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Multifunctional energy landscape for a DNA G-quadruplex: An evolved molecular switch
2017
Journal of Chemical Physics
Preserved Fulltext
characterised G-quadruplex topologies. ...
A new class of enhanced kinetic sampling methods for building Markov state models We explore the energy landscape for a four-fold telomere repeat, obtaining interconversion pathways between six experimentally ...
A systematic exploration of all possible quadruplex organisations, based on their topologies and the anti/syn conformations of the guanines, should now be feasible. ...
doi:10.1063/1.4997377
pmid:29055346
fatcat:zw6p2irhyfaktdi3b7d5rbhtkq
A topological nomenclature for protein structure
1998
Protein Engineering Design & Selection
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Keywords: α-helix/β-sheet/graph theory/protein structure representation/protein topology/topological nomenclature In recent years, technical advances in X-ray crystallography and multi-dimensional NMR, ...
Most recently, I have explored how graph theoretical techniques can be combined with established pattern recognition methods to help automate the analysis of super-secondary structures (Flower, 1995a) ...
The last part of the diagram shows topological summaries corresponding to the acyclic form of the graph with labelling of graph edges. ...
doi:10.1093/protein/11.9.723
pmid:9796819
fatcat:4vfilvw74rbenlgux3ttl7lu6i
Mathematics at the eve of a historic transition in biology
[article]
2017
arXiv
pre-print
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Indeed, algebras, partial differential equations, group theory, and functional analysis underpin the foundation of quantum mechanism. ...
Graph theory is able to go beyond topological connectivity and incorporates harmonic analysis and optimization theory to explore biomolecular structure-function relationships. ...
properties. ...
arXiv:1711.02001v1
fatcat:c7glqysunzhw5cgpoabmuscma4
Interlacing molecular threads on transition metals
1990
Pure and Applied Chemistry
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Catenands display very special coordinating properties, allowing in particular to strongly stabilize low formal oxidation states (for ...
Copper (1) is ideally adapted to a three-dimensional template effect allowing interlacing of 1,lO-phenanthroline based molecular threads. ...
The knotted topology of 12 was fully confirmed by the chirality of its potassium complex. H NMR and mass spectra (FAB) consistent with its structure. 12 -++ Fig. 13 . ...
doi:10.1351/pac199062061027
fatcat:s66ujk25ofegjodkdjugdwe4a4
Network Theory Tools for RNA Modeling
2013
WSEAS Transactions on Mathematics
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Graph connectivity and associated Laplacian eigenvalues relate to biological properties of RNA and help understand RNA motifs as well as build, by computational design, various RNA target structures. ...
By using vertices and edges to define RNA secondary structures as tree and dual graphs, we can enumerate, predict, and design RNA topologies. ...
Acknowledgements: This work is supported by the National Science Foundation (DMS-0201160, CCF-0727001) and the National Institutes of Health (GM081410, GM100469). ...
pmid:25414570
pmcid:PMC4235620
fatcat:olt7kbyxu5frpfunqs6vjrbzoy
Engineering macrocyclic figure-eight motif
2007
Proceedings of the Indian Academy of sciences. Chemical sciences
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Nature presents great deal of complexity in terms of structures in macromolecules like DNA and proteins and also displays intriguing topology in simple natural products. ...
Analysis of structure and folding behaviour will enable chemists to design molecules with intriguing topology. ...
Acknowledgements We thank the Department of Science and technology (DST), Govt of India for financial assistance. ...
doi:10.1007/s12039-007-0029-1
fatcat:sawiqvr2rrgc5gqiphqmtah3tm
A Topological Hierarchy of Molecular Chirality and other Tidbits in Topological Stereochemistry
[chapter]
1991
New Developments in Molecular Chirality
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Acknowledgements The author is greatly indebted to the Office of Naval Research for partial support of this work. ...
This classification is completely rigorous, being based upon Euclidean and topological properties of the graphs. ...
Consider the topological properties of this relatively simple molecule. A more illuminating homeotopic presentation of the graph is shown in 17. ...
doi:10.1007/978-94-011-3698-3_4
fatcat:4zhpt2rrnrhmvclb77cqnskiiu
Page 1188 of Mathematical Reviews Vol. , Issue 92b
[page]
1992
Mathematical Reviews
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The symmetry properties of the paths of steepest descent and transition states of these re- arrangements are derived. ...
From this permutational character, it would be possible to investigate the compatibility of these processes with the results of NMR line shape analysis of the dynamics of heptacoordinate complexes. ...
An effective method for network module extraction from microarray data
2012
BMC Bioinformatics
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We use an effective gene expression similarity measure called NMRS (Normalized mean residue similarity) to construct the CEN. ...
