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Kumar, Prasun and Halder, Swagata and Bansal, Manju (2019) Biomolecular Structures: Prediction, Identification and Analyses. [Book Chapter]
Shelar, Ashish and Kumar, Prasun and Bansal, Manju (2014) DEFINING alpha-HELIX GEOMETRY BY C-alpha ATOM TRACE vs (phi-psi) TORSION ANGLES: A COMPARATIVE ANALYSIS. In: Conference on Biomolecular Forms and Functions - A Celebration of 50 Years of the Ramachandran Map, JAN, 2013, Indian Inst Sci, Bangalore, INDIA, pp. 116-127.
Ghosh, Arindam and Bansal, Manju (2001) Structural features of B-DNA dodecamer crystal structures: Influence of crystal packing versus base sequence. In: Satellite Symposium on Structural Biology and Molecular Recognition, SEP 27-29, 1999, Calcutta, India.
Ghoshdastidar, Debostuti and Bansal, Manju (2019) Dynamics of physiologically relevant noncanonical DNA structures: an overview from experimental and theoretical studies. In: BRIEFINGS IN FUNCTIONAL GENOMICS, 18 (3). pp. 192-204.
Yella, Venkata Rajesh and Kumar, Aditya and Bansal, Manju (2018) Identification of putative promoters in 48 eukaryotic genomes on the basis of DNA free energy. In: SCIENTIFIC REPORTS, 8 .
Yella, Venkata Rajesh and Bansal, Manju (2017) DNA structural features of eukaryotic TATA-containing and TATA-less promoters. In: FEBS OPEN BIO, 7 (3). pp. 324-334.
Bhattacharyya, Dhananjay and Halder, Sukanya and Basu, Sankar and Mukherjee, Debasish and Kumar, Prasun and Bansal, Manju (2017) RNAHelix: computational modeling of nucleic acid structures with Watson-Crick and non-canonical base pairs. In: JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 31 (2). pp. 219-235.
Kumar, Aditya and Bansal, Manju (2017) Unveiling DNA structural features of promoters associated with various types of TSSs in prokaryotic transcriptomes and their role in gene expression. In: DNA RESEARCH, 24 (1). pp. 25-35.
Jena, NR and Bansal, Manju and Mishra, PC (2016) Conformational stabilities of iminoallantoin and its base pairs in DNA: implications for mutagenicity. In: PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18 (18). pp. 12774-12783.
Khanday, Imtiyaz and Das, Sanjukta and Chongloi, Grace L and Bansal, Manju and Grossniklaus, Ueli and Vijayraghavan, Usha (2016) Genome-Wide Targets Regulated by the OsMADS1 Transcription Factor Reveals Its DNA Recognition Properties. In: PLANT PHYSIOLOGY, 172 (1). pp. 372-388.
Shelar, Ashish and Bansal, Manju (2016) Helix perturbations in membrane proteins assist in inter-helical interactions and optimal helix positioning in the bilayer. In: BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1858 (11). pp. 2804-2817.
Gupta, Asmita and Kailasam, Senthilkumar and Bansal, Manju (2016) Insights into the Structural Dynamics of Nucleocytoplasmic Transport of tRNA by Exportin-t. In: BIOPHYSICAL JOURNAL, 110 (6). pp. 1264-1279.
Bairagya, Hridoy R and Bansal, Manju (2016) New insight into the architecture of oxy-anion pocket in unliganded conformation of GAT domains: A MD-simulation study. In: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 84 (3). pp. 360-373.
Kumar, Prasun and Bansal, Manju (2016) Structural and functional analyses of PolyProline-II helices in globular proteins. In: JOURNAL OF STRUCTURAL BIOLOGY, 196 (3). pp. 414-425.
Kumar, Aditya and Manivelan, Vasumathi and Bansal, Manju (2016) Structural features of DNA are conserved in the promoter region of orthologous genes across different strains of Helicobacter pylori. In: FEMS MICROBIOLOGY LETTERS, 363 (18).
Gupta, Asmita and Bansal, Manju (2016) The role of sequence in altering the unfolding pathway of an RNA pseudoknot: a steered molecular dynamics study. In: PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18 (41). pp. 28767-28780.
Kumar, Prasun and Bansal, Manju (2015) Dissecting pi-helices: sequence, structure and function. In: FEBS JOURNAL, 282 (22). pp. 4415-4432.
