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Bansia, H and Ramakumar, S (2023) Homology Modeling of Antibody Variable Regions: Methods and Applications. [Book Chapter]
Bagaria, A and Ramakumar, S (2020) Peptide Nanotubes: A Crystallographic Approach. [Book Chapter]
Bansia, H and Mahanta, P and Yennawar, NH and Ramakumar, S (2021) Small Glycols Discover Cryptic Pockets on Proteins for Fragment-Based Approaches. In: Journal of Chemical Information and Modeling .
Dey, D and Ramakumar, S and Conn, GL (2021) Targeted Redesign of Suramin Analogs for Novel Antimicrobial Lead Development. In: Journal of Chemical Information and Modeling, 61 (9). pp. 4442-4454.
Dey, D and Ramakumar, S and Conn, GL (2021) Targeted Redesign of Suramin Analogs for Novel Antimicrobial Lead Development. In: Journal of Chemical Information and Modeling .
Biswas, T and Misra, A and Das, S and Yadav, P and Ramakumar, S and Roy, RP (2020) Interrogation of 3D-swapped structure and functional attributes of quintessential Sortase A from Streptococcus pneumoniae. In: Biochemical Journal, 477 (24). pp. 4711-4728.
Manikandan, K and Jagtap, S and Rao, M and Ramakumar, S (2006) Crystallization and preliminary X-ray characterization of a thermostable low-molecularweight 1,4-$\beta$-D-glucan glucohydrolase from an alkalothermophilic Thermomonospora sp. In: Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 62 (4). pp. 385-357.
Padyana, Anil K and Ramakumar, S (2006) Lateral energy transfer model for adjacent light-harvesting antennae rods of C-phycocyanins. In: Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1757 (3). pp. 161-165.
Manikandan, K and Bhardwaj, Amit and Ghosh, Amit and Reddy, VS and Ramakumar, S (2005) Crystallization and preliminary X-ray study of a family 10 alkali-thermostable xylanase from alkalophilic Bacillus sp. strain NG-27. In: Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 61 (Part 8). pp. 747-749.
Manikandan, K and Bhardwaj, Amit and Ghosh, Amit and Reddy, VS and Ramakumar, S (2005) Crystallization and preliminary X-ray study of a family 10 alkali-thermostable xylanase from alkalophilic Bacillus sp. strain NG-27. In: Acta Crystallographica F: Structural Biology and Crystallization Communications, 61 (8). pp. 747-749.
Bagaria, A and Ramakumar, S and Gupta, M and Chauhan, VS (2005) Cyclo(L-leucyl-$\alpha$,$\beta$-dehydrophenylalanine): the first diketopiperazine containing an $\alpha$,$\beta$-dehydrophenylalanine residue. In: Acta crystallographica. Section C, Crystal structure communications, 61 (3). pp. 174-176.
Manikandan, K and Ramakumar, S (2004) The occurrence of C-H...O hydrogen bonds in alpha-helices and helix termini in globular proteins. In: Proteins: Structure, Function, and Genetics, 56 (4). pp. 768-781.
Fernando, SA and Selvarani, P and Das, Soma and Kumar, Kiran Ch and Mondal, Sukanta and Ramakumar, S and Sekar, K (2004) THGS:a web-based database of Transmembrane Helices in Genome Sequences. In: Nucleic Acids Research, 32 . D125-D128.
Mathur, Puniti and Ramakumar, S and Chauhan, VS (2004) Peptide Design Using \alpha , \beta - Dehydro Amino Acids: From \beta -Turns to Helical Hairpins. In: Peptide Science, 76 (2). pp. 150-161.
Mondal, Sukanta and Jaishankar, SP and Ramakumar, S (2003) Role of context in the relationship between form and function: structural plasticity of some PROSITE patterns. In: Biochemical and Biophysical Research Communications, 305 (4). pp. 1078-1084.
Natesh, R and Manikandan, K and Bhanumoorthy, P and Viswamitra, MA and Ramakumar, S (2003) Thermostable xylanase from Thermoascus aurantiacus at ultrahigh resolution (0.89 Å) at 100 K and atomic resolution (1.11 Å) at 293 K refined anisotropically to small-molecule accuracy. In: Acta Crystallographica Section D: Biological Crystallography, 59 (Part 1). pp. 105-117.
