Search found 8 matches

by liyangum
Tue Dec 05, 2023 11:09 am
Forum: Main Forum
Topic: About geo.npy file
Replies: 3
Views: 24761

Re: About geo.npy file

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 a...
by liyangum
Sat Jun 03, 2023 2:50 am
Forum: Main Forum
Topic: DeepPotential "Index out of range"
Replies: 3
Views: 6465

Re: DeepPotential "Index out of range"

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 err...
by liyangum
Mon Mar 27, 2023 2:37 pm
Forum: Main Forum
Topic: USalign 的错误提示建议
Replies: 1
Views: 6701

USalign 的错误提示建议

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.
by liyangum
Thu May 05, 2022 4:53 am
Forum: Main Forum
Topic: respre memory issue
Replies: 2
Views: 2031

Re: respre memory issue

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
by liyangum
Wed Oct 27, 2021 11:32 pm
Forum: Main Forum
Topic: ResPre precision matrix
Replies: 1
Views: 1435

Re: ResPre precision matrix

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...
by liyangum
Thu Jun 17, 2021 2:30 pm
Forum: Main Forum
Topic: I have some questions about ResPRE
Replies: 1
Views: 2123

Re: I have some questions about ResPRE

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.
by liyangum
Wed May 26, 2021 7:00 am
Forum: Main Forum
Topic: I have some questions about ResPRE
Replies: 5
Views: 4146

Re: I have some questions about ResPRE

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.
by liyangum
Sun May 23, 2021 8:25 pm
Forum: Main Forum
Topic: I have some questions about the formula in the ResPRE paper
Replies: 2
Views: 2438

Re: I have some questions about the formula in the ResPRE paper

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).