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http://www.wwpdb.org/download/downloads
> Since 1971, the Protein Data Bank archive (PDB) has served as the single repository of information about the 3D structures of proteins, nucleic acids, and co…
ghost updated
8 years ago
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The protein data bank will abruptly stop supporting PDB files at some point this year.
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Hello,
I am trying to run a docking of a receptor whose structure was obtained from protein data bank. I deleted all the water and heteroatoms and followed the receptor processing tutorial in AutoD…
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https://en.wikipedia.org/wiki/Protein_Data_Bank_(file_format)
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The Protein Data Bank `mmcif` standard assigns two identifiers for protein chains, an author assigned chain id `auth_asym_id` and a pdb assigned chain id `label_asym_id`. Base on two examples of the `…
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Download and prepare OpenProteinSet on the cluster, while deleting the old version on S3.
> Multiple sequence alignments (MSAs) for 140,000 unique [Protein Data Bank](https://www.rcsb.org/) (PDB) cha…
NZ99 updated
8 months ago
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I am trying to extract the gold struct from the pdb files.
Where and how to read the protein sequence chain and compare it with the sequence struct predicted by the HMM?
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> http://dx.doi.org/10.1371/journal.pone.0141287
>
> **Motivation:** We introduce a new representation and feature extraction method for biological sequences. Named bio-vectors (BioVec) to refer to…
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SPICE 2 is close to finished, which means this is a good time to discuss possible additions for version 3. Here are some ideas to get things started.
- **Nonbonded interactions between amino acids…
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Please work to debug the step1_pdb_process.py script.
Script: https://github.com/lemaslab/CAMP/blob/master/data_prepare/step1_pdb_process.py
Input Data (RCSB PDB) : Download the fasta files fro…