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3DNALandscapes: a database for exploring the conformational features of DNA

Guohui Zheng, Andrew V. Colasanti, Xiang-Jun Lu, Wilma K. Olson
2009 Nucleic Acids Research  
3DNALandscapes, located at: http://3DNAscapes, is a new database for exploring the conformational features of DNA.  ...  In contrast to most structural databases, which archive the Cartesian coordinates and/or derived parameters and images for individual structures, 3DNALandscapes enables searches of conformational information  ...  (b) One of the downloadable two-dimensional scatter plots, here Roll versus Twist, automatically generated for the above steps in the data set.  ... 
doi:10.1093/nar/gkp959 pmid:19906722 pmcid:PMC2808892 fatcat:445xhsk5tjdulnymczy2jzls74

ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability

Vincent Frappier, Matthieu Chartier, Rafael J. Najmanovich
2015 Nucleic Acids Research  
The inclusion of this layer of information was shown to improve conformational space sampling and apply for the first time a coarse-grained normal mode analysis method to predict the effect of single point  ...  ENCoM is a coarse-grained normal mode analysis method recently introduced that unlike previous such methods is unique in that it accounts for the nature of amino acids.  ...  Normal modes provide a means to generate conformational ensembles. However, care needs to be taken in the details of how the exploration of the relevant modes is performed.  ... 
doi:10.1093/nar/gkv343 pmid:25883149 pmcid:PMC4489264 fatcat:ftzz676gi5celojsthlly2sbpy

Modeling nucleic acids

Adelene YL Sim, Peter Minary, Michael Levitt
2012 Current Opinion in Structural Biology  
Due to their self-assembling characteristics, nucleic acids have also been widely studied in the field of nanotechnology, and a diverse range of intricate three-dimensional nanostructures have been designed  ...  Appropriate choices in each of these key areas in nucleic acid modeling can effectively combine to aid interpretation of experimental data and facilitate prediction of nucleic acid structure.  ...  Acknowledgements We apologize to researchers for being unable to cite all their interesting and relevant work in the field of nucleic acid modeling due to space constraints.  ... 
doi:10.1016/ pmid:22538125 pmcid:PMC4028509 fatcat:3hzwpvlvrzgmxli7kjjyq4crq4

How 'Protein-Docking' Translates into the New Emerging Field of Docking Small Molecules to Nucleic Acids?

Francesca Tessaro, Leonardo Scapozza
2020 Molecules  
Here, we have analyzed literature data on nucleic acid to benchmark some of the widely used docking programs.  ...  Despite the promising therapeutic potential of nucleic acids, molecular docking programs have been optimized mostly for proteins.  ...  The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.  ... 
doi:10.3390/molecules25122749 pmid:32545835 fatcat:rhfd7634qzcuxpsnhmqpzityom

BioExcel Webinar #16 - NAFlex, a web server for the study of nucleic acid flexibility

Federica Battistini
2017 Zenodo  
The server offers a variety of methods to explore nucleic acid flexibility, a base-pair resolution mesoscopic model and atomistic molecular dynamics simulations with a wide variety of protocols and force  ...  The server allows the user to study the flexibility of nucleic acids, either isolated or bound to other molecules.  ... 
doi:10.5281/zenodo.3824299 fatcat:qrj23iiuobernfx2qdhvk2rw2q

SPA-LN: a scoring function of ligand–nucleic acid interactions via optimizing both specificity and affinity

Zhiqiang Yan, Jin Wang
2017 Nucleic Acids Research  
However, the predictive power of nucleic acid-ligand scoring functions is still a challenge compared to other types of biomolecular recognition.  ...  The performance of SPA-LN validates the development strategy and provides a relatively more accurate way to score the nucleic acid-ligand interactions.  ...  ACKNOWLEDGEMENT The authors thank Computing Center of Jilin Province for computational support.  ... 
doi:10.1093/nar/gkx255 pmid:28431169 pmcid:PMC5499587 fatcat:abr54zqyjvc5poz2phr3pbna2q

Twenty-five years of nucleic acid simulations

Thomas E. Cheatham, David A. Case
2013 Biopolymers  
We present a brief, and largely personal, history of computer simulations of DNA and RNA oligonucleotides, with an emphasis on duplex structures and the Amber force fields.  ...  This overview, covering about two decades of work, provides a perspective for a discussion of prospects and obstacles for future simulations of RNA and DNA.  ...  The 50th anniversary of Biopolymers coincides with the 25th year that one of us (DAC) has served on its editorial board, and he takes this opportunity to thank other members of the editorial board for  ... 
doi:10.1002/bip.22331 pmid:23784813 pmcid:PMC3820278 fatcat:gpvn7lvbf5hgddqbvfvwnhd42q

NALDB: nucleic acid ligand database for small molecules targeting nucleic acid

Subodh Kumar Mishra, Amit Kumar
2016 Database: The Journal of Biological Databases and Curation  
NALDB is the first ligand database that contains ligand information for all type of nucleic acid.  ...  Abstract Nucleic acid ligand database (NALDB) is a unique database that provides detailed information about the experimental data of small molecules that were reported to target several types of nucleic  ...  Acknowledgements The authors thank Mr. Eshan Khan and Ms. Arpita Tawani for their help in preparing the manuscript, and designing the database pages.  ... 
doi:10.1093/database/baw002 pmid:26896846 pmcid:PMC4761111 fatcat:2wx4pdzvkzco3kvrrv35me2lgq

