amin-sagar
amin-sagar
Hello. I am working on generating binders for a target which seems like a difficult one as most runs give binders with very low i_ptm. I thought I could increase...
Hello. This is somewhat related to #107 I am fixing the positions of some of the residues using the bias matrix as follows. ``` bias = np.zeros((af_model._binder_len,20)) fixpos = [1,11,15]...
Hello. This is related to #44 I am exploring if there is a possibility to add hundreds of non-canonical amino acids to templates and soft.xml to allow for mutating standard...
Hello. Thanks again for this amazing work. The sequence based potentials are really useful. I am wondering if it's also possible to have structure based potentials. For example, if I...
Hello ADCP developers. Thanks for sharing this program. I am wondering if it is possible to approximately simulate cyclization by crosslinkers by adapting the disulfide bond potential.  If I...
Dear OpenFE team. Thanks for this awesome work. This is related to https://github.com/OpenFreeEnergy/openfe/issues/633 https://github.com/OpenFreeEnergy/openfe/issues/634 and https://github.com/OpenFreeEnergy/openfe/issues/636 I would like to start with a protein-peptide co-crystal structure and modify the peptide...
Hello. Thanks for this awesome work. I tested RDE-PPI on the chains C and B of PDB ID: 8TCG. There is a critical Aspartic acid (D12) in chain C required...
Hello. This is similar to #1 I used both PPIformer and RDE-PPI for predicting the effect of an Alanine scan on the chains B and C of PDB ID: 8TCG...
Hello Everyone. I tried setting up Temperature REMD simulations using two scripts. The first one is using ReplicaExchangeSampler ``` # Set up the temperature range for replicas n_replicas = 20...
Hello. I am trying to run some Temperature replica exchange simulations for small molecules. The relevant part of my script is as follows. ``` # Set up the temperature range...