Results 311 to 320 of about 381,553 (352)

PDB@: An offline toolkit for exploration and analysis of PDB files

Journal of Structural and Functional Genomics, 2013
Protein Data Bank (PDB) is a freely accessible archive of the 3-D structural data of biological molecules. Structure based studies offers a unique vantage point in inferring the properties of a protein molecule from structural data. This is too big a task to be done manually.
Udayakumar, Mani, Sadhana, Ravisankar, Sai Mukund, Ramakrishnan   +2 more
openaire   +2 more sources

Parallel PDB data retriever “PDB diving booster”

1997
A powerful PDB-data-retrieval system “PDB Diving Booster,” which is a collection of functions/methods for data-retrieval and datatransmission, will enhances high-performance parallel-distributed programming in the field of structural biology. This system provides with 1) functions for reading whatever irregular data in PDB file, 2) methods to access ...
Kentaro Onizuka, Tamotsu Noguchi, Minoru Saito, Yutaka Akiyama   +3 more
openaire   +1 more source

PDB: Not All Drivers Are the Same - A Personalized Dataset for Understanding Driving Behavior

arXiv.org
Driving behavior varies across individuals, yet most existing driving datasets do not preserve driver identity or control for factors that may affect driving style.
Chu-Heng Wei, Zi-Ye Qin, Si-Yan Li, Zi-Yan Zhang, Xuan-Peng Zhao, Amr Abdelraouf, Rohit Gupta, Kyungtae Han, Zi-Ran Wang, Matthew J. Barth, Guo-Yuan Wu   +10 more
semanticscholar   +1 more source

PDB-2-PBv3.0: An updated protein block database

J. Bioinform. Comput. Biol., 2020
Our protein block (PB) sequence database PDB-2-PBv1.0 provides PB sequences and dihedral angles for 74,297 protein structures comprising of 103,252 protein chains of Protein Data Bank (PDB) as on 2011.
Muthuvel Prasath Karuppasamy, S. Venkateswaran, Parthasarathy Subbiah   +2 more
semanticscholar   +1 more source

Structural changes of homodimers in the PDB

Journal of Structural Biology, 2018
Protein complexes are involved in various biological phenomena. These complexes are intrinsically flexible, and structural changes are essential to their functions. To perform a large-scale automated analysis of the structural changes of complexes, we combined two original methods.
Ryotaro, Koike, Takayuki, Amemiya, Tatsuya, Horii, Motonori, Ota   +3 more
openaire   +2 more sources

Quantifying intramolecular Halogen Bonds in Nucleic Acids: A combined PDB and theoretical study.

ACS Chemical Biology, 2020
In this study we report experimental (PDB search) and theoretical (RI-MP2/def2-TZVP level of theory) evidence of the nature, stability and directionality properties of intramolecular halogen bonding interactions (XBs) between 5-bromo/5-iodouracil bases ...
María de las Nieves Piña, A. Frontera, Antonio Bauzá   +2 more
semanticscholar   +1 more source

PDB-SQL

Proceedings of the 45th annual southeast regional conference, 2007
The Protein Data Bank (PDB) was established in 1971 as a repository for macromolecular crystal structure data. Recent development of high throughput structural genomic technologies has produced massive quantities of data, and the amount of macromolecular structure data is increasing exponentially.
Edward E. Pryor Jr., Jacquelyn S. Fetrow
openaire   +2 more sources

Water-Mediated Selenium Hydrogen-Bonding in Proteins: PDB Analysis and Gas-Phase Spectroscopy of Model Complexes.

Journal of Physical Chemistry A, 2019
High-resolution X-ray crystallography and two-dimensional NMR studies demonstrate that water-mediated conventional hydrogen-bonding interactions (N-H···N, O-H···N, etc.) bridging two or more amino acid residues contribute to the stability of proteins and
K. Mishra, S. Singh, Satish Kumar, Gulzar Singh, Biplab Sarkar, M. Madhusudhan, Aloke Das   +6 more
semanticscholar   +1 more source

Interrogating the PDB

<p><span style="font-size:12pt"><span calibri="" style="font-family:"><b><span arial="" style="font-family:">ASBMB Learning Objectives</span></b> </span></span></p> <p><span style="font-size:12pt"><span calibri="" style="font-family:"><span arial="" style="font-family ...
Johnson, Keith, Dutta, Shuchismita
openaire   +1 more source

Chalcogen Bonding in Protein-Ligand Complexes: PDB Survey and Quantum Mechanical Calculations.

ChemPhysChem, 2018
A chalcogen bond is a nonclassical noncovalent interaction which can stabilise small-molecule crystals as well as protein structures. Here, we systematically explore the stabilising potential of chalcogen bonding in protein-ligand complexes in the ...
K. Kríz, J. Fanfrlík, M. Lepšík
semanticscholar   +1 more source