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PAST: fast structure-based searching in the PDB
2006
Nucleic Acids Research
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PAST is a new web service providing fast structural queries of the Protein Data Bank. ...
Unlike most established tools, PAST does not prefilter the dataset or exclude parts of the search space based on statistical reasoning. The server is freely available at http://past. in.tum.de/. ...
As well as the improved search functions by Uwe Römers and Anselm Kusser. We al thank the anonymous reviewers for helpful considerations. ...
doi:10.1093/nar/gkl273
pmid:16844992
pmcid:PMC1538836
fatcat:2la22nwrtnflxinsbvislhmuui
Biocrystallography: Past, present, future
2010
HFSP Journal
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Membrane proteins are shown with their trans membrane region emphasized in a schematized membrane ͑notice the lysozyme module fused to the intracellular part of the GPCR structure, see text for details͒ ...
All structures are displayed at the same scale using PyMol ͑Delano Scientific-http://www.pymol.org͒. ...
Marat Yusupov for sharing with us his experience on the structural study of the ribosome. ...
doi:10.2976/1.3369281
pmid:21119764
pmcid:PMC2929629
fatcat:zidp47hib5cf7isdbd6lorcqpm
Protein design: Past, present, and future
2015
Biopolymers
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Building on the pioneering work of Bill DeGrado and colleagues in the late nineteen-eighties, protein design approaches have revealed many fundamental features of protein structure and stability. ...
Here we briefly survey some past milestones in protein design, in addition to highlighting recent progress and future aspirations. ...
distributions from the PDB 33 . ...
doi:10.1002/bip.22639
pmid:25784145
pmcid:PMC4856012
fatcat:x5ecxnecfvfepffebuawfd3v4i
Macrocycles: lessons from the distant past, recent developments, and future directions
2015
Chemical Science
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A noticeable increase in molecular complexity of drug targets has created an unmet need in the therapeutic agents that are larger than traditional small molecules. ...
been the topic of particularly intense efforts over the past decade. ...
hydrogen bonds and transient b-sheet structure, which accelerates the search for contacts among residues distant in sequence. 12 Signicantly, intramolecular hydrogen bonds were found to lower the free ...
doi:10.1039/c4sc03089c
pmid:28553456
pmcid:PMC5424464
fatcat:rl26cgbk55b3lkc2rqjbb7fwpi
Past and ongoing adaptation of human cytomegalovirus to its host
2020
PLoS Pathogens
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Functional characterization of adaptive mutations in the primase gene (UL70) indicated that selection favored amino acid replacements that decrease viral replication in human fibroblasts, suggesting evolution ...
A significant excess of positively selected sites was also detected in the signal peptides (SPs) of viral proteins, indicating that, although they are removed from mature proteins, SPs can contribute to ...
enabling fast, iterative and accurate sequence searches [97] . ...
doi:10.1371/journal.ppat.1008476
pmid:32384127
fatcat:tcu6znrxqnfzxarrljekzuuzxu
Applications of Microbial Laccases: Patent Review of the Past Decade (2009–2019)
2019
Catalysts
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Due to society's increasing environmental awareness and the global intensification of bio-based economies, the biotechnological industry is also expanding. ...
This review summarizes the laccase applications in the last decade, focusing on the published patents during this period. ...
At present, 180 structures are available in Protein Data Bank (PDB) corresponding to the keyword 'laccase', while 86 of them have been added after 2015 (Table 1) . ...
doi:10.3390/catal9121023
fatcat:5rwz273oprgvhcwfa6mzznouci
Bacillus sp. JR3 esterase LipJ: A new mesophilic enzyme showing traces of a thermophilic past
2017
PLoS ONE
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A search for extremophile enzymes from ancient volcanic soils in El Hierro Island (Canary Islands, Spain) allowed isolation of a microbial sporulated strain collection from which several enzymatic activities ...
Nevertheless, the 3D structural model of LipJ displayed the same folding as that of thermophilic lipases, suggesting a common evolutionary origin. ...
Acknowledgments We thank the Serveis Cientifico-Tècnics of the University of Barcelona for technical support in sequencing. Dr. ...
doi:10.1371/journal.pone.0181029
pmid:28742841
pmcid:PMC5526573
fatcat:qalep2bdevhbpesgopi7ad624a
Targeting survivin for therapeutic discovery: past, present, and future promises
2017
Drug Discovery Today
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Acknowledgement This work was supported in part by the grant W81XWH-14-1-0489 from Department of Defense CDMRP.
Conflict of interest The authors declare no conflict interest. ...
Atomic structure of survivin (PDB 1F3H) with domains color in correspondence with that shown in the linear structure in panel A. ...