Kumar, Prasun and Bansal, Manju (2015) Identification of local variations within secondary structures of proteins. In: ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 71 (5). pp. 1077-1086.
Ali, Asfa and Bansal, Manju and 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. In: JOURNAL OF PHYSICAL CHEMISTRY B, 119 (1). pp. 5-14.
Mukherjee, Sanchita and Kailasam, Senthilkumar and Bansal, Manju and Bhattacharyya, Dhananjay (2015) Stacking Interactions in RNA and DNA: Roll-Slide Energy Hyperspace for Ten Unique Dinucleotide Steps. In: BIOPOLYMERS, 103 (3). pp. 134-147.
Mukherjee, Sanchita and Kailasam, Senthilkumar and Bansal, Manju and Bhattacharyya, Dhananjay (2014) Energy Hyperspace for Stacking Interaction in AU/AU Dinucleotide Step: Dispersion-Corrected Density Functional Theory Study. In: BIOPOLYMERS, 101 (1). pp. 107-120.
Gupta, Asmita and Bansal, Manju (2014) Local Structural and Environmental Factors Define the Efficiency of an RNA Pseudoknot Involved in Programmed Ribosomal Frameshift Process. In: JOURNAL OF PHYSICAL CHEMISTRY B, 118 (41). pp. 11905-11920.
Kumar, Prasun and Kailasam, Senthilkumar and Chakraborty, Shaunak and Bansal, Manju (2014) MolBridge: a program for identifying nonbonded interactions in small molecules and biomolecular structures. In: JOURNAL OF APPLIED CRYSTALLOGRAPHY, 47 (5). pp. 1772-1776.
Bansal, Manju and Kumar, Aditya and Yella, Venkata Rajesh (2014) Role of DNA sequence based structural features of promoters in transcription initiation and gene expression. In: CURRENT OPINION IN STRUCTURAL BIOLOGY, 25 . pp. 77-85.
Shelar, Ashish and Bansal, Manju (2014) Sequence and conformational preferences at termini of alpha-helices in membrane proteins: Role of the helix environment. In: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82 (12). pp. 3420-3436.
Yella, Venkata Rajesh and Bansal, Manju (2013) DNA STRUCTURAL FEATURES AND ARCHITECTURE OF PROMOTER REGIONS PLAY A ROLE IN GENE RESPONSIVENESS OF S. CEREVISIAE. In: JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 11 (6, SI).
Kumar, Aditya and 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. In: JOURNAL OF BIOSCIENCES, 37 (3). pp. 423-431.
Kumar, Prasun and Bansal, Manju (2012) HELANAL-Plus: a web server for analysis of helix geometry in protein structures. In: JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 30 (6). pp. 773-783.
Morey, Czuee and Mookherjee, Sushmita and Rajasekaran, Ganesan and Bansal, Manju (2011) DNA Free Energy-Based Promoter Prediction and Comparative Analysis of Arabidopsis and Rice Genomes. In: Plant Physiology, 156 (3). pp. 1300-1315.
Marathe, Arvind and Bansal, Manju (2011) An ensemble of B-DNA dinucleotide geometries lead to characteristic nucleosomal DNA structure and provide plasticity required for gene expression. In: BMC STRUCTURAL BIOLOGY, 11 .
Jena, NR and Bansal, Manju (2011) Mutagenicity associated with O6-methylguanine-DNA damage and mechanism of nucleotide flipping by AGT during repair. In: Physical Biology, 8 (4).
Rangannan, Vetriselvi and Bansal, Manju (2010) High-quality annotation of promoter regions for 913 bacterial genomes. In: Bioinformatics, 26 (24). pp. 3043-3050.
Marathe, Arvind and Bansal, Manju (2010) The 5-Methyl Group in Thymine Dynamically Influences the Structure of A-Tracts in DNA at the Local and Global Level. In: Journal of Physical Chemistry B, 114 (16). pp. 5534-5546.
Rangannan, Vetriselvi and Bansal, Manju (2009) Relative stability of DNA as a generic criterion for promoter prediction: whole genome annotation of microbial genomes with varying nucleotide base composition. In: Molecular BioSystems, 5 (12). pp. 1758-1769.
Marathe, Arvind and Bansal, Manju (2009) Structural Polymorphism of the Nucleosomal DNA and Implications for Protein Binding. In: Journal of Biomolecular Structure & Dynamics, 26 (6). pp. 925-926.
Marathe, Arvind and Karandur, Deepti and 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. In: BMC Structural Biology, 9 (24).
