Chengxin Zhang

I am reading the code of cd-hit-common.c++ and I am puzzled by its aa2idx array: ``` int aa2idx[] = {0, 2, 4, 3, 6, 13,7, 8, 9,20,11,10,12, 2,20,14, 5, 1,15,16,20,19,17,20,18,...

The selection of papers in protein residue-residue contact prediction is biased. 1. The NeBcon paper (Baoji He, S. M. Mortuza, Yanting Wang, Hong-Bin Shen, Yang Zhang."NeBcon: protein contact map prediction...

atom name all left justified

2

**Bug description** In all PDB files provided by ESM atlas, the atom name at column 13-16 of the ATOM record are always left justified, which is not the standard string...

cannot build on ubuntu12.04 using clang3.4

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I am trying to compile maloader using clang-3.4 on Ubuntu 12.04 (precise) amd64. Previously, when I compile maloader using gcc-4.6, all went well. The clang-3.4 were installed by apt as...

uniclust30 is incompatible with hhsuite2.0.15

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Even though the uniclust30 document claim that it is compatible with hhsuite 2.x, it does not seem to like hhsuite2.x at all. For example, I have downloaded http://wwwuser.gwdg.de/~compbiol/uniclust/2017_10/uniclust30_2017_10_hhsuite.tar.gz and search...

AlphaFold DB proteome subset

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Is it possible for https://foldcomp.steineggerlab.workers.dev/ to distribute the subset of AlphaFold database corresponding to the "Model organism proteomes" and "Global health proteomes" listed by https://alphafold.ebi.ac.uk/download? Many of these proteins are...

"diamond --outfmt 6 qseq sseq" will remove all gaps in the aligned regions. This is different from NCBI-BLAST+, where "blastp -outfmt 6 qseq sseq" preserves all gaps. This commit preserves...