Items where Author is "Bansal, Manju"

Article

Ghoshdastidar, Debostuti ; Bansal, Manju (2022) Flexibility of flanking DNA is a key determinant of transcription factor affinity for the core motif Biophysical Journal, 121 (20). pp. 3987-4000. ISSN 0006-3495

Halder, Swagata ; Bansal, Manju (2022) The effect of mutation in the stem of the MicroROSE thermometer on its thermosensing ability: insights from molecular dynamics simulation studies RSC Advances, 12 (19). pp. 11853-11865. ISSN 2046-2069

Kumar, Prasun ; Halder, Swagata ; Bansal, Manju (2019) Biomolecular Structures: Prediction, Identification and Analyses Life Sciences, 3 . pp. 504-534. ISSN 0024-3205

Gupta, Asmita ; Bansal, Manju (2019) RNA-mediated translation regulation in viral genomes: computational advances in the recognition of sequences and structures Briefings in Bioinformatics, 21 (4). pp. 1151-1163. ISSN 1477-4054

Prasad, Manoj ; Das, Sanjukta ; Bansal, Manju (2019) Variation of gene expression in plants is influenced by gene architecture and structural properties of promoters PLoS One, 14 (3). e0212678. ISSN 1932-6203

Ghoshdastidar, Debostuti ; Bansal, Manju (2018) Dynamics of physiologically relevant noncanonical DNA structures: an overview from experimental and theoretical studies Briefings in Functional Genomics, 18 (3). pp. 192-204. ISSN 2041-2657

Yella, Venkata Rajesh ; Bhimsaria, Devesh ; Ghoshdastidar, Debostuti ; Rodríguez-Martínez, José A ; Ansari, Aseem Z ; Bansal, Manju (2018) Flexibility and structure of flanking DNA impact transcription factor affinity for its core motif Nucleic Acids Research, 46 (22). pp. 11883-11897. ISSN 0305-1048

Yella, Venkata Rajesh ; Kumar, Aditya ; Bansal, Manju (2018) Identification of putative promoters in 48 eukaryotic genomes on the basis of DNA free energy Scientific Reports, 8 (1). ISSN 2045-2322

Mishra, Akhilesh ; Siwach, Priyanka ; Misra, Pallavi ; Jayaram, Bhyravabhotla ; Bansal, Manju ; Olson, Wilma K. ; Thayer, Kelly M. ; Beveridge, David L. (2018) Toward a Universal Structural and Energetic Model for Prokaryotic Promoters Biophysical Journal, 115 (7). pp. 1180-1189. ISSN 0006-3495

Yella, Venkata Rajesh ; Bansal, Manju (2017) DNA structural features of eukaryotic TATA-containing and TATA-less promoters FEBS Open Bio, 7 (3). pp. 324-334. ISSN 2211-5463

Bhattacharyya, Dhananjay ; Halder, Sukanya ; Basu, Sankar ; Mukherjee, Debasish ; Kumar, Prasun ; Bansal, Manju (2017) RNAHelix: computational modeling of nucleic acid structures with Watson–Crick and non-canonical base pairs Journal of Computer-Aided Molecular Design, 31 (2). pp. 219-235. ISSN 0920-654X

Gupta, Asmita ; Kailasam, Senthilkumar ; Bansal, Manju (2016) Insights into the structural dynamics of nucleocytoplasmic transport of tRNA by Exportin-t Biophysical Journal, 110 (6). pp. 1264-1279. ISSN 0006-3495

Bairagya, Hridoy R. ; Bansal, Manju (2016) New insight into the architecture of oxy-anion pocket in unliganded conformation of GAT domains: a MD-simulation study Proteins: Structure, Function, and Bioinformatics, 84 (3). pp. 360-373. ISSN 0887-3585

Jena, N. R. ; Bansal, Manju ; Mishra, P. C. (2016) Conformational stabilities of iminoallantoin and its base pairs in DNA: implications for mutagenicity Physical Chemistry Chemical Physics, 18 (18). pp. 12774-12783. ISSN 1463-9076

Shelar, Ashish ; Bansal, Manju (2016) Data on diverse roles of helix perturbations in membrane proteins Data in Brief, 9 . pp. 781-802. ISSN 2352-3409

