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Ligand Depot: a data warehouse for ligands bound to macromolecules

Z. Feng, L. Chen, H. Maddula, O. Akcan, R. Oughtred, H. M. Berman, J. Westbrook
2004 Bioinformatics  
Ligand Depot is an integrated data resource for finding information about small molecules bound to proteins and nucleic acids.  ...  Ligand Depot accepts keyword-based queries and also provides a graphical interface for performing chemical substructure searches.  ...  Here we describe Ligand Depot, a data warehouse that integrates databases, services and tools related to small molecules bound to macromolecules.  ... 
doi:10.1093/bioinformatics/bth214 pmid:15059838 fatcat:5hpxwnwambdupdtl3r4mpknq2e

A structural keystone for drug design

Kristian Rother, Mathias Dunkel, Elke Michalsky, Silke Trissl, Andrean Goede, Ulf Leser, Robert Preissner
2006 Journal of Integrative Bioinformatics  
It consists of three parts: i) A data warehouse on annotation of protein structures that integrates many well-known databases such as Swiss-Prot, SCOP, ENZYME and others. ii) A conformational library of  ...  For this purpose we have built a web resource bridging protein and ligand databases.  ...  Ligand Depot [11] and Relibase [15] provide a graphical interface search among the ligands by two-dimensional similarity and chemical substructure as well as for sequence similarity search among the  ... 
doi:10.1515/jib-2006-19 fatcat:jyng7vcqyje3taz7d5z2t5zxye

Superimpose: a 3D structural superposition server

R. A. Bauer, P. E. Bourne, A. Formella, C. Frommel, C. Gille, A. Goede, A. Guerler, A. Hoppe, E.-W. Knapp, T. Poschel, B. Wittig, V. Ziegler (+1 others)
2008 Nucleic Acids Research  
For this purpose, a number of algorithms were implemented and various databases are provided. Superimposé assists the user regarding the selection of a suitable combination of algorithm and database.  ...  The possibility to find similar binding sites can be of special interest in the functional analysis of proteins.  ...  Nicklaus and Wolf-Dietrich Ihlenfeldt from the NCI for providing data of the Open NCI Database with conformers.  ... 
doi:10.1093/nar/gkn285 pmid:18492720 pmcid:PMC2447795 fatcat:c7ljn4uj6fbsxmmu4qfcwdirqi

Mercury toxicity and antioxidants: Part 1: role of glutathione and alpha-lipoic acid in the treatment of mercury toxicity

Lyn Patrick
2002 Alternative medicine review : a journal of clinical therapeutic  
Alpha-lipoic acid, a coenzyme of pyruvate and alpha-ketoglutarate dehydrogenase, has been used in Germany as an antioxidant and approved treatment for diabetic polyneuropathy for 40 years.  ...  Public health concern over mercury exposure, due to contamination of fish with methylmercury and the elemental mercury content of dental amalgams, has long been a topic of political and medical debate.  ...  inorganic mercury, and become firmly bound to sulfhydryl-containing macromolecules. 21 Both methylmercury and inorganic mercury bind to various molecular weight thiol-containing proteins (glutathione  ... 
pmid:12495372 fatcat:vpyiuwwzjvgu7kkllxnmbyhyb4

Human Health Risk Assessment for Aluminium, Aluminium Oxide, and Aluminium Hydroxide

Daniel Krewski, Robert A Yokel, Evert Nieboer, David Borchelt, Joshua Cohen, Jean Harry, Sam Kacew, Joan Lindsay, Amal M Mahfouz, Virginie Rondeau
2007 Journal of Toxicology and Environmental Health. Part B, Critical Reviews  
A large fraction of the aluminium in tea infusions was very strongly bound to unidentified ligands (Alberti et al., 2003) .  ...  Nielsen et al. (1993) studied 25 welders exposed to aluminium. The exposed workers were matched for age and smoking habits to 25 males employed in a warehouse for wines.  ...  This Section provides a synthesis of data from the salient studies on potential health effects of exposure to aluminium for the purpose of quantifying health risks.  ... 
doi:10.1080/10937400701597766 pmid:18085482 pmcid:PMC2782734 fatcat:bx2pc4zpejclpitv4jkdysmnzy

