Search details
1.
MetBP: a software tool for detection of interaction between metal ion-RNA base pairs.
Bioinformatics
; 38(15): 3833-3834, 2022 08 02.
Article
in English
| MEDLINE | ID: mdl-35695777
2.
Base pair compositional variability influences DNA structural stability and tunes hydration thermodynamics and dynamics.
J Chem Phys
; 159(9)2023 Sep 07.
Article
in English
| MEDLINE | ID: mdl-37655772
3.
Can the jigsaw puzzle model of protein folding re-assemble a hydrophobic core?
Proteins
; 90(7): 1390-1412, 2022 07.
Article
in English
| MEDLINE | ID: mdl-35157344
4.
Understanding the role of non-Watson-Crick base pairs in DNA-protein recognition: Structural and energetic aspects using crystallographic database analysis and quantum chemical calculation.
Biopolymers
; 113(7): e23492, 2022 Jul.
Article
in English
| MEDLINE | ID: mdl-35615897
5.
Contact networks in RNA: a structural bioinformatics study with a new tool.
J Comput Aided Mol Des
; 36(2): 131-140, 2022 02.
Article
in English
| MEDLINE | ID: mdl-35059942
6.
Going beyond base-pairs: topology-based characterization of base-multiplets in RNA.
RNA
; 25(5): 573-589, 2019 05.
Article
in English
| MEDLINE | ID: mdl-30792229
7.
Sequence specificity in DNA-drug intercalation: MD simulation and density functional theory approaches.
J Comput Aided Mol Des
; 34(1): 83-95, 2020 01.
Article
in English
| MEDLINE | ID: mdl-31820194
8.
Structural properties and influence of solvent on the stability of telomeric four-stranded i-motif DNA.
Phys Chem Chem Phys
; 21(38): 21549-21560, 2019 Oct 02.
Article
in English
| MEDLINE | ID: mdl-31536074
9.
Exploring the major cross-talking edges of competitive endogenous RNA networks in human Chronic and Acute Myeloid Leukemia.
Biochim Biophys Acta Gen Subj
; 1862(9): 1883-1892, 2018 09.
Article
in English
| MEDLINE | ID: mdl-29902552
10.
Consequences of Mg2+ binding on the geometry and stability of RNA base pairs.
Phys Chem Chem Phys
; 20(34): 21934-21948, 2018 Aug 29.
Article
in English
| MEDLINE | ID: mdl-30088497
11.
How Does Mg2+ Modulate the RNA Folding Mechanism: A Case Study of the G:C W:W Trans Basepair.
Biophys J
; 113(2): 277-289, 2017 Jul 25.
Article
in English
| MEDLINE | ID: mdl-28506525
12.
RNAHelix: computational modeling of nucleic acid structures with Watson-Crick and non-canonical base pairs.
J Comput Aided Mol Des
; 31(2): 219-235, 2017 02.
Article
in English
| MEDLINE | ID: mdl-28102461
13.
Stacking interactions involving non-Watson-Crick basepairs: dispersion corrected density functional theory studies.
Phys Chem Chem Phys
; 19(42): 28718-28730, 2017 Nov 01.
Article
in English
| MEDLINE | ID: mdl-29043327
14.
Specific DNA sequences allosterically enhance protein-protein interaction in a transcription factor through modulation of protein dynamics: implications for specificity of gene regulation.
Phys Chem Chem Phys
; 19(22): 14781-14792, 2017 Jun 07.
Article
in English
| MEDLINE | ID: mdl-28548177
15.
A comparison of four different conformations adopted by human telomeric G-quadruplex using computer simulations.
Biopolymers
; 105(2): 83-99, 2016 Feb.
Article
in English
| MEDLINE | ID: mdl-26448055
16.
Hybrid simulation approach incorporating microscopic interaction along with rigid body degrees of freedom for stacking between base pairs.
Biopolymers
; 105(4): 212-26, 2016 Apr.
Article
in English
| MEDLINE | ID: mdl-26600167
17.
Conformational selection underpins recognition of multiple DNA sequences by proteins and consequent functional actions.
Phys Chem Chem Phys
; 18(31): 21618-28, 2016 Aug 21.
Article
in English
| MEDLINE | ID: mdl-27426617
18.
Stacking interactions in RNA and DNA: Roll-slide energy hyperspace for ten unique dinucleotide steps.
Biopolymers
; 103(3): 134-47, 2015 Mar.
Article
in English
| MEDLINE | ID: mdl-25257334
19.
Stacking geometry for non-canonical G:U wobble base pair containing dinucleotide sequences in RNA: dispersion-corrected DFT-D study.
Biopolymers
; 103(6): 328-38, 2015 Jun.
Article
in English
| MEDLINE | ID: mdl-25652776
20.
Role of indirect readout mechanism in TATA box binding protein-DNA interaction.
J Comput Aided Mol Des
; 29(3): 283-95, 2015 Mar.
Article
in English
| MEDLINE | ID: mdl-25575717