Khanday, Imtiyaz ; Das, Sanjukta ; Chongloi, Grace L ; Bansal, Manju ; Grossniklaus, Ueli ; Vijayraghavan, Usha (2016) Genome-Wide Targets Regulated by the OsMADS1 Transcription Factor Reveals Its DNA Recognition Properties Plant Physiology, 172 (1). pp. 372-388. ISSN 0032-0889

Shelar, Ashish ; Bansal, Manju (2016) Helix perturbations in membrane proteins assist in inter-helical interactions and optimal helix positioning in the bilayer Biochimica et Biophysica Acta (BBA) - Biomembranes, 1858 (11). pp. 2804-2817. ISSN 0005-2736

Kumar, Prasun ; Bansal, Manju (2016) Structural and functional analyses of PolyProline-II helices in globular proteins Journal of Structural Biology, 196 (3). pp. 414-425. ISSN 1047-8477

Kumar, Aditya ; Manivelan, Vasumathi ; Bansal, Manju ; van Vliet, Arnoud (2016) Structural features of DNA are conserved in the promoter region of orthologous genes across different strains ofHelicobacter pylori FEMS Microbiology Letters, 363 (18). fnw207. ISSN 1574-6968

Kumar, Aditya ; Bansal, Manju (2016) Unveiling DNA structural features of promoters associated with various types of TSSs in prokaryotic transcriptomes and their role in gene expression DNA Research . dsw045. ISSN 1340-2838

Gupta, Asmita ; Bansal, Manju (2016) The role of sequence in altering the unfolding pathway of an RNA pseudoknot: a steered molecular dynamics study Physical Chemistry Chemical Physics, 18 (41). pp. 28767-28780. ISSN 1463-9076

Mukherjee, Sanchita ; Kailasam, Senthilkumar ; Bansal, Manju ; Bhattacharyya, Dhananjay (2015) Stacking interactions in RNA and DNA: roll-slide energy hyperspace for ten unique dinucleotide steps Biopolymers, 103 (3). pp. 134-147. ISSN 0006-3525

Kumar, Prasun ; Bansal, Manju (2015) Identification of local variations within secondary structures of proteins Acta Crystallographica Section D Biological Crystallography, 71 (5). pp. 1077-1086. ISSN 1399-0047

Ali, Asfa ; Bansal, Manju ; Bhattacharya, Santanu (2015) Ligand 5,10,15,20-Tetra(N-methyl-4-pyridyl)porphine (TMPyP4) Prefers the Parallel Propeller-Type Human Telomeric G-Quadruplex DNA over Its Other Polymorphs Journal of Physical Chemistry B, 119 (1). pp. 5-14. ISSN 1520-6106

Ali, Asfa ; Bansal, Manju ; Bhattacharya, Santanu (2015) Ligand 5,10,15,20-tetra(N-methyl-4-pyridyl)porphine (TMPyP4) prefers the parallel propeller-type human telomeric G-quadruplex DNA over its other polymorphs Journal of Physical Chemistry B, 119 (1). pp. 5-14. ISSN 1520-6106

Shelar, Ashish ; Bansal, Manju (2014) Sequence and conformational preferences at termini of α-helices in membrane proteins: role of the helix environment Proteins: Structure, Function, and Bioinformatics, 82 (12). pp. 3420-3436. ISSN 0887-3585

Bansal, Manju ; Kumar, Aditya ; Yella, Venkata Rajesh (2014) Role of DNA sequence based structural features of promoters in transcription initiation and gene expression Current Opinion in Structural Biology, 25 . pp. 77-85. ISSN 0959-440X

Mukherjee, Sanchita ; Kailasam, Senthilkumar ; Bansal, Manju ; Bhattacharyya, Dhananjay (2014) Energy hyperspace for stacking interaction inAU/AU dinucleotide step: dispersion-corrected density functional theory study Biopolymers, 101 (1). pp. 107-120. ISSN 0006-3525

Gupta, Asmita ; Bansal, Manju (2014) Local structural and environmental factors define the efficiency of an RNA pseudoknot involved in programmed ribosomal frameshift process Journal of Physical Chemistry B, 118 (41). pp. 11905-11920. ISSN 1520-6106

Kumar, Prasun ; Kailasam, Senthilkumar ; Chakraborty, Shaunak ; Bansal, Manju (2014) MolBridge: a program for identifying nonbonded interactions in small molecules and biomolecular structures Journal of Applied Crystallography, 47 (5). pp. 1772-1776. ISSN 1600-5767