Atomic structure of dimeric survivin (PDB 1F3H) with one subunit shown in pink and the other in blue. ...
doi:10.1016/j.drudis.2017.05.009
pmid:28577912
fatcat:c7hrpvcbgzbhxgfbsmlvg435pm
DNA repair targeted therapy: The past or future of cancer treatment?
2016
Pharmacology and Therapeutics
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The range of insults to DNA includes small, modest changes in structure including mismatched bases and simple methylation events to oxidized bases, intra-and interstrand DNA crosslinks, DNA double strand ...
Pathways required for the repair of these lesions include mismatch repair, base excision repair, nucleotide excision repair, and the homology directed repair/Fanconi anemia pathway. ...
Acknowledgments Research in the Turchi lab is supported by NIH grants R01-CA180710 and R41-CA162648 and the Tom and Julie Wood Family Foundation. ...
doi:10.1016/j.pharmthera.2016.02.003
pmid:26896565
pmcid:PMC4811676
fatcat:b4sz6w4gwfegrapnfjszinremq
Development of Plasmodium falciparum Protease Inhibitors in the Past Decade (2002–2012)
2013
Current Medicinal Chemistry
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recorded in the past decade in this particular field. ...
New drug targets for the development of antimalarial drugs have emerged after the unveiling of the Plasmodium falciparum genome in 2002. ...
CT and JRBG thank FCT for the post-doctoral fellowship SFRH/BPD/62967/2009 and for Programa Ciência 2007, respectively. BP thanks FCT for the doctoral grant SFRH/BD/86166/2012. ...
doi:10.2174/0929867311320250003
pmid:23514416
fatcat:qcx7cwevdbckpbfpscb24z5o4q
PHI-DAC: protein homology database through dihedral angle conservation
2014
Computer applications in the biosciences : CABIOS
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The search engine is fast, with query times lasting a few seconds, and freely available at http:// ...
Finding related conformations in the Protein Data Bank is essential in many areas of bioscience. To assist this task, we designed a dihedral angle database for searching protein segment homologs. ...
INTRODUCTION Over the past years, structural data in the Protein Data Bank (PDB) has grown exponentially. At the present time, $92 000 structures are available in the PDB (Berman et al., 2002) . ...
doi:10.1093/bioinformatics/btu617
pmid:25252780
fatcat:tst2zuom75bhjbbosbggrmlshu
Three stories about the conduct of science: Past, future, and present
2011
Journal of Cheminformatics
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I find myself at an interesting point in my life and career at the same point as the research community is undergoing massive change. ...
The second story is one of what the world might look like at some point in the future. What might we achieve? What might it look like? And what will be possible? ...
the subscription based publishers. ...
doi:10.1186/1758-2946-3-35
pmid:21999290
pmcid:PMC3198952
fatcat:rsvli4hiafb4bats7jzndmqua4
Biomonitoring Human Albumin Adducts: The Past, the Present, and the Future
2016
Chemical Research in Toxicology
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adducts in animals and humans during the past three decades. ...
The identification and characterization of the adduct structures formed with Alb have served to understand the generation of reactive metabolites and to predict idiosyncratic drug reactions and toxicities ...
Three-dimensional structure of Alb (1A06.pdb) with the subdomains (I−III) and depiction of several reactive nucleophilic amino acid residues, which are displayed as spheres. ...
doi:10.1021/acs.chemrestox.6b00366
pmid:27989119
pmcid:PMC5241710
fatcat:2sjumjjzevfa7gtsy7njqigwyu
Biochemistry and physiological roles of enzymes that 'cut and paste' plant cell-wall polysaccharides
2013
Journal of Experimental Botany
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Some of these enzymes also participate in the 'cutting and pasting' (transglycosylation) of sugar residues-enzyme activities known as transglycosidases and transglycanases. ...
Based on the nature of the substrates, two types of reaction can be distinguished: homo-transglycosylation (occurring between chemically similar polymers) and heterotransglycosylation (between chemically ...
Acknowledgements The authors thank the Leverhulme Foundation for supporting their work in this field. ...
doi:10.1093/jxb/ert201
pmid:23956409
fatcat:4q6wpmyzmrexti5bj75jerf4ve
PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank
2015
Nucleic Acids Research
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The unique design of the language and the provided service could pave the way towards novel PDB-wide analyses, which were either difficult or unfeasible in the past. ...
We introduce Pat-ternQuery, a web-based application designed for detection and fast extraction of such patterns. ...
INTRODUCTION In the past years an overwhelming volume of biomacromolecular structures have been deposited in the worldwide deposition system Protein Data Bank (PDB) (1) . ...
doi:10.1093/nar/gkv561
pmid:26013810
pmcid:PMC4489247
fatcat:sdmbzxp7qvavjp7ol4h5aysxya
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