Bioinformatics and Biomolecular Simulation Laboratory

BSBE, IIT-Kanpur

• P. Singh, V. Ramanathan and R. Sankararamakrishnan*.
  Self-contacting Cys, Ser and Thr residues in high-resolution protein crystal structures: Tertiary constraints or hydrogen bonds?
  Protein Science 33, Art. No. e5218 (2024). [Abstract]
  

• R. Muthukumaran* and R. Sankararamakrishnan*.
  Differences in the membrane-binding properties of flaviviral nonstructural 1 (NS1) protein: Comparative simulations of zika and dengue virus NS1 proteins in explicit bilayers
  ACS Bio & Med Chem Au 4, 137-153 (2024). [Abstract] [FULL TEXT]
  

• I. Avasthi, R. Muthukumaran, R. K. Prajapati, R. Sankararamakrishnan* and S. Verma*.
  Crystal patterns of N9/N7 substituted purine-CdII/HgII frameworks and self-assembled nanoring formation
  Chemistry - An Asian Journal 19, Art. No. e202301119 (2024). [Abstract]
  Also appears in Hot Topic: Crystal Engineering

• A. Gupta and R. Sankararamakrishnan*.
  Substrate selectivity and unique sequence signatures in SWEET/semiSWEET homologs of four taxonomic groups: Sequence analysis and phylogenetic studies
  Proteins: Structure, Function, and Bioinformatics (2024) In press. [Abstract]
  

• R. Dande and R. Sankararamakrishnan*.
  dbAQP-SNP: A database of missense single nucleotide polymorphisms in human aquaporins
  Database: The Journal of Biological Databases and Curation. 2023. Art. ID: baad012 (2023). [Abstract] [FULL TEXT]
  

• C. N. Reddy and R. Sankararamakrishnan*.
  Molecular dynamics studies of CED-4/CED-9/EGL-1 ternary complex reveal CED-4 release mechanism in the linear apoptotic pathway of Caenorhabditis elegans
  Proteins: Structure, Function, and Bioinformatics 91, 679-693 (2023). [Abstract]
  

• C. N. Reddy and R. Sankararamakrishnan*.
  Designing BH3-mimetic peptide inhibitors for the viral Bcl-2 homologs A179L and BHRF1: Importance of long-range electrostatic interactions
  ACS Omega 6, 26976-26989 (2021). [Abstract]
  

• C. N. Reddy, N. Manzar, B. Ateeq and R. Sankararamakrishnan*.
  Computational design of BH3-mimetic peptide inhibitors that can bind specifically to Mcl-1 or Bcl-X_L: Role of non-hot spot residues.
  Biochemistry 59, 4379-4394 (2020). [Abstract]
  

• M. Mukherjee^#, A. Gupta^# and R. Sankararamakrishnan*.
  Is the E. coli homolog of the formate/nitrite transporter family an anion channel? A computational study.
  Biophysical Journal 118, 846-860 (2020). (^#Equal Contribution). Cover Illustration [Abstract]
  
  A blog for the cover image can be found here

• A. Jain^#, R. K. Verma^# and R. Sankararamakrishnan*.
  Presence of intra-helical salt-bridge in loop E half-helix can influence the transport properties of AQP1 and GlpF channels: Molecular dynamics simulations of in silico mutants.
  Journal of Membrane Biology 252, 17-29 (2019). (^#Equal Contribution). [Abstract]

• M. Vajpai^#, M. Mukherjee^# and R. Sankararamakrishnan*.
  Cooperativity in plant plasma membrane intrinsic proteins (PIPs): Mechanism of increased water transport in maize PIP1 channels in hetero-tetramers.
  Scientific Reports 8, Art. No. 12055 (2018). (^#Equal Contribution). [Abstract] [FULL TEXT]

• A. Gupta and R. Sankararamakrishnan*.
  dbSWEET: An Integrated resource for SWEET superfamily to understand, analyze and predict the function of sugar transporters in prokaryotes and eukaryotes.
  Journal of Molecular Biology 430, 2203-2211 (2018). [Abstract]

