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GEOMETRIC ANALYSIS OF CROSS-LINKABILITY FOR PROTEIN FOLD DISCRIMINATION
2003
Biocomputing 2004
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We are pursuing a minimalist approach to protein fold identification that characterizes possible folds in terms of consistency of their geometric features with restraints derived from relatively cheap, ...
This paper presents a suite of novel lower-and upper-bounding algorithms for analyzing the distance between surface cross-link sites and thereby validating predicted models against experimental cross-linking ...
Thanks to Mike Stoppelman, Xiaoduan Ye, and other members of our labs for helpful discussions and related work. ...
doi:10.1142/9789812704856_0042
fatcat:s7puzvflsja7be6ou275yfotq4
Geometric analysis of cross-linkability for protein fold discrimination
2004
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
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We are pursuing a minimalist approach to protein fold identification that characterizes possible folds in terms of consistency of their geometric features with restraints derived from relatively cheap, ...
This paper presents a suite of novel lower- and upper-bounding algorithms for analyzing the distance between surface cross-link sites and thereby validating predicted models against experimental cross-linking ...
Thanks to Mike Stoppelman, Xiaoduan Ye, and other members of our labs for helpful discussions and related work. ...
pmid:14992524
fatcat:pk2ixt6u4fa6lav5nopyri2u7a
Protein structure prediction guided by crosslinking restraints – A systematic evaluation of the impact of the crosslinking spacer length
2015
Methods
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In this study, the number of cross-links and their discriminative power was systematically analyzed in silico on a set of 2,055 non-redundant protein folds considering Lys-Lys, Lys-Asp, Lys-Glu, Cys-Cys ...
Next, simulated restraints of variable length were used to de novo predict the tertiary structure of fifteen proteins using the BCL::Fold algorithm. ...
Further, 605 the geometrical restraints derived from XL-MS allow for the discrimination of a significant 606 fraction of models representing incorrect topologies and therefore improve the 607 discriminative ...
doi:10.1016/j.ymeth.2015.05.014
pmid:25986934
pmcid:PMC4803439
fatcat:k6otwxpasjaflelxt3rt73t3kq
Trapped translocation intermediates establish the route for export of capsular polysaccharides across Escherichia coli outer membranes
2014
Proceedings of the National Academy of Sciences of the United States of America
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Residues within the lumen of Wza were targeted for site-specific incorporation of the UV photo-cross-linkable unnatural amino acid p-benzoyl-L-phenylalanine. ...
Wza is the prototype for the large family of OM polysaccharide export proteins. ...
We thank Catrien Bouwman for construction of the ΔgalE mutant of E. coli E69, Bradley R. Clarke for technical advice, and members of the laboratory of C.W. for helpful discussions. ...
doi:10.1073/pnas.1400341111
pmid:24843147
pmcid:PMC4050593
fatcat:ybabs3movnhddnmxejsgvtxypy
High-density chemical cross-linking for modeling protein interactions
2019
Proceedings of the National Academy of Sciences of the United States of America
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The resulting model suggests a scaffold for development of a class of protein-based inhibitors of the CA family of enzymes. ...
coverage of 1 unique cross-linked position pair for every 7 amino acids at a 1% false discovery rate. ...
Finley for the proteasome sample and critical reading of the manuscript. We are also grateful to J. Paolo and R. Kunz for instrument help. We thank A.B. Mason and M.P. ...
doi:10.1073/pnas.1902931116
pmid:31848235
pmcid:PMC6955236
fatcat:g72u2fg6p5aqnahmz747w2ha6e
The trimeric solution structure and fucose-binding mechanism of the core fucosylation-specific lectin PhoSL
2018
Scientific Reports
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NMR analysis with an excess amount of fucose revealed the structural basis for the molecular recognition. ...
The structure possesses a β-prism motif with a three-fold rotational symmetry, where three antiparallel β-sheets are tightly connected by swapping of β-strands. ...
Acknowledgements This project was supported by Leading Engine program for Accelerating Drug discovery (LEAD) of AIST. We thank Mr. O. Tani of AIST for his support in the mass spectrometry, and Drs. ...
doi:10.1038/s41598-018-25630-2
pmid:29773815
pmcid:PMC5958098
fatcat:wjgbjyybn5b4fodml4u4hg4kc4
Non‐homology‐based prediction of gene functions in maize ( Zea mays ssp. mays )
2020
The Plant Genome
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Advances in genome sequencing and annotation have eased the difficulty of identifying new gene sequences. Predicting the functions of these newly identified genes remains challenging. ...
As a result, homology is widely used for gene function prediction. This means functional annotation errors also propagate from one species to another. ...