Kailasam, Senthilkumar ; Bhattacharyya, Dhananjay ; Bansal, Manju (2014) Sequence dependent variations in RNA duplex are related to non-canonical hydrogen bond interactions in dinucleotide steps BMC Research Notes, 7 . Article ID 83. ISSN 1756-0500

Yella, Venkata Rajesh ; Bansal, Manju (2013) DNA structural features and architecture of promoter regions play a role in gene responsiveness of S. cerevisiae Journal of Bioinformatics and Computational Biology, 11 (06). Article ID 1343001. ISSN 0219-7200

Kumar, Aditya ; Bansal, Manju (2012) Characterization of structural and free energy properties of promoters associated with Primary and Operon TSS in Helicobacter pylori genome and their orthologs Journal of Biosciences, 37 (2). pp. 423-431. ISSN 0250-5991

Kumar, Prasun ; Bansal, Manju (2012) HELANAL-Plus: a web server for analysis of helix geometry in protein structures Journal of Biomolecular Structure and Dynamics, 30 (6). pp. 773-783. ISSN 0739-1102

Bansal, Manju ; Jayaram, B. ; Mittal, Aditya (2012) Nucleic acids in disease and disorder: Understanding the language of life emerging from the ‘ABC’ of DNA Journal of Biosciences, 37 (3). pp. 375-378. ISSN 0250-5991

Jena, N. R. ; Bansal, Manju (2011) Mutagenicity associated with O6-methylguanine-DNA damage and mechanism of nucleotide flipping by AGT during repair Physical Biology, 8 (4). 046007. ISSN 1478-3967

Morey, Czuee ; Mookherjee, Sushmita ; Rajasekaran, G. ; Bansal, Manju (2011) DNA free energy based promoter prediction and comparative analysis of Arabidopsis and rice genomes Plant Physiology . No pp. given. ISSN 0032-0889

Arvind, Marathe ; Bansal, Manju (2011) An ensemble of B-DNA dinucleotide geometries lead to characteristic nucleosomal DNA structure and provide plasticity required for gene expression BMC Structural Biology, 11 . pp. 1_1-1_21. ISSN 1472-6807

Rangannan, Vetriselvi ; Bansal, Manju (2011) PromBase: a web resource for various genomic features and predicted promoters in prokaryotic genomes BMC Research Notes, 4 (1). p. 257. ISSN 1756-0500

Marathe, Arvind ; Bansal, Manju (2010) The 5-methyl group in thymine dynamically influences the structure of A-tracts in DNA at the local and global level Journal of Physical Chemistry B, 114 (16). pp. 5534-5546. ISSN 1520-6106

Rangannan, Vetriselvi ; Bansal, Manju (2010) High-quality annotation of promoter regions for 913 bacterial genomes Bioinformatics, 26 (24). pp. 3043-3050. ISSN 1367-4803

Marathe, Arvind ; Karandur, Deepti ; Bansal, Manju (2009) Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs BMC Structural Biology, 9 . pp. 24_1-24_26. ISSN 1472-6807

Rangannan, Vetriselvi ; Bansal, Manju (2007) Identification and annotation of promoter regions in microbial genome sequences on the basis of DNA stability Journal of Biosciences, 32 (5). pp. 851-862. ISSN 0250-5991

Vidyasagar, M. ; Balakrishnan, N. ; Bansal, Manju ; et., al (2007) BioSuite: a comprehensive bioinformatics software package (A unique industry-academia collaboration) Current Science, 92 (1). pp. 29-38. ISSN 0011-3891

Mukherjee, Shayantani ; Bansal, Manju ; Bhattacharyya, Dhananjay (2006) Conformational specificity of non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis Journal of Computer-Aided Molecular Design, 20 (10-11). pp. 629-645. ISSN 0920-654X

Bansal, Anil K. ; Bansal, Manju ; Soni, Giridhar ; Bhatnagar, Deepak (2005) Protective role of Vitamin E pre-treatment on N-nitrosodiethylamine induced oxidative stress in rat liver Chemico-Biological Interactions, 156 (2-3). pp. 101-111. ISSN 0009-2797

Madhumalar, A. ; Bansal, Manju (2005) Sequence preference for BI/BII conformations in DNA: MD and crystal structure data analysis Journal of Biomolecular Structure & Dynamics, 23 (1). pp. 1-112. ISSN 0739-1102

