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PAST: fast structure-based searching in the PDB

H. Taubig, A. Buchner, J. Griebsch
2006 Nucleic Acids Research  
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.  ...  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

Richard Giegé, Claude Sauter
2010 HFSP Journal  
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-͒.  ...  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

Lynne Regan, Diego Caballero, Michael R. Hinrichsen, Alejandro Virrueta, Danielle M. Williams, Corey S. O'Hern
2015 Biopolymers  
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

Andrei K. Yudin
2015 Chemical Science  
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 Signicantly, 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

Alessandra Mozzi, Matteo Biolatti, Rachele Cagliani, Diego Forni, Valentina Dell'Oste, Chiara Pontremoli, Chiara Vantaggiato, Uberto Pozzoli, Mario Clerici, Santo Landolfo, Manuela Sironi, Edward Mocarski
2020 PLoS Pathogens  
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)

Zerva, Simić, Topakas, Nikodinovic-Runic
2019 Catalysts  
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

Judit Ribera, Mónica Estupiñán, Alba Fuentes, Amanda Fillat, Josefina Martínez, Pilar Diaz, Monika Oberer
2017 PLoS ONE  
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

Robert C. Peery, Jing-Yuan Liu, Jian-Ting Zhang
2017 Drug Discovery Today  
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?

Navnath S. Gavande, Pamela S. VanderVere-Carozza, Hilary D. Hinshaw, Shadia I. Jalal, Catherine R. Sears, Katherine S. Pawelczak, John J. Turchi
2016 Pharmacology and Therapeutics  
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)

B. Perez, C. Teixeira, J. Gomes, P. Gomes
2013 Current Medicinal Chemistry  
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

Noa Maatuk, Yitav Glantz-Gashai, Maya Rotman, Meirav Baydany, Gennadiy Fonar, Amir Shechvitz, Karin Shemer, Aviva Peleg, Eli Reuveni, Abraham O. Samson
2014 Computer applications in the biosciences : CABIOS  
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

Cameron Neylon
2011 Journal of Cheminformatics  
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

Gabriele Sabbioni, Robert J. Turesky
2016 Chemical Research in Toxicology  
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

Lenka Franková, Stephen C. Fry
2013 Journal of Experimental Botany  
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

David Sehnal, Lukáš Pravda, Radka Svobodová Vařeková, Crina-Maria Ionescu, Jaroslav Koča
2015 Nucleic Acids Research  
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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