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Sharma, A and Chandrashekar, CR and Krishna, S and Sowdhamini, R (2024) Computational Analysis of the Accumulation of Mutations in Therapeutically Important RNA Viral Proteins During Pandemics with Special Emphasis on SARS-CoV-2. In: Journal of Molecular Biology, 436 (19).
Panda, S and Anandan, A and Shafi, KM and Naika, MBN and Sowdhamini, R and Vanishree, G and Sarkar, S and Travis, AJ and Norton, GJ and Price, AH (2024) Genome-wide association study reveals effect of nsSNPs on candidate genes in rice during iron deficiency. In: Functional & integrative genomics, 24 (6). p. 198.
Subhadarshini, S and Tandon, H and Srinivasan, N and Sowdhamini, R (2024) Normal Mode Analysis Elicits Conformational Shifts in Proteins at Both Proximal and Distal Regions to the Phosphosite Stemming from Single-Site Phosphorylation. In: ACS Omega .
Sidhanta, SPD and Sowdhamini, R and Srinivasan, N (2023) Comparative analysis of permanent and transient domain–domain interactions in multi-domain proteins. In: Proteins: Structure, Function and Bioinformatics .
Chauhan, PK and Sowdhamini, R (2023) Transcriptome data analysis of primary cardiomyopathies reveals perturbations in arachidonic acid metabolism. In: Frontiers in Cardiovascular Medicine, 10 .
Meenakshi S, I and Rao, M and Mayor, S and Sowdhamini, R (2023) A census of actin-associated proteins in humans. In: Frontiers in Cell and Developmental Biology, 11 .
Chauhan, PK and Sowdhamini, R (2023) Computational analysis of the flexibility in the disordered linker region connecting LIM domains in cysteine–glycine-rich protein. In: Frontiers in Genetics, 14 .
Parvathy, J and Yazhini, A and Srinivasan, N and Sowdhamini, R (2023) Interfacial residues in protein�protein complexes are in the eyes of the beholder. In: Proteins: Structure, Function and Bioinformatics .
Prabantu, VM and Tandon, H and Sandhya, S and Sowdhamini, R and Srinivasan, N (2023) The alteration of structural network upon transient association between proteins studied using graph theory. In: Proteins: Structure, Function and Bioinformatics .
Shafi, KM and Sowdhamini, R (2022) Computational analysis of potential candidate genes involved in the cold stress response of ten Rosaceae members. In: BMC Genomics, 23 (1).
Chauhan, PK and Sowdhamini, R (2022) Integrative network analysis interweaves the missing links in cardiomyopathy diseasome. In: Scientific Reports, 12 (1).
Bheemireddy, S and Sandhya, S and Srinivasan, N and Sowdhamini, R (2022) Computational tools to study RNA-protein complexes. In: Frontiers in Molecular Biosciences, 9 .
Kalmankar, NV and Gehi, BR and Sowdhamini, R (2022) Effects of a plant cyclotide on conformational dynamics and destabilization of β-amyloid fibrils through molecular dynamics simulations. In: Frontiers in Molecular Biosciences, 9 .
Naveenkumar, N and Prabantu, VM and Vishwanath, S and Sowdhamini, R and Srinivasan, N (2022) Structures of distantly related interacting protein homologs are less divergent than non-interacting homologs. In: FEBS Open Bio .
Kalmankar, NV and Pavalam, M and Indrakumar, S and Srinivasan, N and Sowdhamini, R (2022) DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins. In: Database : the journal of biological databases and curation, 2022 .
Rebehmed, J and de Brevern, AG and Sowdhamini, R and Joseph, AP (2022) Editorial: Advances in Molecular Docking and Structure-Based Modelling. In: Frontiers in Molecular Biosciences, 9 .
Sankaradoss, A and Jagtap, S and Nazir, J and Moula, SE and Modak, A and Fialho, J and Iyer, M and Shastri, JS and Dias, M and Gadepalli, R and Aggarwal, A and Vedpathak, M and Agrawal, S and Pandit, A and Nisheetha, A and Kumar, A and Bordoloi, M and Shafi, M and Shelar, B and Balachandra, SS and Damodar, T and Masika, MM and Mwaura, P and Anzala, O and Muthumani, K and Sowdhamini, R and Medigeshi, GR and Roy, R and Pattabiraman, C and Krishna, S and Sreekumar, E (2022) Immune profile and responses of a novel dengue DNA vaccine encoding an EDIII-NS1 consensus design based on Indo-African sequences. In: Molecular Therapy .
Harini, K and Jayashree, S and Tiwari, V and Vishwanath, S and Sowdhamini, R (2021) Ligand Docking Methods to Recognize Allosteric Inhibitors for G-Protein-Coupled Receptors. In: Bioinformatics and Biology Insights, 15 .
Kalmankar, NV and Venkatesan, R and Balaram, P and Sowdhamini, R (2020) Transcriptomic profiling of the medicinal plant Clitoria ternatea: identification of potential genes in cyclotide biosynthesis. In: Scientific Reports, 10 (1).
Lakshmi, B and Ramakrishnan, C and Archunan, G and Sowdhamini, R and Srinivasan, N (2014) Investigations of Ramachandran disallowed conformations in protein domain families. In: INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES, 63 . pp. 119-125.
