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A series of PDB-related databanks for everyday needs

Wouter G. Touw, Coos Baakman, Jon Black, Tim A. H. te Beek, E. Krieger, Robbie P. Joosten, Gert Vriend
2014 Nucleic Acids Research  
PDB files are not the optimal presentation of the underlying data for many studies. We therefore made a series of databanks that hold PDB files in an easier to use or more consistent representation.  ...  A large number of databanks have been added to aid computational structural biology; some examples are lists of residues that make crystal contacts, lists of contacting residues using a series of contact  ...  ACKNOWLEDGEMENT We thank our colleagues at the CMBI and at Bio-Prodict for many stimulating discussions and help with coding and checking. FUNDING  ... 
doi:10.1093/nar/gku1028 pmid:25352545 pmcid:PMC4383885 fatcat:m62obb3oyjhevftn544ikvn2ia

A series of PDB related databases for everyday needs

R. P. Joosten, T. A. H. te Beek, E. Krieger, M. L. Hekkelman, R. W. W. Hooft, R. Schneider, C. Sander, G. Vriend
2010 Nucleic Acids Research  
The Protein Data Bank (PDB) is the world-wide repository of macromolecular structure information. We present a series of databases that run parallel to the PDB.  ...  HSSP holds a multiple sequence alignment for all proteins. The PDBFINDER holds easy to parse summaries of the PDB file content, augmented with essentials from the other systems.  ...  ACKNOWLEDGEMENTS The authors are especially grateful to those users of these databases who cite the related articles and who report problems.  ... 
doi:10.1093/nar/gkq1105 pmid:21071423 pmcid:PMC3013697 fatcat:jl2ocrg3v5avbgz7cdxbs3rsie

Visualization of macromolecular structures

Seán I O'Donoghue, David S Goodsell, Achilleas S Frangakis, Fabrice Jossinet, Roman A Laskowski, Michael Nilges, Helen R Saibil, Andrea Schafferhans, Rebecca C Wade, Eric Westhof, Arthur J Olson
2010 Nature Methods  
For comparing different complexes, LIGPLOT 65 and MOE allow the user to generate a series of plots for related proteins binding the same or different ligands.  ...  (a,b) For example, in PDB 2C2A Figure 3 | 3 Visualization of an NMR ensemble for SH3 (ref. 108).  ... 
doi:10.1038/nmeth.1427 pmid:20195256 fatcat:6cdm4zkmwfe5hpo5bl4ea3vonq

Visualization of Biomedical Data

Seán I. O'Donoghue, Benedetta Frida Baldi, Susan J. Clark, Aaron E. Darling, James M. Hogan, Sandeep Kaur, Lena Maier-Hein, Davis J. McCarthy, William J. Moore, Esther Stenau, Jason R. Swedlow, Jenny Vuong (+1 others)
2018 Annual Review of Biomedical Data Science  
The eye of a Master, will do more Work than his Hand. -Benjamin Franklin, Poor Richard's Almanack (1744) 276 O'Donoghue et al.  ...  We then survey how visualization is being used in a selection of emerging biomedical research areas, including three-dimensional genomics, single-cell RNA sequencing (RNA-seq), the protein structure universe  ...  We are grateful for funding organizations that have supported the VIZBI meeting series, especially NIH, EMBO, the University of Sydney, and the Garvan Institute of Medical Research.  ... 
doi:10.1146/annurev-biodatasci-080917-013424 fatcat:fegyfgpvlneupgowzqnwk5opv4

From Structure to Function: Methods and Applications

Haim Wolfson, Maxim Shatsky, Dina Schneidman-Duhovny, Oranit Dror, Alexandra Shulman-Peleg, Buyong Ma, Ruth Nussinov
2005 Current protein and peptide science  
The review presents the up-to-date advances in computational methods for structural pattern discovery and for prediction of molecular associations.  ...  We focus on their applications toward a range of biological problems and highlight the advantages of the combination of these methods and their integration with biological experiments.  ...  The research of H.J.W. is partially supported by the Hermann Minkowski-Minerva Center for Geometry at Tel Aviv University.  ... 
doi:10.2174/1389203053545435 pmid:15853653 fatcat:t6se7n6msnhsfe54rss2xrvnhe

