Using the Tools and Resources of the RCSB Protein Data Bank

Abstract

The Protein Data Bank (PDB; http://www.pdb.org) is the worldwide repository for threedimensional structural data determined using various experimental methods. The options and procedures for searching and downloading structural data from the Research Collaboratory for Structural Bioinformatics (RCSB) PDB are described here, along with tools for assessing the quality of structures. Several types of information are associated with each structure deposition, including atomic coordinates of the structure, experimental data used to solve it, sequences of all macromolecules in the structures, details about the structure solution method, images showing different views of the structure, derived geometric data, and a variety of links to other resources. These data and resources may be used for understanding the function and stability of the molecule and for designing biochemical, genetic, or other experiments. They can also be used for molecular modeling and drug design.

LTR Retrotransposons in Fungi

“…Since the order of the encoded proteins and the sequence similarity of the reverse transcriptase form the base for LTR retrotransposon classification, repetitive elements were screened for retrotransposon-related protein domains. Each putative LTR retrotransposon was translated in 6 frames with transeq from the EMBOSS package [49] and searched with HMMsearch (from HMMer3.0 package [50] ) against 13 HMM (Hidden Markov Model) profiles corresponding to 8 different protein domains (INT, RT, AP, RNase H, Gag, Chromo, and two RT-related: RVT_thumb and RVT_connect) included in the Pfam25 database [51] and one developed specially for this project: the Pfam RNase H profile does not include retrotransposon RNase H sequences which are known to vary from canonical RNase H sequences [34] , so we made our own RNase H profile, using known fungal retrotransposon RNase H sequences together with two PDB [52] non-fungal structures for alignment guiding purposes. Sequence searches were automated with pfam_scan.pl, a tool available at the Pfam database site [51] , which enables the user to create a database of HMM profiles to be searched with a database of protein sequences.…”

Identification of Functional SNPs in BARD1 Gene and In Silico Analysis of Damaging SNPs: Based on Data Procured from dbSNP Database

“…BARD1 gene SNPs and their protein sequences in the FASTA format were retrieved from the dbSNP database [15] , [45] ( http://www.ncbi.nlm.nih.gov/SNP/ ), and “.pdb” files for BARD1 subunits were retrieved from the RCSB Protein Data Base [46] ( http://www.rcsb.org/pdb/home/home.do ) for computational analysis in this study.…”

Species-Specificity in Myoglobin Oxygenation and Reduction Potential Properties

“…This homology-based modeling study with I-TASSER involves 3 steps: template identification from PDB library, assembly of iterative structures, and structure-based function annotation. I-TASSER identifies the homologous structure models from PDB database (Dutta et al, 2007) using an algorithm Local Meta-Threading-Server (LOMETS; Wu and Zhang, 2007). The secondary structure of the target protein was predicted based on sequence information from the Protein Secondary Structure PREDiction (PSSpred) algorithm (Yang, Yan, Roy, Xu, Poisson & Zhang, 2015).…”