Rangannan, Vetriselvi and Bansal, Manju (2007) Identification and annotation of promoter regions in microbial genome sequences on the basis of DNA stability. In: Journal of Biosciences, 32 (5). pp. 871-881.
Mukherjee, Shayantani and Bansal, Manju and Bhattacharyya, Dhananjay (2006) Conformational specificity of non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis. In: Journal of Computer-Aided Molecular Design, 20 (10-11). pp. 629-645.
Madhumalar, A and Bansal, Manju (2005) Sequence preference for BI/BII conformations in DNA: MD and crystal structure data analysis. In: Journal of Biomolecular Structure & Dynamics, 23 (1). pp. 13-27.
Kanhere, Aditi and Bansal, Manju (2005) Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes. In: Nucleic Acids Research, 33 (10). pp. 3165-3175.
Bhattacharjee, Arnab and Bansal, Manju (2005) Collagen Structure: The Madras Triple Helix and the Current Scenario. In: International Union of Biochemistry and Molecular Biology: Life, 57 (3). pp. 161-72.
Kanhere, Aditi and Bansal, Manju (2005) A novel method for prokaryotic promoter prediction based on DNA stability. In: BMC bioinformatics, 6 (1). pp. 1-10.
Bansal, Manju (2003) DNA structure: Revisiting the Watson–Crick double helix. In: Current Science, 85 (11). pp. 1556-1563.
Madhumalar, A and Bansal, Manju (2003) Structural Insights into the Effect of Hydration and Ions on A-Tract DNA: A Molecular Dynamics Study. In: The Biophysical Journal, 85 (3). pp. 1805-1816.
Kanhere, Aditi and Bansal, Manju (2003) An assessment of three dinucleotide parameters to predict DNA curvature by quantitative comparison with experimental data. In: Nucleic Acids Research, 31 (10). pp. 2647-2658.
Paul, Bindu D and Kanhere, Aditi and Chakraborty, Atanu and Bansal, Manju and Nagaraja, Valakunja (2003) Identification of the Domains for DNA Binding and Transactivation Function of C Protein from Bacteriophage Mu. In: Proteins: Structure, Function, and Genetics, 52 (2). pp. 272-282.
Chowdhury, Shibasish and Bansal, Manju (2001) Modelling studies on neurodegenerative disease causing triplet repeat sequences d(CGG/GCC) and d(CAG/CTG): Duplexes vs Quadruplexes. In: Journal of Biosciences, 26 (5). pp. 649-665.
Chowdhury, Shibasish and Bansal, Manju (2001) G-quadruplex structure can be stable with only some coordination sites being occupied by cations: A six-nanosecond molecular dynamics study. In: Journal Of Physical Chemistry B, 105 (31). pp. 7572-7578.
Bansal, Manju (2001) The Madras Triple Helix:Origins and Current Status. In: Resonance, 6 . pp. 38-47.
Chowdhury, Shibasish and Bansal, Manju (2000) Effect of coordinated ions on structure and flexibility of parallel G-quadruplexes: A molecular dynamics study. In: Journal of Biomolecular Structure & Dynamics, 18 (1). pp. 11-28.
Chowdhury, Shibasish and Bansal, Manju (2000) Effect of coordinated ions on structure and flexiblity of parallel G-quandruplexes: a molecular dynamics study. In: Journal of Biomolecular Structure & Dynamics, 18 (1). pp. 11-28.
Bansal, Manju and Kumar, Sandeep and Velavan, R (2000) HELANAL: A Program to Characterize Helix Geometry in Proteins. In: Journal of Biomolecular Structure and Dynamics, 17 (5). pp. 811-819.
Bansal, Manju and Sandeep Kumar, * and Velavan, R (2000) HELANAL: A program to characterise helix geometry in proteins,. In: Journal of Biomolecular Structure & Dynamics, 17 (5). pp. 769-932.
Ghosh, Anirban and Bansal, Manju (1999) C-H..O Hydrogen Bonds in Minor Groove of A-tracts in DNA Double Helices. In: Journal of Molecular Biology, 294 (5). pp. 1149-1158.
Ghosh, Anirban and Bansal, Manju (1999) Three-centre C-H...O hydrogen bonds in the DNA minor groove: analysis of oligonucleotide crystal structures. In: Acta Crystallographica Section D-Biological Crystallography, 55 (12). pp. 2005-2012.