• A. H. Iyer^#, R. N. V. Krishna Deepak^# and R. Sankararamakrishnan*.
  Imidazole nitrogens of two histidine residues participating in N-H...N hydrogen bonds in protein structures: Structural bioinformatics approach combined with quantum chemical calculations
  Journal of Physical Chemistry B 122, 1205-1212 (2018). (^#Equal Contribution). [Abstract]

• M. Mukherjee, M. Vajpai and R. Sankararamakrishnan*.
  Anion-selective formate/nitrite transporters: Taxonomic distribution, phylogenetic analysis and subfamily-specific conservation pattern in prokaryotes
  BMC Genomics 18, Art. No. 560 (2017) [Abstract] [FULL TEXT]

• R. N. V. Krishna Deepak^#, B. Chandrakar^# and R. Sankararamakrishnan*.
  Comparison of metal-binding strength between methionine and cysteine residues: Implications for the design of metal-binding motifs in proteins.
  Biophysical Chemistry. 224, 32-39 (2017) (^#Equal contribution). [Abstract]

• V. Modi and R. Sankararamakrishnan*.
  Binding affinity of pro-apoptotic BH3 peptides for the anti-apoptotic Mcl-1 and A1 proteins: Molecular dynamics simulations of Mcl-1 and A1 in complex with six different BH3 peptides.
  Journal of Molecular Graphics and Modelling. 73, 115-128 (2017). [Abstract]

• R. N. V. Krishna Deepak and R. Sankararamakrishnan*.
  N-H...N hydrogen bonds involving histidine imidazole nitrogen atoms: A new structural role for histidine residues in proteins.
  Biochemistry 55, 3774-3783 (2016). [Abstract]

• R. N. V. Krishna Deepak and R. Sankararamakrishnan*.
  Unconventional N-H...N hydrogen bonds involving proline backbone nitrogen in protein structures.
  Biophysical Journal 110, 1967-1979 (2016). [Abstract]

• N. K. Mishra, R. N. V. Krishna Deepak, R. Sankararamakrishnan* and S. Verma*.
  Controlling in vitro insulin amyloidosis with stable peptide conjugates: A combined experimental and computational study.
  Journal of Physical Chemistry B 119, 15395-15406 (2015). [Abstract]

• R. K. Verma, N. D. Prabh and R. Sankararamakrishnan*.
  Intra-helical salt-bridge and helix destabilizing residues within the same helical turn: Role of functionally important loop E half-helix in channel regulation of major intrinsic proteins.
  Biochimica et Biophysia Acta (BBA) - Biomembranes 1848, 1436-1449 (2015). [Abstract]

• R. K. Verma^#, A. B. Gupta^# and R. Sankararamakrishnan*.
  Major intrinsic protein superfamily: Channels with unique structural features and diverse selectivity filters.
  Methods in Enzymology 557, 485-520 (2015) [Abstract] (^#Equal contribution)

• R. K. Verma, N. D. Prabh and R. Sankararamakrishnan*.
  New subfamilies of major intrinsic proteins in fungi suggest novel transport properties in fungal channels: Implications for the host-fungal interactions.
  BMC Evolutionary Biology 14, Art. No. 173 (2014). Highly Accessed [Abstract] [FULL TEXT]

• A. Jain, R. N. V. Krishna Deepak and R. Sankararamakrishnan*.
  Oxygen-aromatic contacts in intra-strand base pairs: Analysis of high-resolution DNA crystal structures and quantum chemical calculations.
  Journal of Structural Biology 187, 49-57 (2014). [Abstract]

• V. Modi and R. Sankararamakrishnan*.
  Anti-apoptotic Bcl-2 homolog CED-9 in Caenorhabditis elegans : Dynamics of BH3 and CED-4 binding regions and comparison with mammalian anti-apoptotic Bcl-2 proteins.
  Proteins: Structure, Function, and Bioinformatics 82, 1035-1047 (2014). [Abstract]

• D. Lama^#, V. Modi^# and R. Sankararamakrishnan*.
  Behavior of solvent-exposed hydrophobic groove in the anti-apoptotic Bcl-X_L protein: Clues for its ability to bind diverse BH3 ligands from MD simulations.
  PLoS One 8, e54397 (2013) [Abstract] [FULL TEXT] (^#Equal contribution)