The development of high-throughput Microarray technologies has provided various opportunities to systematically characterize diverse types of computational biological networks. ...
Acknowledgment This paper is an outcome of a research project supported by (1) DST, Govt. of India in collaboration with ISI, Kolkata and (2) National Science Foundation, USA under grants CNS-095876 and ...
doi:10.1186/1471-2105-13-s13-s4
pmid:23320896
pmcid:PMC3426802
fatcat:yvmndjtygjgevp3bm3hz3xu4rm
Probabilistic Interaction Network of Evidence Algorithm and its Application to Complete Labeling of Peak Lists from Protein NMR Spectroscopy
2009
PLoS Computational Biology
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The PINE-NMR server accepts as input the sequence of the protein plus user-specified combinations of data corresponding to an extensive list of NMR experiments; it provides as output a probabilistic assignment ...
PINE-NMR achieves robust and consistent results that have been shown to be effective in subsequent steps of NMR structure determination. ...
Acknowledgments We thank the members of NMRFAM and CESG who provided NMR data for this study and are pleased to acknowledge the many users of the PINE-NMR server, who provided useful feedback on its operation ...
doi:10.1371/journal.pcbi.1000307
pmid:19282963
pmcid:PMC2645676
fatcat:s6zqy7o3xvgx3m5zjgc6k2rgoy
Targeting Promoter G-Quadruplex DNAs by Indenopyrimidine-Based Ligands
2014
ChemMedChem
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Fluorescence titration experiments Fluorescence spectroscopy was used to explore the binding properties of ligands with various quadruplex and duplex DNAs. [44, 45] Interaction of ligands with quadruplex ...
Titration of the human telomeric DNA with InPy1 in the absence of added monovalent cations was carried out to explore the capacity of the ligand to induce a particular quadruplex topology. ...
Acknowledgements We are thankful to the Computer Centre, IIT Bombay, for use of the HPC facility; to Prof. David A. Case (Rutgers University) for waiving the licensing fee for AMBER 12; and to Prof. ...
doi:10.1002/cmdc.201402394
pmid:25359695
fatcat:lu57dzmmbzexpmohvt7aum3wfq
Protonation of Borylated Carboxonium Derivative [2,6-B10H8O2CCH3]−: Theoretical and Experimental Investigation
2022
International Journal of Molecular Sciences
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The structure of the resulting complex [2,6-B10H8O2CCH3*Hfac]0 was established using NMR data and the results of DFT calculations. ...
The process of protonation was carried out in the presence of an excess of trifluoromethanesulfonic acid CF3SO3H at room temperature in dichloromethane solution. ...
Acknowledgments: NMR Studies were performed within the framework of the State Assignment of the Kurnakov Institute (IGIC RAS) in the field of fundamental scientific research. ...
doi:10.3390/ijms23084190
pmid:35457007
pmcid:PMC9025682
fatcat:i5g7d3f56fdjfkh2u3gcdvhuia
Network alignment and similarity reveal atlas-based topological differences in structural connectomes
2021
Network Neuroscience
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First, the graph Jaccard index (GJI), a graph similarity measure based on the well-established Jaccard index between sets; the GJI exhibits natural mathematical properties that are not satisfied by previous ...
The edges of the graph encode the strength of the axonal connectivity between regions of the atlas that can be estimated via diffusion magnetic resonance imaging (MRI) tractography. ...
Vogelstein for the discussion on the use of FAQ. ...
doi:10.1162/netn_a_00199
pmid:34746624
pmcid:PMC8567827
fatcat:b4z2je5ibrb3fnsfzv7yiyp2z4
Ordering Protein Contact Matrices
2018
Computational and Structural Biotechnology Journal
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During the exploration of DFS that starts at node r, there are three possible states for each node, which are not explored, partially explored and completely explored. ...
These 8 architectures correspond only to 11 topologies over the 1391 topologies of CATH. Thus, the PDB select list corresponds to the majority of CATH folds. ...
doi:10.1016/j.csbj.2018.03.001
pmid:29632657
pmcid:PMC5889711
fatcat:tfmtqe23zjdbzkszey4nqvmngm
Page 49 of Library & Information Science Abstracts Vol. , Issue 6
[page]
1993
Library & Information Science Abstracts
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(LT)
9303836
Topological approach of C13 NMR spectral simulation: application to fuzzy substructures. A. Panaye, J-P. Doucet and B. T. Fan. ...
(LT)
9303835
Sequential assignment of 2D-NMR spectra of proteins using genetic algorithms. R. Wehrens et al. ...
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