BioSilicoSystems – A Multipronged Approach Towards Analysis and Representation of Biological Data (PhD Thesis)

Sridhar Hariharaputran, Sridhar Hariharaputran
2010 Nature Precedings  
If more than two sequences are given we initially If all this could be done, then we are in a very good position to mine or fish the databanks for the related sequences.  ...  Figure 32 : 32 The related information table from different sources such as Protein DataBank (PDB), SCOP, CATH, Gene Ontology and other external links are provided as * Parts of the work have been published  ... 
doi:10.1038/npre.2010.5164 fatcat:72ufu6ycfba55gi6bvhatcld3e

BioSilicoSystems – A Multipronged Approach Towards Analysis and Representation of Biological Data (PhD Thesis)

Sridhar Hariharaputran, Sridhar Hariharaputran
2010 Nature Precedings  
If more than two sequences are given we initially If all this could be done, then we are in a very good position to mine or fish the databanks for the related sequences.  ...  Figure 32 : 32 The related information table from different sources such as Protein DataBank (PDB), SCOP, CATH, Gene Ontology and other external links are provided as * Parts of the work have been published  ... 
doi:10.1038/npre.2010.5164.1 fatcat:bo3ri2crajb5xk7kukxhe6affa

BioExcel-2 Deliverable 2.1 – State of the Art and Initial Roadmap

Adam Hospital, Stian Soiland-Reyes, Josep Lluís Gelpí, Pau Andrio, Daniele Lezzi, Sarah Butcher, Ania Niewielska, Yvonne Westermaier
2019 Zenodo  
, and presenting a roadmap for WP2 in the first period (18 months) of the BioExcel-2 project.  ...  , success stories reached for a set of workflows built using this library, and finding and using BioExcel workflows through the BioExcel Cloud Portal.  ...  Reduce is a program for adding hydrogens to a Protein DataBank (PDB) molecular structure file, included in the AmberTools package.Package to compute classical molecular interaction potentials (electrostatic  ... 
doi:10.5281/zenodo.4604607 fatcat:u3yplgrepzfytda2zwzu37phge

Structural and evolutionary analysis unveil functional adaptations in the promiscuous behavior of serum albumins [article]

Ana Julia Velez Rueda, Guillermo Ignacio Benítez, Leandro Matías Sommese, Sebastián M. Ardanaz, Estefanía L. Borucki, Nicolas Palopoli, Luis E Iglesias, Gustavo Parisi
2021 bioRxiv   pre-print
AbstractPromiscuous activities have been related to the capacity to catalyze reactions different from those a protein has evolved to sustain.  ...  Structural and evolutionary analysis indicates that the involved residues could have evolved for a still unknown biological function.  ...  A series of PDB-related databanks for everyday needs. Nucleic Acids Res. 2015;43: D364-8. doi:10.1093/nar/gku1028 28. Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, Gascuel O.  ... 
doi:10.1101/2021.05.01.442285 fatcat:rmq3gg24wbdjxg275w2nfs5ksq

A natural chalcone induces apoptosis in lung cancer cells: 3D-QSAR, docking and an in vivo/vitro assay

Gang Chen, Di Zhou, Xue-Zheng Li, Zhe Jiang, Chengyu Tan, Xiu-Yan Wei, Junhong Ling, Jing Jing, Fen Liu, Ning Li
2017 Scientific Reports  
These results suggest that lonchocarpin is a potentially useful natural agent for cancer treatment.  ...  the crucial factor for the antitumor activity of lonchocarpin.  ...  for Chemistry and Molecular Engineering of Medicinal Resources (CMEMR2017-B03).  ... 
doi:10.1038/s41598-017-11369-9 pmid:28878321 pmcid:PMC5587747 fatcat:jodulgxvljgaxb6qowospadpsy