Padyana, Anil K and Ramakumar, S and Mathur, Puniti and Jagannathan, NR and Chauhan, VS (2003) Role of a two-residue spacer in an \alpha, \beta -didehydrophenylalanine containing hexapeptide: crystal and solution structure of Boc-Val- \bigtriangleup Phe-Leu-Ala- \bigtriangleup Phe-Ala-OMe. In: Journal of Peptide Science, 9 (1). pp. 54-63.
Kant, Shashi and Bagaria, Ashima and Ramakumar, S (2002) Putative homeodomain proteins identified in prokaryotes based on pattern and sequence similarity. In: Biochemical and Biophysical Research Communications, 299 (2). pp. 229-232.
Rudresh, * and Jain, Rinku and Dani, Vardhan and Mitra, Ashima and Srivastava, Sarika and Sarma, Siddhartha P and Varadarajan, R and Ramakumar, S (2002) Structural consequences of replacement of an \alpha-helical Pro residue in Escherichia coli thioredoxin. In: Protein Engineering, 15 (8). pp. 627-633.
Padyana, Anil K and Bhat, Vadiraja B and Madyastha, KM and Rajashankar, KR and Ramakumar, S (2001) Crystal Structure of a Light-Harvesting Protein C-Phycocyanin from Spirulina platensis. In: Biochemical and Biophysical Research Communications, 282 (4). pp. 893-898.
Jain, Rinku and Ramakumar, S (1999) Stochastic dynamics modeling of the protein sequence length distribution in genomes: implications for microbial evolution. In: Physica A: Statistical Mechanics and its Applications, 273 (3-4). pp. 476-485.
Natesh, R and Bhanumoorthy, P and Vithayathil, PJ and Sekar, K and Ramakumar, S and Viswamitra, MA (1999) Crystal structure at $1.8 \AA$ resolution and proposed amino acid sequence of a thermostable xylanase from Thermoascus aurantiacus. In: Journal of Molecular Biology, 288 (5). pp. 999-1012.
Ramagopal, UA and Ramakumar, S and Joshi, R and Chauhan, VS (1998) Crystal structure of Boc-LAla-Delta Phe-Delta Phe-Delta Phe-Delta Phe-NHMe: a left-handed helical peptide. In: Journal of Peptide Research, 52 (3). pp. 208-215.
Rajashankar, KR and Ramakumar, S and Jain, RM and Chauhan, VS (1997) Role of two consecutive alpha,beta-dehydrophenylalanines in peptide structure: Crystal and molecular structure of Boc-Leu-Delta Phe-Delta Phe-Ala-Phe-NHMe. In: Biopolymers, 42 (3). pp. 373-382.
Eswaran, SV and Neela, HY and Ramakumar, S and Viswamitra, MA (1996) The unusual formation of methyl alpha-(5,6-dimethoxycarbonyl-2,3-dimethoxyazepin-7-ylidene)-alpha-[5-methoxycarbonyl-2,3-dimethoxypyrid-6-yl)acetate during the pyrolysis of ''azido-meta-hemipinate'' - First example of a reaction involving a concomitant ring expansion and ring extrusion. In: Journal of Heterocyclic Chemistry, 33 (4). 1333-1337 .
Rajashankar, KR and Ramakumar, S (1996) Pi-turns in proteins and peptides: Classification, conformation, occurrence, hydration and sequence. In: Protein Science, 5 (5). pp. 932-946.
Rajashankar , KR and Ramakumar, S and Jain, RM and Chauhan, VS (1996) Helix termination and chain reversal: Crystal and molecular structure of the alpha,beta-dehydrooctapeptide Boc-Val Delta Phe-Phe-Ala-Leu-Ala-Delta Phe-Leu-OH. In: Journal of Biomolecular Structure & Dynamics, 13 (4). 641-647 .
Rajashankar, KR and Chauhan, VS and Ramakumar, S (1995) Crystal and molecular structure of Boc-Phe-Val-OMe; comparison of the peptide conformation with its dehydro analogue. In: International Journal of Peptide & Protein Research, 46 (6). pp. 487-493.
Rajashankar, KR and Ramakumar, S and Jain, RM and Chauhan, VS (1995) Observation of Water-Mediated Helix-Terminating Conformation in a Dehydrophenylalanine Peptide: Crystal and Solution Structure of the Octapeptide Ac-.DELTA.Phe-Val-.DELTA.Phe-Phe-Ala-Val-.DELTA.Phe-Gly-OMe. In: Journal of the American Chemical Society, 117 (47). pp. 11773-11779.
