Results 301 to 310 of about 381,553 (352)

Redocking the PDB

Journal of Chemical Information and Modeling, 2023
Molecular docking is a standard technique in structure-based drug design (SBDD). It aims to predict the 3D structure of a small molecule in the binding site of a receptor (often a protein). Despite being a common technique, it often necessitates multiple
F. Flachsenberg, C. Ehrt, Torben Gutermuth, M. Rarey   +3 more
semanticscholar   +4 more sources

PSAC-PDB: Analysis and classification of protein structures

Computers in Biology and Medicine, 2023
This paper presents a novel framework, called PSAC-PDB, for analyzing and classifying protein structures from the Protein Data Bank (PDB). PSAC-PDB first finds, analyze and identifies protein structures in PDB that are similar to a protein structure of ...
Muhammad Saqib Nawaz, Yu-Lin He, Philippe Fournier-Viger   +2 more
exaly   +2 more sources

PDB-tools web: A user-friendly interface for the manipulation of PDB files [PDF]

Proteins: Structure, Function and Bioinformatics, 2021
The Protein Data Bank (PDB) file format remains a popular format used and supported by many software to represent coordinates of macromolecular structures. It however suffers from drawbacks such as error-prone manual editing.
Mikael Trellet, Alexandre Bonvin, Brian Jimenez   +2 more
exaly   +1 more source

Protein Repair and Analysis Server: A Web Server to Repair PDB Structures, Add Missing Heavy Atoms and Hydrogen Atoms, and Assign Secondary Structures by Amide Interactions

Journal of Chemical Information and Modeling, 2022
The Protein Data Bank (PDB) file format developed at Brookhaven National Laboratory is the most popular file format to store biological data and is widely supported by many software programs for the editing and visualization of macromolecular structures.
Osita Sunday Nnyigide, Tochukwu Olunna Nnyigide, Sun-Gu Lee, K. Hyun   +3 more
semanticscholar   +1 more source

Ultrathin and Wavy PdB Alloy Nanowires with Controlled Surface Defects for Enhanced Ethanol Oxidation Electrocatalysis.

ACS Applied Materials and Interfaces, 2021
Engineering crystalline structures/defects and elemental compositions is synthetically critical to optimize surface features of noble metal nanocrystals and thus improve their catalytic performances in various reactions.
Yaru Wang, Hao Lv, Li-Zhi Sun, Xuwen Guo, Dong-Dong Xu, Ben Liu   +5 more
semanticscholar   +1 more source

Building a Structured PDB: The RS-PDB Database

2006 International Conference of the IEEE Engineering in Medicine and Biology Society, 2006
A method for automatically analyzing structures deposited in the Protein Data Bank is presented. The method is capable to detect missing atoms, bond length deviations, atom bumps and to correctly identify protein-ligand complexes. The results are organized into a database, called the Rich Structure PDB (RS-PDB in short) from which one can easily select
Zoltan Szabadka, Vince Grolmusz
openaire   +2 more sources

Overhauling the PDB

Nature Biotechnology, 2007
The Brookhaven Protein Data Bank was once a pioneering database, but its organization of structural data is now outdated and in need of an upgrade.
Schierz, Amanda C., Soldatova, Larisa N., King, Ross D.   +2 more
openaire   +2 more sources

PDB Data Curation

2006 International Conference of the IEEE Engineering in Medicine and Biology Society, 2006
In this paper, we propose two architectures for curating PDB data to improve its quality. The first one, PDB Data Curation System, is developed by adding two parts, Checking Filter and Curation Engine, between User Interface and Database. This architecture supports the basic PDB data curation.
Yan Chao Wang, Rajshekhar Sunderraman
openaire   +2 more sources