Re: [Rdkit-discuss] Structure-Based Drug Design

Hi James, Since you got many answers in regards to visualization, I might offer some help on other end, namely the computations in SBDD. For this we have created ODDT https://github.com/oddt/oddt in my previous group, and it offers many protein ligand interaction and scoring functionality among ma

Re: [Rdkit-discuss] Structure-Based Drug Design

Hi James, As Paul mentioned about RDKit-3Dmol.js integration, I would like to share additional information. I wrote those scripts about 2 years ago and those do not have structure editing capabilities. I have plan to update those after June this year. Thank you. Best regards, - malitha On Mon, M

Re: [Rdkit-discuss] Structure-Based Drug Design

2) For visualization nglview has lot of capabilities. I run simulation on a cluster and with nglview in a Notebook, the final trajectories can be directly be loaded in the notebook for visualization. Here is a gallery of different usages for visualization with ng

Re: [Rdkit-discuss] Structure-Based Drug Design

On Sun, 17 Mar 2019 at 21:27, Czodrowski, Paul < paul.czodrow...@tu-dortmund.de> wrote: > Dear James, > > > > Ad 1) Paolo Tosco did an integration of openMM and also was able to run a > MD within Jupyter (partly covering (3)). Here is a link: > > > https://github.com/rdkit/UGM_2017/blob/master/Pre

Re: [Rdkit-discuss] Structure-Based Drug Design

estm...@aol.com" Betreff: [Rdkit-discuss] Structure-Based Drug Design RDkit Discussion Group, RDkit has quite a number of useful tools and algorithms for ligand-based drug design (LBDD). However, what about structure-based drug design (SBDD)? Perhaps a few questions to motivate the discussio

[Rdkit-discuss] Structure-Based Drug Design

RDkit Discussion Group,     RDkit has quite a number of useful tools and algorithms for ligand-based drug design (LBDD).  However, what about structure-based drug design (SBDD)?   Perhaps a few questions to motivate the discussion.     1) Since RDkit supposedly includes the force field MMFF, does t