# Full idresidue=chain[(" ",100," ")]# Shortcut idreside=chain[100] Atom id就是原子的名字,比如'CA'。 处理disorder信息 使用Bio.PDB的一个很重要的功能就是他可以处理点突变和无序的原子信息(ie. a Gly and an Ala residue in the same position)。一般disorder信息可以从两个角度进行考虑,一个...
Insertions and deletions (indels) represent a common type of sequence variations, which are less studied and pose many important biological questions. Recent research has shown that the presence of sizable indels in protein sequences may be indicative of
Bioinformatics Group, Metaphorics LLC, Santa Fe, New Mexico.1. Abstract A automated method for extracting small molecule ligands, including assigning hybridization states and bond orders, from the PDB is presented. This processing proceeds in two distinct phases. The first phase results in the bonde...
Full size image The second check analyses the reported data for completeness. For each hetero-atom its distances to all other atoms are determined. In case this distance is within the usual bond length range, and the connection is not listed in the CONECT records, a warning is displayed. In...
Note that these proteins were collected from NCBI Protein or UniProt database, which may or may not be in their full-length form. During this step, we extracted complete sequences by searching the accession numbers in NCBI Protein or UniProt database. In addition, a number of entries ...
Full size image Because most PDB-entries contain thousands of atoms which would require explicit calculation of many millions of atom pair distances (Fig.1d), the 3DP calculation was simplified by computing the fingerprint using formal “sum atoms”. A maximum of 1728 sum atoms (resulting in a...
This file format is largely used in Bioinformatics to exchange protein coordinates. It contains thousands of lines describing a protein structure. Now, if you want to read or view PDB files on Windows PC, you need to use a dedicated third-party tool as there is no native application to do...
Those resources may correspond to data extracted from databases, flat files, DAS tracks, or even results returned by local or remote bioinformatics analysis tools. WikiOpener has already been successfully used in the frame of another biological database that aims at depicting the relationships between...
PDBe also works closely with its collaborators at the European Bioinformatics Institute and the scientific community around the world to enhance its databases and services by adding curated and actively maintained derived data to the existing structural data in the PDB. We have developed a new data...
Full size image Often in many proteins, several domains are tandemly repeated38. Additionally, researchers also synthesise structures where even the entire protein is repeated for specific research purposes39,40. Previously, there was no automated way to find corresponding UniProtKB mappings for multiple...