Rajashankar, KR and Ramakumar, S and Mal, TK and Jain, RM and Chauhan, VS (1995) Synthesis, and Crystal and Molecular Structure of the $ 3_{10}-Helical \aplha,\beta $-dehydro pentapeptide Boc-Leu-Phe-Ala- \bigtriangleup Phe-Leu-Ome. In: Biopolymers, 35 (2). pp. 141-147.
Rao, Rama AV and Reddy, Ashok K and Srinivas, NR and Gurjar, MK and Padmaja, N and Ramakumar, S and Viswamitra, MA and Swapna, GVT and Jagannadh, B and Kunwar, AC (1993) Chiral polyhydroxylated tetrahydrothiophene derivatives: novel synthesis and structural elucidation by X-ray crystallography, NMR spectroscopy and molecular mechanics calculations. In: Perkin Transactions 1 (11). pp. 1255-1259.
Mande, Sharmila S and Lalitha, HN and Viswamitra, MA and Ramakumar, S (1992) Influence of acetyl and bromine substitutions on stacking. Crystal and molecular structures of 8-bromo-2',3',5'-triacetyl adenosine and 8-bromo 2',3',5'-triacetyl guanosine. In: Nucleosides & Nucleotides, 11 (5). pp. 1089-1101.
Padmaja, N and Ramakumar, S and Viswamitra, MA (1991) Structure of 5-methylcytidine. In: Acta Crystallographica Section C, 47 . pp. 1445-1448.
Padmaja, N and Ramakumar, S and Viswamitra, MA (1990) Space-group frequencies of proteins and of organic compounds with more than one formula unit in the asymmetric unit. In: Acta Crystallographica Section A, 46 (9). pp. 725-730.
Neela, BS and Manjula, MV and Ramakumar, S and Balasubramanian, D and Viswamitra, MA (1990) Conformation of cyclolinopeptide dihydrate: An antamanide analogue. In: Biopolymers, 29 (10-11). pp. 1499-1501.
Swaminathan, K and Sinha, UC and Ramakumar, S and Bhatt, RK and Sabata, BK (1989) Structure of columbin, a diterpenoid furanolactone from Tinospora cordifolia Miers. In: Acta Crystallographica Section C, 45 . 300 -303.
Padmaja, N and Ramakumar, S and Viswamitra, MA (1988) Structure of Puromycin Aminonucleoside. In: Acta Crystallographica, Section C: Crystal Structure Communications, C44 (12). pp. 2176-2178.
Begum, Sameena A and Jain, VK and Ramakumar, S and Khetrapal, CL (1988) A plausible mechanism of thermal decomposition of oxalohydroxamic acid and formation of novel products. In: Journal of Solid State Chemistry, 75 (2). pp. 432-434.
Begum, Sameena A and Jain, VK and Ramakumar, S and Khetrapal, CL (1988) The structure of ammonium oxalohydroxamate - a monopropellant. In: Acta Crystallographica Section C, 44 . pp. 1047-1049.
Padmaja, N and Ramakumar, S and Viswamitra, MA (1987) Reinvestigation of the structure of 2-hydroxyquinoxaline. In: Acta Crystallographica Section C, C43 (11). pp. 2239-2240.
Padmaja, N and Ramakumar, S and Viswamitra, MA (1987) Structure of 5-methylcytosine hydrochloride. In: Acta Crystallographica, Section C: Crystal Structure Communications, C43 (11). 2157-2160.
Suguna, K and Ramakumar, S and Nagaraj, R and Balaram, P (1985) Structure of cyclo(\alpha- Aminoisobutyryl-L-phenylalanyl-), $C_{13}H_{16}N_2O_2$. In: Acta Crystallographica Section C: Crystal Structure Communications, 41 (2). pp. 284-286.
Suguna, K and Ramakumar, S and Nagaraj, R and Balaram, P (1985) Structure Of Cyclo(-Alpha-Aminoisobutyryl-L-Phenylalanyl-), C13h16n2o2. In: ACTA Crystallographica Section C-Crystal Structure Communications, 41 (Feb). pp. 284-286.
Suguna, K and Ramakumar, S and Kopple, KD (1984) Structure of cyclo(-L-leucyl-L-tyrosyl-) monohydrate, $C_{15}H_{20}N_2O_3.H_2O$. In: Acta Crystallographica - C, 40 (12). pp. 2053-2056.