• V. Modi, D. Lama and R. Sankararamakrishnan*.
  Relationship between helix stability and binding affinities: Molecular dynamics simulations of Bfl-1/A1-binding pro-apoptotic BH3 peptide helices in explicit solvent.
  Journal of Biomolecular Structure & Dynamics 31, 65-77 (2013). [Abstract]

• A. V. Kochetov*, P. D. Prayaga, O. A. Volkova and R. Sankararamakrishnan*.
  Hidden coding potential of eukaryotic genomes: non-AUG started ORFs.
  Journal of Biomolecular Structure & Dynamics 31 103-114 (2013). [Abstract]

• A. B. Gupta, R. K. Verma, V. Agarwal, M. Vajpai, V. Bansal and R. Sankararamakrishnan*.
  MIPModDB: A central resource for the superfamily of major intrinsic proteins.
  Nucleic Acids Research 40, D362-D369 (2012). [Abstract] [FULL TEXT]

• A. Jain and R. Sankararamakrishnan*.
  Dynamics of non-covalent interactions in all-alpha and all-beta class proteins: Implications for the stability of amyloid aggregates.
  Journal of Chemical Information and Modeling 51, 3208-3216 (2011) [Abstract]

• D. Lama and R. Sankararamakrishnan*.
  Molecular dynamics simulations of pro-apoptotic BH3 peptide helices in aqueous medium: Relationship between helix stability and their binding affinities to the anti-apoptotic protein Bcl-X_L.
  Journal of Computer-Aided Molecular Design 25, 413-426 (2011). [Abstract]

• D. Lama and R. Sankararamakrishnan*.
  Identification of core structural residues in sequentially diverse and structurally homologous Bcl-2 family of proteins.
  Biochemistry 49, 2574-2584 (2010). [Abstract]

• T. K. Pal and R. Sankararamakrishnan*.
  Quantum chemical investigations on intra-residue carbonyl-carbonyl contacts in aspartates of high-resolution protein structures.
  Journal of Physical Chemistry B 114, 1038-1049 (2010). [Abstract]

• P. Prakash and R. Sankararamakrishnan*.
  Force field dependence of phospholipid headgroup and acyl Chain properties: Comparative molecular dynamics simulations of DMPC bilayers.
  Journal of Computational Chemistry 31, 266-277 (2010). [Abstract]

• A. B. Gupta and R. Sankararamakrishnan*.
  Genome-wide analysis of major intrinsic proteins in the tree plant Populus trichocarpa: Characterization of XIP subfamily of aquaporins from evolutionary perspective.
  BMC Plant Biology 9, 134 (2009). [Abstract] [FULL TEXT]

• T. S. Ghosh, S. K. Chaitanya and R. Sankararamakrishnan*.
  End-to-end and end-to-middle inter-helical interactions: New classes of interacting helix pairs in protein structures.
  Acta Crystallographica D Biological Crystallography D65, 1032-1041 (2009). [Abstract]

• A. Jain, V. Ramanathan and R. Sankararamakrishnan*.
  Lone pair ... pi interactions between water oxygens and aromatic residues: Quantum chemical studies based on high-resolution protein structures and model compounds.
  Protein Science 18, 595-605 (2009). [Abstract]
  Also appeared in the Virtual Issue: Focus on the Pacific Rim, Issue 4, May 2011.

• D. Lama and R. Sankararamakrishnan*.
  Anti-apoptotic Bcl-X_L protein in complex with BH3 peptides of pro-apoptotic Bak, Bad and Bim proteins: Comparative molecular dynamics simulations.
  Proteins: Structure, Function, and Bioinformatics 73, 492-514 (2008). [Abstract]

• T. K. Pal and R. Sankararamakrishnan*.
  Self-contacts in Asx and Glx residues of high-resolution protein structures: Role of local environment and tertiary interactions.
  Journal of Molecular Graphics and Modelling 27, 20-33 (2008). [Abstract]

• S. Tikole and R. Sankararamakrishnan*.
  Prediction of translation initiation sites in human mRNA sequences with AUG start codon in weak Kozak context: A neural network approach.
  Biochemical and Biophysical Research Communications 369, 1166-1168 (2008). [Abstract]

