| Year |
Citation |
Score |
| 2019 |
Mukherjee M, Gupta A, Sankararamakrishnan R. Is the E. coli Homolog of the Formate/Nitrite Transporter Family an Anion Channel? A Computational Study. Biophysical Journal. PMID 31968229 DOI: 10.1016/J.Bpj.2019.12.024 |
0.397 |
|
| 2019 |
Gupta A, Sankararamakrishnan R. Selectivity and Substrate Translocation Mechanism in Eukaryotic Sweet Proteins: Bioinformatics and Molecular Dynamics Studies Biophysical Journal. 116. DOI: 10.1016/J.Bpj.2018.11.1142 |
0.328 |
|
| 2018 |
Jain A, Verma RK, Sankararamakrishnan R. 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. The Journal of Membrane Biology. PMID 30470864 DOI: 10.1007/S00232-018-0054-7 |
0.436 |
|
| 2018 |
Vajpai M, Mukherjee M, Sankararamakrishnan R. Cooperativity in Plant Plasma Membrane Intrinsic Proteins (PIPs): Mechanism of Increased Water Transport in Maize PIP1 Channels in Hetero-tetramers. Scientific Reports. 8: 12055. PMID 30104609 DOI: 10.1038/S41598-018-30257-4 |
0.424 |
|
| 2018 |
Gupta A, Sankararamakrishnan R. 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. PMID 29665371 DOI: 10.1016/J.Jmb.2018.04.013 |
0.381 |
|
| 2018 |
Iyer AH, Krishna Deepak RNV, Sankararamakrishnan R. Imidazole Nitrogens of Two Histidine Residues Participating in N-H···N Hydrogen Bonds in Protein Structures: Structural Bioinformatics Approach Combined with Quantum Chemical Calculations. The Journal of Physical Chemistry. B. 122: 1205-1212. PMID 29278913 DOI: 10.1021/Acs.Jpcb.7B11737 |
0.348 |
|
| 2017 |
Krishna Deepak RNV, Chandrakar B, Sankararamakrishnan R. 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. PMID 28363089 DOI: 10.1016/J.Bpc.2017.02.007 |
0.309 |
|
| 2017 |
Modi V, Sankararamakrishnan R. 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 & Modelling. 73: 115-128. PMID 28279820 DOI: 10.1016/J.Jmgm.2016.12.006 |
0.346 |
|
| 2016 |
Krishna Deepak RN, Sankararamakrishnan R. N-H···N Hydrogen Bonds Involving Histidine Imidazole Nitrogen Atoms: A New Structural Role for Histidine Residues in Proteins. Biochemistry. 55: 3774-83. PMID 27305350 DOI: 10.1021/Acs.Biochem.6B00253 |
0.363 |
|
| 2016 |
Deepak RN, Sankararamakrishnan R. Unconventional N-H…N Hydrogen Bonds Involving Proline Backbone Nitrogen in Protein Structures. Biophysical Journal. 110: 1967-79. PMID 27166805 DOI: 10.1016/J.Bpj.2016.03.034 |
0.333 |
|
| 2015 |
Mishra NK, Krishna Deepak RN, Sankararamakrishnan R, Verma S. Controlling In Vitro Insulin Amyloidosis with Stable Peptide Conjugates: A Combined Experimental and Computational Study. The Journal of Physical Chemistry. B. PMID 26569375 DOI: 10.1021/Acs.Jpcb.5B08215 |
0.307 |
|
| 2015 |
Verma RK, Gupta AB, Sankararamakrishnan R. Major intrinsic protein superfamily: channels with unique structural features and diverse selectivity filters. Methods in Enzymology. 557: 485-520. PMID 25950979 DOI: 10.1016/Bs.Mie.2014.12.006 |
0.425 |
|
| 2015 |
Verma RK, Prabh ND, Sankararamakrishnan R. 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 Biophysica Acta. 1848: 1436-49. PMID 25797519 DOI: 10.1016/J.Bbamem.2015.03.013 |
0.464 |
|
| 2015 |
Verma RK, Sankararamakrishnan R. Molecular Dynamics Simulations of Wild-Type and Mutant AQP6 Channels: Investigation of Anion Transport in Human AQP6 Biophysical Journal. 108. DOI: 10.1016/J.Bpj.2014.11.2049 |
0.402 |
|
| 2014 |
Verma RK, Prabh ND, Sankararamakrishnan R. 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: 173. PMID 25112373 DOI: 10.1186/S12862-014-0173-4 |
0.336 |
|
| 2014 |
Jain A, Krishna Deepak RNV, Sankararamakrishnan R. 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. PMID 24816369 DOI: 10.1016/J.Jsb.2014.04.008 |
0.343 |
|
| 2014 |
Modi V, Sankararamakrishnan R. Antiapoptotic Bcl-2 homolog CED-9 in Caenorhabditis elegans: Dynamics of BH3 and CED-4 binding regions and comparison with mammalian antiapoptotic Bcl-2 proteins Proteins: Structure, Function and Bioinformatics. 82: 1035-1047. PMID 24218065 DOI: 10.1002/Prot.24476 |
