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3DNALandscapes: a database for exploring the conformational features of DNA
2009
Nucleic Acids Research
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3DNALandscapes, located at: http://3DNAscapes .rutgers.edu, 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
2015
Nucleic Acids Research
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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
2012
Current Opinion in Structural Biology
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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/j.sbi.2012.03.012
pmid:22538125
pmcid:PMC4028509
fatcat:3hzwpvlvrzgmxli7kjjyq4crq4
How 'Protein-Docking' Translates into the New Emerging Field of Docking Small Molecules to Nucleic Acids?
2020
Molecules
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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
2017
Zenodo
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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
2017
Nucleic Acids Research
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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
2013
Biopolymers
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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
2016
Database: The Journal of Biological Databases and Curation
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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
2013
PLoS ONE
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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
2016
ChemBioChem
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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
2011
Journal of Nucleic Acids
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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
2013
Biophysical Journal
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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
2004
Pure and Applied Chemistry
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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
2017
FEBS Letters
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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
2014
Life
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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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