Gu, Jiande and Leszczynski, Jerzy and Bansal, Manju (1999) A new insight into the structure and stability of Hoogsteen hydrogen-bonded G-tetrad: an ab initio SCF study. In: Chemical Physics Letters, 311 (3-4). pp. 209-214.
Bansal, Manju (1999) DNA structure: Yet another avatar? In: Current Science, 76 (9). pp. 1178-1181.
Ravi Kiran, M and Bansal, Manju (1998) Molecular dynamics simulations on parallel and antiparallel C.G*G triplexes. In: Journal of Biomolecular Structure & Dynamics, 16 (3). pp. 511-526.
Kumar, Sandeep and Bansal, Manju (1998) Geometrical and Sequence Characteristics of $\alpha$-Helices in Globular Proteins. In: Biophysical Journal, 75 (4). pp. 1935-1944.
Kumar, Sandeep and Bansal, Manju (1996) Structural and Sequence Characteristics of Long alpha Helices in Globular Proteins. In: Biophysical Journal., 71 (03). pp. 1574-1586.
Bansal, Manju and Bhattacharyya, D and Ravi, B (1995) NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures. In: CABIOS / Computer Applications in the Biosciences, 11 (3). pp. 281-287.
Anachi, RB and Bansal, Manju and Easwaran, KRK and Namboodri, K and Gaber, BP (1995) Molecular Modeling Studies on Amphotericin B and its Complex with Phospholipid,. In: Journal of Biomolecular Structure & Dynamics, 12 (5). pp. 957-970.
Mohanty, Debasisa and Bansal, Manju (1994) Conformational Polymorphism in Telomeric Structures: Loop Orientation and Interloop Pairing in d(G4TnG4),. In: Biopolymers, 34 (9). pp. 1187-1211.
Nagaich, Akhilesh K. and Bhattacharyya, Dhanaqjay and Brahmachari, Samir K and Bansal, Manju (1994) CA\TG Sequence at the 5'end of Oligo(A)-tracts Strongly Modulates DNA Curvature. In: Journal of Biological Chemistry , 269 (10). 7824-7833. .
Nagaich, AK and Bhattacharyya, D and Brahmachari, SK and Bansal, Manju (1994) CA/TG sequence at the 5' end of oligo(A)-tracts strongly modulates DNA curvature. In: Journal of Biological Chemistry, 269 (10). pp. 7824-7833.
Mohanty, Debasisa and Bansal, Manju (1994) Conformational Polymorphism in Telomeric Structures: Loop Orientation and Interloop Ppairing in $d(G_4T_nG_4)$. In: Biopolymers, 34 (9). pp. 1187-1211.
Mohanty, D and Bansal, Manju (1993) Conformational Polymorphism in G-tetraplex Structures: Strand Reversal by Base Flipover or Sugar Flipover. In: Nucleic Acids Research, 21 (8). pp. 1767-1774.
Mohanty, Debasisa and Bansal, Manju (1993) Conformational polymorphism in G-tetraplex structures: strand reversal by base flipover or sugar flipover. In: Nucleic Acids Research, 21 (8). pp. 1767-1774.
Balagurumoorthy, P and Brahmachari, Samir K and Mohanty, Debasisa and Bansal, Manju and Sasisekharan, V (1992) Hairpin and parallel quartet structures for telomeric sequences. In: Nucleic Acids Research, 20 (15). pp. 4061-4067.
Heinemann, U and Alings, C and Bansal, Manju (1992) Double helix conformation, groove dimensions and ligand binding potential of a G/C stretch in B-DNA. In: The EMBO Journal, 11 (5). 1931-1939 .
Bhattacharyya, Dhananjay and Bansal, Manju (1992) Groove width and depth of B-DNA structures depend on local variation in slide. In: Journal of Biomolecular Structure & Dynamics, 10 (1). pp. 213-226.
Bhattacharyya, D and Bansal, Manju (1989) A self-consistent formulation for analysis and generation of non-uniform DNA structure. In: Journal of Biomolecular Structure & Dynamics, 6 (4). pp. 635-653.
Bansal, Manju and Pattabiraman, N (1989) Molecular mechanics studies on poly(purine) poly(pyrimidine) sequences in DNA: Polymorphism and local variability. In: Biopolymers, 28 (2). pp. 531-548.
Bhattacharyya, Dhananjay and Bansal, Manju (1988) Why do DNA helical models exhibit wedge rolls? A mathematical rationale. In: Current Science, 57 (21). pp. 1159-1162.