0.401 |
|
| 2014 |
Deepak K, Jain A, Sankararamakrishnan R. Affinities of Selective-Serotonin Reuptake Inhibitor (SSRI) for Human Transporters: Molecular Modeling and Quantum Chemical Studies Biophysical Journal. 106: 2-5. DOI: 10.1016/J.Bpj.2013.11.1499 |
0.333 |
|
| 2013 |
Lama D, Modi V, Sankararamakrishnan R. Behavior of solvent-exposed hydrophobic groove in the anti-apoptotic Bcl-XL protein: clues for its ability to bind diverse BH3 ligands from MD simulations. Plos One. 8: e54397. PMID 23468841 DOI: 10.1371/Journal.Pone.0054397 |
0.397 |
|
| 2013 |
Modi V, Lama D, Sankararamakrishnan R. 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. PMID 22803956 DOI: 10.1080/07391102.2012.691363 |
0.406 |
|
| 2012 |
Gupta AB, Verma RK, Agarwal V, Vajpai M, Bansal V, Sankararamakrishnan R. MIPModDB: a central resource for the superfamily of major intrinsic proteins. Nucleic Acids Research. 40: D362-9. PMID 22080560 DOI: 10.1093/Nar/Gkr914 |
0.373 |
|
| 2012 |
Verma RK, Jain A, Sankararamakrishnan R. Distinguishing Features of Aquaglyceroporin in Plasmodium Falciparum: Comparative Molecular Dynamics Simulations of Three Aquaporins Biophysical Journal. 102. DOI: 10.1016/J.Bpj.2011.11.2478 |
0.456 |
|
| 2011 |
Jain A, Sankararamakrishnan R. Dynamics of noncovalent interactions in all-α and all-β class proteins: implications for the stability of amyloid aggregates. Journal of Chemical Information and Modeling. 51: 3208-16. PMID 22017310 DOI: 10.1021/Ci200302Q |
0.389 |
|
| 2011 |
Lama D, Sankararamakrishnan R. 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: 413-26. PMID 21523491 DOI: 10.1007/S10822-011-9428-Y |
0.373 |
|
| 2011 |
Modi V, Lama D, Sankararamakrishnan R. Differential Binding Affinities of Anti-Apoptotic MCL-1 and A1 Proteins for the Pro-Apoptotic BH3 Peptides: Understanding the Molecular Basis using MD Simulations Biophysical Journal. 100: 3-6. DOI: 10.1016/J.Bpj.2010.12.2351 |
0.389 |
|
| 2010 |
Lama D, Sankararamakrishnan R. Identification of core structural residues in the sequentially diverse and structurally homologous Bcl-2 family of proteins. Biochemistry. 49: 2574-84. PMID 20141168 DOI: 10.1021/Bi100029K |
0.39 |
|
| 2010 |
Pal TK, Sankararamakrishnan R. Quantum chemical investigations on intraresidue carbonyl-carbonyl contacts in aspartates of high-resolution protein structures. The Journal of Physical Chemistry. B. 114: 1038-49. PMID 20039723 DOI: 10.1021/Jp909339R |
0.415 |
|
| 2010 |
Prakash P, Sankararamakrishnan R. Force field dependence of phospholipid headgroup and acyl chain properties: Comparative molecular dynamics simulations of DMPC bilayers Journal of Computational Chemistry. 31: 266-277. PMID 19475632 DOI: 10.1002/Jcc.21313 |
0.304 |
|
| 2010 |
Jain A, Sankararamakrishnan R. Non-Covalent Interactions Involving Aromatic Residues in Protein Structures: Stability and Dynamics in Membrane and Globular Proteins using Molecular Dynamics Simulations Biophysical Journal. 98. DOI: 10.1016/J.Bpj.2009.12.3480 |
0.413 |
|
| 2009 |
Ghosh TS, Chaitanya SK, Sankararamakrishnan R. End-to-end and end-to-middle interhelical interactions: new classes of interacting helix pairs in protein structures. Acta Crystallographica. Section D, Biological Crystallography. 65: 1032-41. PMID 19770500 DOI: 10.1107/S0907444909027012 |
0.408 |
|
| 2009 |
Jain A, Ramanathan V, Sankararamakrishnan R. Lone pair ... pi interactions between water oxygens and aromatic residues: quantum chemical studies based on high-resolution protein structures and model compounds. Protein Science : a Publication of the Protein Society. 18: 595-605. PMID 19241386 DOI: 10.1002/Pro.67 |
0.38 |
|
| 2008 |
Lama D, Sankararamakrishnan R. Anti-apoptotic Bcl-XL protein in complex with BH3 peptides of pro-apoptotic Bak, Bad, and Bim proteins: comparative molecular dynamics simulations. Proteins. 73: 492-514. PMID 18452209 DOI: 10.1002/Prot.22075 |
0.411 |
|
| 2008 |