• A. Jain, C. S. Purohit, S. Verma and R. Sankararamakrishnan*.
  Close contacts between carbonyl oxygen atoms and aromatic centers in protein structures: pi-pi or lone-pair-pi interactions?
  Journal of Physical Chemistry B 111, 8680-8683 (2007). [Abstract]

• P. Prakash and R. Sankararamakrishnan*.
  Molecular dynamics simulations of C-terminal decapeptide of gastrin-releasing peptide in DMPC bilayers: Structure, stability and orientation of the peptide hormone within the bilayers.
  Protein & Peptide Letters 14, 590-596 (2007). [Abstract]

• A. Bansal and R. Sankararamakrishnan*.
  Homology modeling of major intrinsic proteins in rice, maize and Arabidopsis: comparative analysis of transmembrane helix association and aromatic/arginine selectivity filters.
  BMC Structural Biology 7, 27 (2007). Highly Accessed [Abstract] [FULL TEXT]

• S. Tikole and R. Sankararamakrishnan*.
  A survey of mRNA sequences with a non-AUG start codon in RefSeq database.
  Journal of Biomolecular Structure and Dynamics 24, 33-41 (2006). [Abstract]

• R. Sankararamakrishnan*.
  Recognition of GPCRs by peptide ligands and membrane compartments theory: Structural studies of endogenous peptide hormones in membrane environment.
  Bioscience Reports 26, 131-158 (2006). [Abstract]

• K.K. Prasad, C.S. Purohit, A. Jain, R. Sankararamakrishnan and S. Verma.
  Enforcing solution phase nanoscopic aggregation in a palindromic tripeptide.
  Chemical Communications 2564-2566 (2005). [Abstract]

• R. Sankararamakrishnan*, S. Verma and S. Kumar.
  ATCUN-like metal-binding motifs in proteins: Identification and characterization by crystal structure and sequence analysis.
  Proteins: Structure, Function, and Bioinformatics 58, 211-221 (2005). [Abstract]

• R. Sankararamakrishnan* and H. Weinstein*.
  Surface tension parameterization in molecular dynamics simulations of a phospholipid-bilayer membrane: Calibration and effects.
  Journal of Physical Chemistry B 108, 11802 - 11811 (2004).

• R. Sankararamakrishnan and H. Weinstein.
  Positioning and stabilization of dynorphin peptides in membrane bilayers: the mechanistic role of aromatic and basic residues revealed from comparative MD simulations.
  Journal of Physical Chemistry B 106, 209 - 218 (2002).

• R. Sankararamakrishnan and H. Weinstein.
  Molecular dynamics simulations predict a tilted orientation for the helical region of dynorphin A(1-17) in dimyristoylphosphatidylcholine bilayers.
  Biophysical Journal 79, 2331 - 2344 (2000). Cover Illustration [Abstract]

• R. Sankararamakrishnan, K. Konvicka, E.L. Mehler and H. Weinstein.
  Solvation in simulated annealing and high-temperature molecular dynamics of proteins: A restrained water droplet model.
  International Journal of Quantum Chemistry 77, 174-186 (2000).

• C. Singh, R. Sankararamakrishnan, S. Subramaniam and E. Jakobsson.
  Solvation, water permeation, and ionic selectivity of a putative model for the pore region of the voltage-gated sodium channel.
  Biophysical Journal 71, 2276-2288 (1996). [Abstract]

• R. Sankararamakrishnan, C. Adcock and M.S.P. Sansom.
  The pore domain of the nicotinic acetylcholine receptor: Molecular modeling, pore dimensions and electrostatics.
  Biophysical Journal 71, 1659-1671 (1996). [Abstract]

• I.D. Kerr, H.S. Son, R. Sankararamakrishnan and M.S.P. Sansom.
  Molecular dynamics simulations of isolated transmembrane helices of potassium channels.
  Biopolymers 39, 503-515 (1996). [Abstract]

• I.D. Kerr, D.G. Doak, R. Sankararamakrishnan, J. Breed and M.S.P. Sansom.
  Molecular modeling of staphylococcal delta-toxin ion channels by restrained molecular dynamics.
  Protein Engineering 9, 161-171 (1996). [Abstract]