Sandhya, S and Mudgal, R and Jayadev, C and Abhinandan, KR and Sowdhamini, R and Srinivasan, N (2012) Cascaded walks in protein sequence space: use of artificial sequences in remote homology detection between natural proteins. In: MOLECULAR BIOSYSTEMS, 8 (8). pp. 2076-2084.
Madan, Lalima L and Veeranna, S and Shameer, Khader and Reddy, Chilamakuri CS and Sowdhamini, R and Gopal, B (2011) Modulation of Catalytic Activity in Multi-Domain Protein Tyrosine Phosphatases. In: PLos One, 6 (9).
Rajkumar, R and Prakash, S and Archunan, G and Sowdhamini, R (2010) Primary Structural Documentation of the Major Urinary Protein of the Indian Commensal Rat (Rattus rattus) Using a Proteomics Platform. In: Protein and Peptide Letters, 17 (4). pp. 449-457.
Thangudu, Ratna R and Manoharan, Malini and Srinivasan, N and Cadet, Frederic and Sowdhamini, R and Offmann, Bernard (2008) Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families. In: BMC Structural Biology, 8 .
Srinivasan, N and Sowdhamini, R and Bhattacharya, Alok (2007) Computational biology: More than just a set of techniques. In: Journal of Biosciences, 32 (1). pp. 1-2.
Gadkari, Rupali A and Sandhya, S and Sowdhamini, R and Dighe, Rajan R (2007) The antigen binding sites of various hCG monoclonal antibodies show homology to different domains of LH receptor. In: Molecular and Cellular Endocrinology, 260-26 . pp. 23-32.
Bhadra, R and Sandhya, S and Abhinandan, KR and Chakrabarti, Sandip and Sowdhamini, R and Srinivasan, N (2006) Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains. In: Nucleic Acids Research, 34 (Sp. Is). W143-W146.
Pugalenthi, G and Shameer, K and Srinivasan, N and Sowdhamini, R (2006) HARMONY: a server for the assessment of protein structures. In: Nucleic Acids Research, 34 (Sp. Is). W231-W234.
Pugalenthi, G and Shameer, K and Srinivasan, N and Sowdhamini, R (2006) HARMONY: a server for the assessment of protein structures. In: Nucleic Acids Research, 34 . W231-W234.
Sandhya, S and Chakrabarti, S and Abhinandan, KR and Sowdhamini, R and Srinivasan, N (2005) Assessment of a rigorous transitive profile based search method to detect remotely similar proteins. In: Journal of Biomolecular Structure & Dynamics, 23 (3). pp. 283-298.
Sandhya, S and Kishore, S and Sowdhamini, R and Srinivasan, N (2003) Effective detection of remote homologues by searching in sequence dataset of a protein domain fold. In: FEBS Letters, 552 (2-3). pp. 225-230.
Pandit, Shashi B and Gosar, Dilip and Abhiman, Saraswathi and Sujatha, S and Dixit, Sayali S and Mhatre, Natasha S and Sowdhamini, R and Srinivasan, N (2002) SUPFAM—a database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: implications for structural genomics and function annotation in genomes. In: Nucleic Acids Research, 30 (1). pp. 289-293.
Natraj, DV and Srinivasan, N and Sowdhamini, R and Ramakrishnan, C (1995) Alpha-Turns In Protein Structures. In: Current Science, 69 (5). pp. 434-447.
Srinivasan, N and Anuradha, VS and Ramakrishnan, C and Sowdhamini, R and Balaram, P (1994) Conformational characteristics of asparaginyl residues in proteins. In: International Journal of Peptide & Protein Research, 24 (2). pp. 112-122.
Sowdhamini, R and Ramakrishnan, C and Balaram, P (1993) Modelling multiple disulphide loop containing polypeptides by random conformation generation. The test cases of α-conotoxin GI and edothelin I. In: Protein Engineering, 6 (8). pp. 873-882.
Nagarajaram, HA and Sowdhamini, R and Ramakrishnan, C and Balaram, P (1993) Termination of right handed helices in proteins by residues in left handed helical conformations. In: FEBS Letters, 321 (1). pp. 79-83.
Sowdhamini, R and Srinivasan, N and Ramakrishnan, C and Balaram, P (1992) Orthogonal beta-beta motifs in proteins. In: Journal of Molecular Biology, 223 (4). pp. 845-851.
Srinivasan, N and Sowdhamini, R and Ramakrishnan, C and Balaram, P (1990) Conformations of disulfide bridges in proteins. In: International Journal of Peptide and Protein Research, 36 (2). pp. 147-155.
Sowdhamini, R and Srinivasan, N and Shoichet, Brian and Santi, Daniel V and Ramakrishnan, C and Balaram, P (1989) Stereochemical modeling of disulfide bridges. Criteria for introduction into proteins by site-directed mutagenesis. In: Protein Engineering, 3 (2). pp. 95-103.
Srinivasan, N and Mudgal, R and Kumar, G and Chandra, NR and Sowdhamini, R and Sandhya, S (2015) Bridging the islands of protein families in sequence space using artificial sequences. In: JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33 (1). pp. 103-104.