Optimizing Scoring Function of Protein-Nucleic Acid Interactions with Both Affinity and Specificity

Zhiqiang Yan, Jin Wang, Freddie Salsbury
2013 PLoS ONE  
Protein-nucleic acid (protein-DNA and protein-RNA) recognition is fundamental to the regulation of gene expression.  ...  In this work, we developed an accurate scoring function (named as SPA-PN, SPecificity and Affinity of the Protein-Nucleic acid interactions) for protein-nucleic acid interactions by incorporating both  ...  acid conformation, l mn is the ISR representing the specificity of the protein-nucleic acid conformation [19] [20] [21] . c is a parameter which balances the values of E mn and l mn and set as 0.1.  ... 
doi:10.1371/journal.pone.0074443 pmid:24098651 pmcid:PMC3787031 fatcat:wziyj7iqfzejlink6iyywkzyea

Nanostructures from Synthetic Genetic Polymers

Alexander I. Taylor, Fabienne Beuron, Sew-Yeu Peak-Chew, Edward P. Morris, Piet Herdewijn, Philipp Holliger
2016 ChemBioChem  
Keywords: chemical biology · DNA nanotechnology · electron microscopy · self-assembly · xeno nucleic acids (XNAs)  ...  Here, we explore the construction of nano-objects made entirely from alternative building blocks:s ynthetic genetic polymers not found in nature,a lso called xeno nucleic acids (XNAs).  ...  nucleic acids.  ... 
doi:10.1002/cbic.201600136 pmid:26992063 pmcid:PMC4973672 fatcat:bu6ktv5dl5e7pbenavyuvcoknu

Use of Nucleic Acid Analogs for the Study of Nucleic Acid Interactions

Shu-ichi Nakano, Masayuki Fujii, Naoki Sugimoto
2011 Journal of Nucleic Acids  
This paper briefly summarizes nucleic acid analogs in which the base is modified or replaced by an unnatural stacking group for the study of nucleic acid interactions.  ...  The base pair-mimic nucleosides can be used to study the mechanism responsible for the base stacking and the flipping of bases out of a nucleic acid duplex.  ...  Acknowledgments The authors thank Yuuki Uotani, Hirohito Oka, Shoji Nakashima, Kazuya Uenishi, and Yosuke Anno for their contributions to the investigations of the base pair-mimic nucleosides.  ... 
doi:10.4061/2011/967098 pmid:21822475 pmcid:PMC3142669 fatcat:cm6uymgkr5dexbcvtz7o7sf7su

Nucleic Acid Conformation Ensembles Revealed by Au-SAXS Interferometry

Xuesong Shi, Pehr Harbury, Daniel Herschlag
2013 Biophysical Journal  
While practical challenges remain, this breakthrough opens the possibility of using SAXS with new, high brightness X-ray sources for high throughput applications. 2568-Pos Board B587 Nucleic Acid Conformation  ...  A central challenge in modern biology is to develop physical models that faithfully reproduce this landscape, and that are capable of predicting the dynamical behavior of proteins and nucleic acids intrinsic  ... 
doi:10.1016/j.bpj.2012.11.2770 fatcat:walxw4mbrzdppiv57opevkerza

Conformationally restricted cationic polyamide analogs of nucleic acids: Design, synthesis, and DNA/RNA binding studies

V. A. Kumar, Moneesha D'Costa, P. S. Lonkar, Meena, P. S. Pallan, K. N. Ganesh
2004 Pure and Applied Chemistry  
The remarkable medicinal importance of the achiral, acyclic, and uncharged aminoethylglycyl peptide nucleic acids (  ...  ACKNOWLEDGMENTS VAK thanks the Department of Science and Technology, Indian National Science Academy and National Chemical Laboratory for research and travel grants.  ...  This caused aegPNA-III to be highly soluble in water, but reduced binding affinity with target nucleic acids due to unrestricted conformational freedom.  ... 
doi:10.1351/pac200476071599 fatcat:jdh55o3x7jadter2btrydorhq4

Investigating the nucleic acid interactions of histone-derived antimicrobial peptides

Sukin Sim, Penny Wang, Brittany N. Beyer, Kara J. Cutrona, Mala L. Radhakrishnan, Donald E. Elmore
2017 FEBS Letters  
Moreover, the lack of binding specificity may make it more difficult for bacteria to evolve resistance to these and other similar AMPs.  ...  Buforin II and DesHDAP1 are thought to kill bacteria by interacting with nucleic acids.  ...  S.S. was supported through the Arnold Beckman Scholars Program. B.N.B. was supported by National Science Foundation award CHE-1005032. D.E.E. is a Henry Dreyfus Teacher-Scholar.  ... 
doi:10.1002/1873-3468.12574 pmid:28130840 pmcid:PMC5371511 fatcat:raus6v3hxba27cbuyxo2jiwvsy

Looked at Life from Both Sides Now

Jillian Smith, Allisandra Mowles, Anil Mehta, David Lynn
2014 Life  
Hydrogen-bond donor/acceptor pairs bias the folding pathways of nucleic acids to optimally store "digital-like" information in the genome.  ...  The origins of this protein/nucleic acid biopolymer mutualism can now be reconsidered in light of the discovery of protein-only infectious agents known as prions [13] .  ...  Department of Energy through Grant DE-ER15377. Conflicts of Interest The authors declare no conflict of interest.  ... 
doi:10.3390/life4040887 pmid:25513758 pmcid:PMC4284472 fatcat:iir6cskiljcjjl5gmgxn3k6cki
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