Bhattacharjee, Arnab ; Bansal, Manju (2005) Collagen structure: the Madras triple helix and the current scenario IUBMB Life, 57 (3). pp. 161-172. ISSN 1521-6543

Kanhere, Aditi ; Bansal, Manju (2005) A novel method for prokaryotic promoter prediction based on DNA stability BMC Bioinformatics, 6 . pp. 1_1-1_10. ISSN 1471-2105

Bansal, Manju ; Rangannan, Vetriselvi (2005) Relative stability of DNA as a generic criterion for promoter prediction: whole genome annotation of microbial genomes with varying nucleotide base composition Molecular Biosystems, 5 . pp. 1758-1769. ISSN 1742-206X

Kanhere, Aditi ; Bansal, Manju (2005) Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes Nucleic Acids Research, 33 (10). pp. 3165-3175. ISSN 0305-1048

Kanhere, Aditi ; Bansal, Manju (2004) DNA bending and curvature: a 'turning point' in DNA function? Proceedings of the Indian National Science Academy - Part B: Biological Sciences, 70 (2). pp. 239-254. ISSN 0073-6600

Bansal, Manju (2003) DNA structure: revisiting the Watson-Crick double helix Current Science, 85 (11). pp. 1556-1563. ISSN 0011-3891

Madhumalar, A. ; Bansal, Manju (2003) Structural insights into the effect of hydration and ions on A-tract DNA: a molecular dynamics study Biophysical Journal, 85 (3). pp. 1805-1816. ISSN 0006-3495

Paul, Bindu Diana ; Kanhere, Aditi ; Chakraborty, Atanu ; Bansal, Manju ; Nagaraja, Valakunja (2003) Identification of the domains for DNA binding and transactivation function of C protein from bacteriophage Mu Proteins: Structure, Function, and Bioinformatics, 52 (2). pp. 272-282. ISSN 0887-3585

Kanhere, Aditi ; Bansal, Manju (2003) An assessment of three dinucleotide parameters to predict DNA curvature by quantitative comparison with experimental data Nucleic Acids Research, 31 (10). pp. 2647-2658. ISSN 0305-1048

Chowdhury, Shibasish ; Bansal, Manju (2001) Modelling studies on neurodegenerative disease causing triplet repeat sequences d(GGC/GCC)_n and d(CAG/CTG)_n Journal of Biosciences, 26 (5). pp. 649-665. ISSN 0250-5991

Chowdhury, Shibasish ; Bansal, Manju (2001) Modelling studies on neurodegenerative disease-causing triplet repeat sequences d(GGC/GCC)_n and d(CAG/CTG)_n Journal of Biosciences, 26 (5). pp. 649-665. ISSN 0250-5991

Bansal, Manju (2001) The Madras triple helix: origins and current status Resonance - Journal of Science Education, 6 (10). pp. 38-47. ISSN 0971-8044

Chowdhury, Shibasish ; Bansal, Manju (2001) A nanosecond molecular dynamics study of antiparallel d(G)₇ quadruplex structures: effect of the coordinated cations Journal of Biomolecular Structure & Dynamics, 18 (5). pp. 647-782. ISSN 0739-1102

Chowdhury, Shibasish ; Bansal, Manju (2001) G-Quadruplex structure can be stable with only some coordination sites being occupied by cations: a six-nanosecond molecular dynamics study Journal of Physical Chemistry B, 105 (31). pp. 7572-7578. ISSN 1089-5647

Bansal, Manju ; Kumar, Sandeep ; Velavan, R. (2000) HELANAL: a program to characterize helix geometry in proteins Journal of Biomolecular Structure & Dynamics, 17 (5). pp. 769-932. ISSN 0739-1102

Ghosh, Anirban ; Bansal, Manju (1999) C-H..O hydrogen bonds in minor groove of A-tracts in DNA double helices Journal of Molecular Biology, 294 (5). pp. 1149-1158. ISSN 0022-2836

Gu, Jiande ; Leszczynski, Jerzy ; Bansal, Manju (1999) A new insight into the structure and stability of Hoogsteen hydrogen-bonded G-tetrad: an ab initio SCF study Chemical Physics Letters, 311 (3-4). pp. 209-214. ISSN 0009-2614

Kumar, Sandeep ; Bansal, Manju (1998) Geometrical and sequence characteristics of α-helices in globular proteins Biophysical Journal, 75 (4). pp. 1935-1944. ISSN 0006-3495