The remaining 80% of data was used to train each algorithm for each GO term. A 10-fold cross validation was used. ...
doi:10.1002/tpg2.20015
pmid:33016608
fatcat:lldl4wonu5eh3fll27ebd4hhma
Role of integrative structural biology in understanding transcriptional initiation
2019
Methods
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The precision of these modelled solutions is limited by the sparseness of cross-links observed, the length of the cross-linking reagent, the ambiguity arisen from the presence of multiple copies of the ...
same protein, and structural and compositional heterogeneity. ...
fluctuations (RMSF), and protein-protein contact analysis. ...
doi:10.1016/j.ymeth.2019.03.009
pmid:30890443
pmcid:PMC6617507
fatcat:pgdbipcqmbfzdmqhg22fzs6hsy
The 13th International Conference on Advances in Quantitative Laryngology, Voice and Speech Research (June 2–4, 2019, Montreal, Quebec, Canada)
2019
Applied Sciences
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The conference and workshops provide a unique opportunity for partnership and collaboration in the advancement of quantitative methods for the measurement and modelling of voice and speech. ...
The AQL accomplishes this mandate by facilitating an interprofessional scientific conference and training intended for an international community of otolaryngologists, speech–language pathologists and ...
for vowel voicing (at least at the speech planning level). ...
doi:10.3390/app9132665
fatcat:xg47la5zkngzxaqe4cdeyv63rq
Advances in Non-Animal Testing Approaches towards Accelerated Clinical Translation of Novel Nanotheranostic Therapeutics for Central Nervous System Disorders
2021
Nanomaterials
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This review aims to identify the most contemporary non-invasive approaches for BBB crossing using nanotheranostics as a novel drug delivery strategy and current non-animal-based models for assessing the ...
By generating predictive data for prospective nanomedicines using validated in vitro models for supporting clinical applications in lieu of requiring extensive use of in vivo animal models that have notable ...
They would also like to acknowledge the work of all researchers included in this review, and to Elsevier Publications and Richard Kollath for the reproduction of figures. ...
doi:10.3390/nano11102632
pmid:34685073
fatcat:oecwqiht3vgklixirhp35lnc6q
DOCK 6: Combining techniques to model RNA-small molecule complexes
2009
RNA: A publication of the RNA Society
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With an increasing interest in RNA therapeutics and for targeting RNA to treat disease, there is a need for the tools used in protein-based drug design, particularly DOCKing algorithms, to be extended ...
Our studies also suggest that RNA-directed ligands often differ from typical protein-ligand complexes in their electrostatic properties, but these differences can be accommodated through the choice of ...
This work was supported in part by an allocation of computing time from the Ohio Supercomputer Center. Received January 18, 2009; accepted February 25, 2009. ...
doi:10.1261/rna.1563609
pmid:19369428
pmcid:PMC2685511
fatcat:7u6e5l3gonchpd23mt2xipseka
Liprotides: a New Class of Protein Lipid-Complexes
2016
Biophysical Journal
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, Python based beamline control, web based applications for data acquisition and analysis, virtualization, and new sample environments. ...
The set of coordinates is used for the calculation of the scattering intensity, either for an oriented particle (as shown in figure 1 ) for for randomly oriented systems. ...
influence the folding and compactness of the protein. ...
doi:10.1016/j.bpj.2015.11.3085
fatcat:eqeeb47atfc4lisnurb25n55gu
Deutsche Gesellschaft für Experimentelle und Klinische Pharmakologie und Toxikologie e.V. Abstracts of the 81th Annual Meeting, March 10-12, 2015, Kiel, Germany
2015
Naunyn-Schmiedeberg's Archives of Pharmacology
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Acknowledgement: This work was supported by the German Research Foundation (DFG, FOR 1406, FU 691/9-2). Acknowledgements: Bavarian State Ministry of the Environment and Consumer Protection. ...
Indeed, disulfide trapping confirmed that the side chains of the pairs Glu84/Arg290 and Glu167/Arg290 are in close proximity when the channel is in the apo closed state, but in weakly cross-linkable and ...
The 90 % CI of the ratio of the geometric means for MRFLB (with/without omeprazole) was between 115 and 127 %. ...
doi:10.1007/s00210-015-1087-4
pmid:25630830
fatcat:wxewzlugk5hvbglugeap75es5u
Guidelines for the use of flow cytometry and cell sorting in immunological studies
2017
European Journal of Immunology
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Guidelines for the use of flow cytometry and cell sorting in immunological studies ...
By using covalently-linkable DNA staining probes (such as ethidium monoazide bromide), it is also possible to combine live/dead discrimination with cell fixation [409] . ...
In contrast, stimulation of CD8 + T cells with whole proteins is not reliable, since MHC class I epitopes are not easily generated from endocytosed proteins which depends on cross-presenting capacity of ...
doi:10.1002/eji.201646632
pmid:29023707
pmcid:PMC9165548
fatcat:2lswztuwwzfnnjomgr2cxnhugu
One-pot synthesis of hyperbranched polyamines based on novel amino glycidyl ether
2017
Journal of Polymer Science Part A: Polymer Chemistry
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We present a recently developed, universal approach for the preparation of a new class of protein-based nanoparticles for the delivery of therapeutics. ...
It features a new concept for the formation of particles based on the assembly of surface-modified proteins. ...
On the material level, a recent
development covering urethane-containing
cross-linkable macromonomers for 3D printing will be
highlighted. ...
doi:10.1002/pola.28865
fatcat:r5jaobn7tzg7rojmelsdnr5v2u
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