• J. Breed, R. Sankararamakrishnan, I.D. Kerr and M.S.P. Sansom.
  Molecular dynamics simulations of water within models of ion channels.
  Biophysical Journal 70, 1643-1661 (1996). Cover Illustration [Abstract]

• M.S.P. Sansom, I.D. Kerr, J. Breed and R. Sankararamakrishnan.
  Water in channel-like cavities - Structure and dynamics.
  Biophysical Journal 70, 693-702 (1996). [Abstract]

• J. Breed, I.D. Kerr, R. Sankararamakrishnan and M.S.P. Sansom.
  Packing interactions of Aib-containing helices: Molecular modeling of parallel dimers of simple hydrophobic helices and of alamethicin.
  Biopolymers 35, 639-655 (1995). [Abstract]

• M.S.P. Sansom, R. Sankararamakrishnan and I.D. Kerr.
  Modelling membrane proteins using structural restraints.
  Nature Structural Biology 2, 624-631 (1995). [Abstract]

• R. Sankararamakrishnan and M.S.P. Sansom.
  Water-mediated conformational transitions in nicotinic receptor M2 helix bundles - A molecular dynamics study.
  FEBS Letters 377, 377-382 (1995). [Abstract]

• R. Sankararamakrishnan and M.S.P. Sansom.
  Modelling packing interactions in parallel helix bundles: Pentameric bundles of nicotinic receptor M2 helices.
  Biochimca et Biophysica Acta (BBA) - Biomembranes 1239, 122-132 (1995). [Abstract]

• R. Sankararamakrishnan and M.S.P. Sansom.
  Structural features of isolated M2 helices of nicotinic receptors. Simulated annealing via molecular dynamics studies.
  Biophysical Chemistry 55, 215-230 (1995). [Abstract]

• M.S.P. Sansom, H.S. Son, R. Sankararamakrishnan, I.D. Kerr and J. Breed.
  Seven-helix bundles: molecular modelling via restrained molecular dynamics.
  Biophysical Journal 68, 1295-1310 (1995). [Abstract]

• R. Sankararamakrishnan and M.S.P. Sansom.
  Kinked structures of isolated nicotinic receptor M2 helices: A molecular dynamics study.
  Biopolymers 34, 1647-1657 (1994). [Abstract]

• I.D. Kerr, R. Sankararamakrishnan, O.S. Smart and M.S.P. Sansom.
  Parallel helix bundles and ion channels: Molecular modelling via simulated annealing and restrained molecular dynamics.
  Biophysical Journal 67, 1501-1515 (1994). [Abstract]

• R. Sankararamakrishnan and S. Vishveshwara.
  Characterization of proline-containing alpha-helix (helix F model of bacteriorhodopsin) by molecular dynamics studies.
  Proteins: Structure, Function, and Genetics 15, 26-41 (1993). [Abstract]

• R. Sankararamakrishnan and S. Vishveshwara.
  The structures of bacteriorhodopsin with different retinal-schiff base orientations - Computer modelling and energy minimization studies.
  Journal of Biomolecular Structure and Dynamics 9, 1073-1095 (1992). [Abstract]

• R. Sankararamakrishnan and S. Vishveshwara.
  Geometry of proline-containing alpha-helices.
  International Journal of Peptide and Protein Research 39, 356-363 (1992). [Abstract]

• R. Sankararamakrishnan, N. Sreerama and S. Vishveshwara.
  Characterization of proline-containing right-handed alpha-helix by molecular dynamics studies.
  Biophysical Chemistry 40, 97-108 (1991). [Abstract]

• R. Sankararamakrishnan and S. Vishveshwara.
  Conformational studies on peptides with proline in the right-handed alpha-helical region.
  Biopolymers 30, 287-298 (1990). [Abstract]

• R. Sankararamakrishnan and S. Vishveshwara.
  A hydrogen bonded chain in bacteriorhodopsin by computer modelling approach.
  Journal of Biomolecular Structure and Dynamics 7, 187-205 (1989). [Abstract]