Zhanglab forum

After obtaining the output of the sequence using DRfold, in geo.npy file there are array with name: pp,cc, nn, pcc, pnn, cnn, pccp,pnnp,cnnc. I don't know what these terms mean, and I could not find any online resource stating what these are. Can anyone help me on this and help me understand what ...

Hi, Such error happens when CCMpred did not run successfully. You can check the following: 1. Check if CCMpred have the exe permission 2. Check if CCMpred can run successfully, for example, check the stdout file generated by CCMpred. If the output file does not contain anything or there are some ...

当pdb文件中不存在C3‘原子时，USalign给出的错误提示是cannot parse file xxx Chain number 0. 这个似乎没问题，但是我想一个可能更好的提示是 C3‘ does not exist in your pdb files.

Hi,

Thank you for the feedback. Can you send us the MSA? ResPRE may use large memory with long sequences, but it should not reach up to 550G.
You can also send me the MSA by email.

Thanks,
Yang Li

Hi, Thanks for the interest. In fact, the plot in Fig.1 was at the size of LX21 by Lx21. You can plot the output matrix of ROPE in https://github.com/leeyang/ResPRE/blob/master/precision.py (LINE43) for the raw precision matrix for visualization. If you need an L x L matrix, you may check Text S4 of ...

We did see the existence of imbalanced positive and negative samples. But we do not think that it is a problem.
Of course, you can set larger weights or other regular settings to try to make it more balance during the training.

We used supervised machine learning to train ResPRE models for contact map predictioon. The supervised information should be the contact maps (binary matrix, 1 for being in contact) from pdb structures.

The calculation of frequencies with pseudo count has been used in many papers for coevolution analysis. For example, Eq 21 in plmDCA (https://arxiv.org/pdf/1211.1281.pdf), and Eq 1 in DCA paper (https://www.pnas.org/content/108/49/e1293).