Kumar, Sandeep ; Bansal, Manju (1998) Dissecting α-helices: position-specific analysis of α-helices in globular proteins Proteins: Structure, Function, and Genetics, 31 . pp. 460-476. ISSN 0887-3585

Venkateswarlu, Divi ; Duncan, R. H. ; Bansal, Manju (1997) A semi-empirical SCF-MO study on the base-pairing properties of 8-oxopurines: significance for mutagenicity Journal of the Chemical Society, Perkin Transactions 2 (3). pp. 621-626. ISSN 0300-9580

Mohanty, Debasisa ; Bansal, Manju (1994) Conformational polymorphism in telomeric structures: loop orientation and interloop pairing in d(G₄T_nG₄) Biopolymers, 34 (9). pp. 1187-1211. ISSN 0006-3525

Bansal, Manju ; Mukerji, Krishna G. (1994) Efficacy of root litter as a biofertiliser Biology and Fertility of Soils, 18 (3). pp. 228-230. ISSN 0178-2762

Mohanty, Debasisa ; Bansal, Manju (1993) Conformational polymorphism in G-tetraplex structures: strand reversal by base flipover or sugar flipover Nucleic Acids Research, 21 (8). pp. 1767-1774. ISSN 0305-1048

Heinemann, Udo ; Alings, Claudia ; Bansal, Manju (1992) Double helix conformation, groove dimensions and ligand binding potential of a G/C stretch in B-DNA EMBO Journal, 11 (5). pp. 1931-1939. ISSN 0261-4189

Balagurumoorthy, P. ; Brahmachari, Samir K. ; Mohanty, Debasisa ; Bansal, Manju ; Sasisekharan, V. (1992) Hairpin and parallel quartet structures for telomeric sequences Nucleic Acids Research, 20 (15). pp. 4061-4067. ISSN 0305-1048

Bansal, Manju ; Pattabiraman, N. (1989) Molecular mechanics studies on poly(purine)·poly(pyrimidine) sequences in DNA: polymorphism and local variability Biopolymers, 28 (2). pp. 531-548. ISSN 0006-3525

Majumder, Kumud ; Mishra, Rakesh K. ; Bansal, Manju ; Brahmachari, Samir K. (1989) Sequence criteria for Z-DNA formation: studies on poly d(ACGT) Nucleic Acids Research, 17 (1). p. 450. ISSN 0305-1048

Bhattacharyya, Dhananjay ; Bansal, Manju (1988) Why do DNA helical models exhibit wedge rolls? A mathematical rationale Current Science, 57 (21). pp. 1159-1162. ISSN 0011-3891

Bansal, Manju ; Gupta, Goutam (1981) Structure factor calculations of various DNA duplexes International Journal of Quantum Chemistry, 20 (2). pp. 407-417. ISSN 0020-7608

Sasisekharan, V. ; Gupta, Goutam ; Bansal, Manju (1981) Sequence-dependent molecular conformation of polynucleotides: right and left-handed helices International Journal of Biological Macromolecules, 3 (1). pp. 2-8. ISSN 0141-8130

Gupta, Goutam ; Bansal, Manju ; Sasisekharan, V. (1980) Reversal of handedness in DNA: a stable link between RU and LZ helices Biochemical and Biophysical Research Communications, 97 (4). pp. 1258-1267. ISSN 0006-291X

Gupta, Goutam ; Bansal, Manju ; Sasisekharan, V. (1980) Polymorphism and conformational flexibility of DNA: right and left handed duplexes International Journal of Biological Macromolecules, 2 (6). pp. 368-380. ISSN 0141-8130

Gupta, Goutam ; Bansal, Manju ; Sasisekharan, V. (1980) A novel Z-structure for poly d(GC).poly d(GC) Biochemical and Biophysical Research Communications, 95 (2). pp. 728-733. ISSN 0006-291X

Bansal, Manju ; Brahmachari, Samir K. ; Sasisekharan, V. (1979) Structural investigations on poly(4-hydroxy-L-proline). 1. Theoretical studies Macromolecules, 12 (1). pp. 19-23. ISSN 0024-9297

Brahmachari, Samir K. ; Bansal, Manju ; Ananthanarayanan, V. S. ; Sasisekharan, V. (1979) Structural investigations on poly(4-hydroxy-L-proline). 2. Physicochemical studies Macromolecules, 12 (1). pp. 23-28. ISSN 0024-9297