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Multifunctional energy landscape for a DNA G-quadruplex: An evolved molecular switch

Tristan Cragnolini, Debayan Chakraborty, Jiří Šponer, Philippe Derreumaux, Samuela Pasquali, David J. Wales
2017 Journal of Chemical Physics  
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

D. R. Flower
1998 Protein Engineering Design & Selection  
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]

Guo-Wei Wei
2017 arXiv   pre-print
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

J.-C. Chambron, C. O. Dietrich-Buchecker, Catherine Hemmert, A.-K. Khemiss, D. Mitchell, J.-P. Sauvage, J. Weiss
1990 Pure and Applied Chemistry  
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

Namhee Kim, Louis Petingi, Tamar Schlick
2013 WSEAS Transactions on Mathematics  
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

V. Haridas, Harinder Singh, Yogesh K. Sharma, Kashmiri Lal
2007 Proceedings of the Indian Academy of sciences. Chemical sciences  
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]

David M. Walba
1991 New Developments in Molecular Chirality  
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  
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

Priyakshi Mahanta, Hasin A Ahmed, Dhruba K Bhattacharyya, Jugal K Kalita
2012 BMC Bioinformatics  
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

Arash Bahrami, Amir H. Assadi, John L. Markley, Hamid R. Eghbalnia, David Cowburn
2009 PLoS Computational Biology  
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

K. V. Diveshkumar, Saaz Sakrikar, S. Harikrishna, V. Dhamodharan, P. I. Pradeepkumar
2014 ChemMedChem  
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

Ilya N. Klyukin, Anastasia V. Kolbunova, Alexander S. Novikov, Aleksey V. Nelyubin, Nikita A. Selivanov, Alexander Yu. Bykov, Alexandra A. Klyukina, Andrey P. Zhdanov, Konstantin Yu. Zhizhin, Nikolay T. Kuznetsov
2022 International Journal of Molecular Sciences  
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

Matteo Frigo, Emilio Cruciani, David Coudert, Rachid Deriche, Emanuele Natale, Samuel Deslauriers-Gauthier
2021 Network Neuroscience  
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

Chuan Xu, Guillaume Bouvier, Benjamin Bardiaux, Michael Nilges, Thérèse Malliavin, Abdel Lisser
2018 Computational and Structural Biotechnology Journal  
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  
(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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