THEA: ontology-driven analysis of microarray data

C. Pasquier, F. Girardot, K. Jevardat de Fombelle, R. Christen
2004 Bioinformatics  
Currently, data interpretation clearly constitutes the bottleneck of such analyses and there is an obvious need for tools able to fill the gap between data processed with mathematical methods and existing  ...  Once microarray data are quantified, normalized and classified, the analysis phase is essentially a manual and subjective task based on visual inspection of classes in the light of the vast amount of information  ...  The relational database MySQL is used to store the information needed by the software. The architecture of THEA is based on the Model-View-Controller (MVC) design paradigm.  ... 
doi:10.1093/bioinformatics/bth295 pmid:15130932 fatcat:ld26jmjo3zakrmi2q2hiw3orte

MENSADB: A Thorough Structural Analysis of Membrane Protein Dimers [article]

Pedro Matos-Filipe, António J. Preto, Panagiotis I. Koukos, Joana Mourão, Alexandre M.J.J. Bonvin, Irina S. Moreira
2019 arXiv   pre-print
Membrane Proteins (MPs) account for around 15-39% of the human proteome and assume a critical role in a vast set of cellular and physiological mechanisms, including molecular transport, nutrient uptake  ...  While roughly 60% of all FDA-approved drugs target MPs, there is a shortage of structural and biochemical data on them mainly hindered by their localization in the lipid bilayer.  ...  A series of PDB-related databanks for everyday needs. Nucleic Acids Res. 43, D364-D368. doi:10.1093/nar/gku1028. Ulmschneider, M. B., and Sansom, M. S. P. (2001).  ... 
arXiv:1902.02321v1 fatcat:n4ekobjs3zb6fbicbvj2yjb23a

Biological Information—Definitions from a Biological Perspective

Jan Charles Biro
2011 Information  
The objective of this paper is to analyze the properties of information in general and to define biological information in particular.  ...  It could be a very discrete change such as storage of the information in a databank for later use, or extensive modification of the receiver's behavior.  ...  There are 3 × 10 9 base pairs in the human genome (100% data), but only a tiny fraction (0.5%) are needed for protein synthesis.  ... 
doi:10.3390/info2010117 fatcat:twvueeyjffg2thuwliafd4d6la

Hidden information on protein function in censuses of proteome foldedness [article]

Dezerae Cox, Ching-Seng Ang, Nadinath B. Nillegoda, Gavin E. Reid, Danny M. Hatters
2021 bioRxiv   pre-print
Paradoxically, up to one third decreased reactivity, which were enriched in proteins with functions relating to unfolded protein stress.  ...  Unmasking this hidden information should improve efforts to understand both folding and the remodeling of protein function directly in complex biological settings  ...  Vriend, A series of 416 PDB-related databanks for everyday needs. Nucleic Acids Res. 43, D364-D368 (2015). 417 40. B. Mészáros, G. Erdos, Z.  ... 
doi:10.1101/2021.02.24.432609 fatcat:ovs57qibwrc3lka23mq533cbpq

A Proton Wire and Water Channel Revealed in the Crystal Structure of Isatin Hydrolase

Kaare Bjerregaard-Andersen, Theis Sommer, Jan K. Jensen, Bjarne Jochimsen, Michael Etzerodt, J. Preben Morth
2014 Journal of Biological Chemistry  
IMBG), University of Aarhus, as part of a double degree agreement. The thesis is divided into two parts.  ...  Part I describes my work on the crystallization and biophysical characterization of the N-terminal cytoplasmic domains of the membrane proteins NCBE.  ...  Significant levels of disorder have been identified in disease-associated protein and these are underrepresented in the protein databank (PDB) (Uversky, Oldfield et al. 2008) .  ... 
doi:10.1074/jbc.m114.568824 pmid:24917679 pmcid:PMC4118100 fatcat:hpcxamzg2zdafdmnnkjiai42gi
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