Bhattacharya, D and Bansal, Manju (1988) A general procedure for generation of curved DNA molecules. In: Journal of Biomolecular Structure & Dynamics, 6 (1). pp. 93-104.
Bhattacharyya, Dhananjoy and Bansal, Manju (1987) Energetics of left and right handed models of DNA. In: Journal of Biomolecular Structure & Dynamics, 4 (6). pp. 1027-1040.
Bryan, RK and Bansal, Manju and Folkhard, , W and Nave, C and Marvin , DA (1983) Maximum-entropy calculation of the electron density at 4 A resolution of Pf1 filamentous bacteriophage. In: Proceedings Of The National Academy Of Sciences of the United States of America-Biological Sciences , 80 (15). 4728-4731 .
Ramaswamy, N and Bansal, Manju and Gupta, Goutam and Sasisekharan, V (1983) Structure of D-DNA: 8-fold or 7-fold helix? In: The EMBO Journal, 2 (9). pp. 1557-1560.
Sasisekharan, V and Bansal, Manju and Gupta, Goutam (1981) A need for re-examination of the fibre diffraction data of A-DNA. In: Biochemical and Biophysical Research Communications, 102 (3). pp. 1087-1095.
Sasisekharan, V and Gupta, Goutam and Bansal, Manju (1981) Sequence-dependent molecular conformation of polynucleotides: right and left-handed helices. In: International Journal of Biological Macromolecules, 3 (1). pp. 2-8.
Bansal, Manju and Gupta, Goutam (1981) Structure factor calculations of various DNA duplexes. In: International Journal of Quantum Chemistry, 20 (2). pp. 407-417.
Gupta, Goutam and Bansal, Manju and Sasisekharan, V (1980) Polymorphism and conformational flexibility of DNA: right and left handed duplexes. In: International Journal of Biological Macromolecules, 2 (6). pp. 368-380.
Gupta, Goutam and Bansal, Manju and Sasisekharan, V (1980) Reversal of handedness in DNA: A stable link between RU and LZ helices. In: Biochemical and Biophysical Research Communications, 97 (4). pp. 1258-1267.
Gupta, Goutam and Bansal, Manju and Sasisekharan, V (1980) A novel Z-structure for poly d(GC).poly d(GC). In: Biochemical and Biophysical Research Communications, 95 (2). pp. 728-733.
Bansal, Manju and Brahmachari, Samir K and Sasisekharan, V (1979) Structural Investigations on Poly(4-hydroxy-L-proline). 1. Theoretical Studies. In: Macromolecules, 12 (1). pp. 19-23.
Brahmachari, Samir K and Bansal, Manju and Ananthanarayanan, VS and Sasisekharan , V (1979) Structural Investigations on Poly(4-hydroxy-L-proline). 2. Physicochemical Studies. In: Macromolecules, 12 (1). pp. 23-28.
Gupta, Asmita and Bansal, Manju (2015) Molecular basis for nucleocytoplasmic transport of tRNA by Exportin-t. In: JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33 (1). pp. 59-60.
Amaro, Rommie E and Bansal, Manju (2014) Theory and simulation: Tools for solving the insolvable. In: CURRENT OPINION IN STRUCTURAL BIOLOGY, 25 . IV-V.
Bansal, Manju and Jayaram, B and Mittal, Aditya (2012) Nucleic acids in disease and disorder: Understanding the language of life emerging from the `ABC' of DNA. In: JOURNAL OF BIOSCIENCES, 37 (3). pp. 375-378.
Jena, Nihar Ranjan and Bansal, Manju (2011) How does AGT detect and repair O6-methyguanine-DNA damage. In: American Chemical Society, National Meeting, 242 .
Marathe, Arvind and Bansal, Manju (2011) Intrinsic structural variability of DNA allows multiple genomic encoding for nucleosomes Comment on ``Cracking the chromatin code: Precise rule of nucleosome positioning'' by EN Trifonov. In: Physics of Life Reviews, 8 (1). pp. 67-68.
Majumder, K and Mishra, RK and Bansal, Manju and Brahmachari, SK (1989) Sequence criteria for Z-DNA formation: studies on poly d(ACGT). In: Nucleic Acids Research, 17 (1). p. 450.
Dickerson, RE and Bansal, Manju (1989) Definitions and nomenclature of nucleic acid structure parameters. In: EMBO Journal, 8 (1). pp. 1-4.
