactions at the molecular level.

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Latest changes

Latest changes

  • Implemented missing glycan 1-6 linkage
  • Shortened the distance cutoff for automatic detection of glycan linkages
  • Added missing improper parameter for D-amino acid
  • Added missing param for HYP (all atoms)
  • Added missing improper for D-Ala
  • Added missing impropers for D-amino acids and cis-peptide bond

Changes - version August 2023

  • Implemented missing glycan params into solvated docking generate-water.inp
  • Added support for GLC-GLC alpha 1-1 linkage
  • Added missing improper for NME methyl group
  • Corrected read_noes.cns to take into account the lastit parameter for distance restraints
  • Corrected linkage files (noter and noNter) to have an uncharged PRO when at the N-ter

Changes - version January 2023

  • Added missing SIA-NGA 2-6 glycosilic linkages
  • Added support for SIA-SIA 2-8 linkages
  • Implemented automatic DNA/RNA restraints definition

changes- version August 2022

  • Added support for 3-Hydroxyproline (HY3 residue)
  • Added improper to tensor topology
  • Extended support for 10 RDC restraint sets
  • Implemented move of RDC and DANI tensors after it1 for numerical stability

changes - version January 2022

  • Minor changes in occupancy treatment for pharmacophore-based shape docking
  • Added support for 2-N-acetyl-beta-D-galactopyranose (NGA)
  • Added support for N-methylated Cter (NME residue)
  • Various changes to support DPP membranes
  • Made glycan rings rigid for torsion angle dynamics
  • Corrected issue with initialisation of contact probabilities for solvated docking
  • Corrected issue when using the DNA-RNA linkage file to keep the terminal 5’phosphate
  • Corrected issue with BSA calculation in the presence of tensors
  • Corrected issue with Rg energy in PDB output files

Changes - version May 2021

  • Fixed issue with grid package submission for model-specific ambig files
  • Added carbohydrates to scoring scripts
  • Fixed clustering issue in case of single model runs
  • Improvements, optimizations and fixes to the internal scheduler subroutines

Changes - version January 2021

  • Added support ASN-BGC glycosilic linkage
  • Fixed an issue in which clustering would fail if complexes had too many chains
  • Added an extra check for solvated docking and waterdock
  • Fixed a bug where simulations would fail if too many ions were restrained
  • Improvements, optimizations and fixes to the internal scheduler subroutines

Changes - version September 2020

  • Added beta sialic acid (SIB), and additional linkages between glycans
  • Added modified DNA baseJ (DJ)
  • Corrected issue with automatic his protonation state
  • Added automatic definition of restraints to maintain ions in their coordination sphere.
  • Modified analysis scripts to work with a single ligand molecule

Changes - version July 2020

  • Added support for glycosylated proteins
  • Improved diagnostics
  • Minor fixes and code cleaning

Changes - version June 2020

  • Adapted the CG-to-AA conversion script to allow to morph larger conformational changes and use secondary structure restraints
  • Corrected an issue in automatic secondary structure definition leading failures for very large systems
  • Exposed a new parameter in run.cns (flcut_nb) that allows to control the distance cutoff to automatically define semi-flexible regions

Changes with respect to version 2.2

  • Extension to up to 20 molecules docking
  • Coarse grained docking implemented based on the Martini force field v2.2 for both proteins and nucleic acids
  • Z-restraining potential as implicit membrane restraining potential
  • Cryo-EM restraints implementation
  • Added option to turn off (partially) analysis (speeds up the overall running time) Default settings only perform clustering
  • For refinement (randorien=false), missing atoms are now rebuilt in the context of the complex
  • Added automatic identification of cyclic peptides
  • Added automatic idenfification of D-amino acids
  • Added support for C6 symmetry
  • Added support for shapes
  • Added option to automatically define HIS protonation states based on electrostatic energy
  • Changed default dielectric treatment to distance dependent dielectric with eps=10 for it0 and 1 for it1 (Note should not be used for nucleic acids and coarse graining)
  • Turn off by default explicit solvent final refinement (only EM performed)
  • Switched nucleic acid support to use 1/2 letter code for RNA/DNA
  • Added option to fix molecules in their original position
Please send any suggestions or enquiries to Alexandre Bonvin