Efficient use of a protein structure annotation database [article]

Kristian Rother, Humboldt-Universität Zu Berlin, Humboldt-Universität Zu Berlin
2017
A dataset of ligands and coenzymes bound to proteins was packed as least as tightly as the reference data. By these results, several contradictions in the literature have been resolved.  ...  Rules for creating datasets of proteins efficiently have been derived. These rules were applied to create datasets for analyzing the packing of proteins.  ...  ., 2002] and Ligand Depot [Feng et al., 2004] just offer a catalog of the PDB ligands in a conveniently searchable way. The latter employs Marvin, a 2D-structure editor.  ... 
doi:10.18452/15657 fatcat:kxmdsya7vzcr3o7y2owe7xn3ae

Health Technology Assessment of pathogen reduction technologies applied to plasma for clinical use

Americo Cicchetti, Alexandra Berrino, Marina Casini, Paola Codella, Giuseppina Facco, Alessandra Fiore, Giuseppe Marano, Marco Marchetti, Emanuela Midolo, Roberta Minacori, Pietro Refolo, Federica Romano (+7 others)
2016 Blood Transfusion  
Evidence on efficacy is only available for the solvent/detergent method, which proved to be non-inferior to untreated fresh-frozen plasma in the treatment of a wide range of congenital and acquired bleeding  ...  Pathogen reduction technologies may offer a new approach to increase blood safety.  ...  bound to lipids and 2% to proteins Does not appear to bind Source: 232  ... 
doi:10.2450/2016.0065-16 pmid:27403740 pmcid:PMC4942318 fatcat:gpeqfbgzcbb2popabool642s64

Midwest Clinical and Translational Research Meeting of CSCTR and MWAFMR

2020 Journal of Investigative Medicine  
Approach: We utilized VHA Corporate Data Warehouse (CDW), a national repository that includes clinical and administrative data from VHA.  ...  Methods This study looked at 1000 dystonia patient encounters from Health Facts Cerner national data warehouse.  ...  These inserts were exposed to aerosolized solutions of 1 mM, 10 nM, and 100 pM MC-LR for 3 minutes a day for 3 days (9 minutes total over 3 days).  ... 
doi:10.1136/jim-2020-mw fatcat:yhmhfirgwjcm7p5jjdmenygq2q

Acute Toxicity [chapter]

Gerald A. Leblanc
A Textbook of Modern Toxicology  
If the affinity for the target tissue is high, then the chemical will accumulate or form a depot.  ...  For example, if a toxicant is 99% bound to plasma proteins, then 1% is free, but if there is toxicant interaction (e.g., competitive binding) that results in 94% bound, 6% is now free.  ...  However, ongoing studies of xenobiotic-metabolizing enzymes were attracting more attention and techniques for chemical analysis of toxicants were starting to undergo a remarkable metamorphosis.  ... 
doi:10.1002/0471646776.ch11 fatcat:hxu6el6mojckxpnl55pgsk2hn4

Dimensions of drug information

Mark E. Sharp
2011
Based on these dimensions, we integrated this information in an experimental database and showed that it was useful (1) as a training set for automating the normalization of additional raw data from the  ...  We argue for a broad view of OM that makes room not only for the "pre-formal" phase/type of multi-ontology integration exemplified by RxNorm and the UMLS Metathesaurus, but also for an even earlier phase  ...  Our data warehouse approach was adopted as an expedient, since the main challenge was to get a grip on "what is there?" and put some of it into a consistent human-readwrite format.  ... 
doi:10.7282/t38c9vws fatcat:hf4yhrsomnexnlsocygifoelnq

Hadrian vs. Apollodorus of Damascus: Who built the Pantheon? Breaking the Fast The Cost of Eating

Alison Burg, Savannah Fielder, Stephanie Hoke, Carlton Troutman, Christopher Duvall, Virginia Nagy, Jocelyn Hofstra, Robert Heller, Tiara Holt, Robert Heller
unpublished
Yes, breakfast is about nourishing the body for the day, but it also tells a story of what a person's life is like day to day.  ...  lining up for a charitable donation.  ...  a change in ligand concentration.  ... 
fatcat:c25lnk6byfgtrldf32zxjuolzq