Suguna, K and Ramakumar, S and Kopple, KD (1984) Structure Of Cyclo(-L-Leucyl-L-Tyrosyl-) Monohydrate, C15h20n2o3.H2o. In: Acta Crystallographica Section C, 40 (Dec). pp. 2053-2056.
Suguna, K and Ramakumar, S and Shamala, N and Prasad, Venkataram BV and Balaram, P (1982) Crystal Structures of Diketopiperazines Containing \alpha-Aminoisobutyric Acid: Cyclo(Aib-Aib) and Cyclo(Aib-L-Ile). In: Biopolymers, 21 (9). pp. 1847-1855.
Suguna, K and Ramakumar, S and Rajappa, S (1982) Structure of (6S,13bR)-1,2,3,5,6,13b-hexahydro-6-isopropyl-8H-pyrrolo[1',2':1,2]pyrazino[3,4,-b]quinazoline-5,8-dione. In: Acta Crystallographica Section B: Structural Crystallography and Crystal Chemistry, 38 (8). pp. 2304-2306.
Suguna, K and Ramakumar, S and Rajappa, S (1982) Structure of (4S)-2,4-dimethyl-1,2-dihydropyrazino[2,1-b]quinazoline-3(4H),6-dione. In: Acta Crystallographica Section B: Structural Crystallography and Crystal Chemistry, 38 (5). pp. 1654-1656.
Suguna, K and Ramakumar, S and Rajappa, S (1982) Structure of (4S)-2,4-dimethyl-1,2-dihydropyrazino[2,1-b]quinazoline-3(4H),6-dione. In: Acta Crystallographica Section B, 38 (5). pp. 1654-1656.
Suguna, K and Ramakumar, S and Rajappa, Srinivasachari (1982) Structure of (6S,13bR)-1,2,3,5,6,13b-hexahydro-6-isopropyl-8H-pyrrolo[1',2':1,2]pyrazino[3,4,-b]quinazoline-5,8-dione. In: Acta Crystallographica Section B, 38 (8). pp. 2304-2306.
Blaha , K and Malon , P and Tichy , M and Fric , I and Usha , R and Ramakumar , S and Venkatesan , K (1978) Crystal- structure and chiroptical properties of (+)-(3S)-4-Azatrtcyclo[4,3,1,03,7]Decan-5-One. In: Collection of Czechoslovak Chemical Communications, 43 (12). 3241-3251 .
Ramakumar, S and Venkatesan, K and Shamala, Narayanaswamy (1973) Determination Of Crystal And Molecular-Structure Of L-Serine Using Rotation And Translation Functions. In: Indian Journal of Pure & Applied Physics, 11 (7). pp. 461-464.
Hegde, Raghurama P and Pavithra, Gowribidanur C and Dey, Debayan and Almo, Steven C and Ramakumar, S and Ramagopal, Udupi A (2017) Can the propensity of protein crystallization be increased by using systematic screening with metals? In: PROTEIN SCIENCE, 26 (9). pp. 1704-1713.
Khare, H and Ramakumar, S (2015) Edge strands and indents of beta-sheets: A comparative analysis of sequence and structural features. In: FEBS JOURNAL, 282 (1, SI). p. 346.
Viswamitra, MA and Bhanumoorthy, P and Ramakumar, S and Manjula, MV and Vithayathil, PJ and Murthy, SK and Naren, AP (1993) Crystallization and Preliminary X-ray Diffraction Analysis of Crystals of Thermoascus aurantiacus Xylanase. In: Journal of Molecular Biology, 232 (3). pp. 987-988.
Rajashankar , KR and Ramakumar, S and Chauhan, VS (1992) Design of a helical motif using .alpha.,.beta.-dehydrophenylalanine residues: crystal structure of Boc-Val-.DELTA.Phe-Phe-Ala-Phe-.DELTA.Phe-Val-.DELTA.PHe-Gly-OCH3, a 310-helical nonapeptide. In: Journal of the American Chemical Society, 114 (23). pp. 9225-9226.
Lalitha, HN and Ramakumar, S and Viswamitra, MA (1989) Structure of 5-methyl-2'-deoxycytidine 5'-monophosphate dihydrate. In: Acta Crystallographica Section C, 45 (Part 1). pp. 1652-1655.
Begum, Sameena A and Jain, VK and Ramakumar, S and Khetrapal, CL (1988) Structure of 1,2,4-oxadiazolidine-3,5-dione monohydrate. In: Acta Crystallographica Section C, 44 . pp. 195-196.