Pal TK, Sankararamakrishnan R. Self-contacts in Asx and Glx residues of high-resolution protein structures: role of local environment and tertiary interactions. Journal of Molecular Graphics & Modelling. 27: 20-33. PMID 18343699 DOI: 10.1016/J.Jmgm.2008.02.001 |
0.392 |
|
| 2007 |
Prakash P, Sankararamakrishnan R. 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 and Peptide Letters. 14: 590-596. PMID 17627601 DOI: 10.2174/092986607780989868 |
0.401 |
|
| 2007 |
Jain A, Purohit CS, Verma S, Sankararamakrishnan R. Close contacts between carbonyl oxygen atoms and aromatic centers in protein structures: pi...pi or lone-pair...pi interactions? The Journal of Physical Chemistry. B. 111: 8680-3. PMID 17616223 DOI: 10.1021/Jp072742L |
0.376 |
|
| 2007 |
Bansal A, Sankararamakrishnan R. 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. PMID 17445256 DOI: 10.1186/1472-6807-7-27 |
0.368 |
|
| 2006 |
Sankararamakrishnan R. Recognition of GPCRs by peptide ligands and membrane compartments theory: structural studies of endogenous peptide hormones in membrane environment. Bioscience Reports. 26: 131-58. PMID 16773462 DOI: 10.1007/S10540-006-9014-Z |
0.351 |
|
| 2005 |
Prasad KK, Purohit CS, Jain A, Sankararamakrishnan R, Verma S. Enforcing solution phase nanoscopic aggregation in a palindromic tripeptide. Chemical Communications (Cambridge, England). 2564-6. PMID 15900327 DOI: 10.1039/B500654F |
0.304 |
|
| 2005 |
Sankararamakrishnan R, Verma S, Kumar S. ATCUN-like metal-binding motifs in proteins: identification and characterization by crystal structure and sequence analysis. Proteins. 58: 211-21. PMID 15508143 DOI: 10.1002/Prot.20265 |
0.345 |
|
| 2004 |
Sankararamakrishnan R, Weinstein H. Surface tension parameterization in molecular dynamics simulations of a phospholipid-bilayer membrane: Calibration and effects Journal of Physical Chemistry B. 108: 11802-11811. DOI: 10.1021/Jp048969N |
0.36 |
|
| 2002 |
Sankararamakrishnan R, Weinstein H. 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. DOI: 10.1021/Jp012174O |
0.356 |
|
| 2000 |
Sankararamakrishnan R, Weinstein H. Molecular dynamics simulations predict a tilted orientation for the helical region of dynorphin A(1-17) in dimyristoylphosphatidylcholine bilayers Biophysical Journal. 79: 2331-2344. PMID 11053113 DOI: 10.1016/S0006-3495(00)76479-4 |
0.474 |
|
| 2000 |
Sankararamakrishnan R, Konvicka K, Mehler EL, Weinstein H. Solvation in simulated annealing and high‐temperature molecular dynamics of proteins: A restrained water droplet model International Journal of Quantum Chemistry. 77: 174-186. DOI: 10.1002/(Sici)1097-461X(2000)77:1<174::Aid-Qua16>3.0.Co;2-C |
0.414 |
|
| 1997 |
Kerr ID, Doak DG, Sankararamakrishnan R, Breed J, Sansom MS. Molecular modelling of Staphylococcal delta-toxin ion channels by restrained molecular dynamics. Protein Engineering. 9: 161-71. PMID 9005437 DOI: 10.1093/Protein/9.2.161 |
0.59 |
|
| 1997 |
Sankararamakrishnan R, Adcock C, Sansom MS. The pore domain of the nicotinic acetylcholine receptor: molecular modeling, pore dimensions, and electrostatics. Biophysical Journal. 71: 1659-71. PMID 8889144 DOI: 10.1016/S0006-3495(96)79370-0 |
0.554 |
|
| 1996 |
Singh C, Sankararamakrishnan R, Subramaniam S, Jakobsson E. Solvation, water permeation, and ionic selectivity of a putative model for the pore region of the voltage-gated sodium channel. Biophysical Journal. 71: 2276-88. PMID 8913570 DOI: 10.1016/S0006-3495(96)79438-9 |
0.56 |
|
| 1996 |
Kerr ID, Son HS, Sankararamakrishnan R, Sansom MS. Molecular dynamics simulations of isolated transmembrane helices of potassium channels. Biopolymers. 39: 503-15. PMID 8837517 DOI: 10.1002/(Sici)1097-0282(199610)39:4<503::Aid-Bip3>3.0.Co;2-0 |
0.582 |
|
| 1996 |
Sansom MSP, Kerr ID, Breed J, Sankararamakrishnan R. Water in channel-like cavities: structure and dynamics. Biophysical Journal. 70: 693-702. PMID 8789086 DOI: 10.1016/S0006-3495(96)79609-1 |
0.394 |
|
| 1996 |
Breed J, Sankararamakrishnan R, Kerr ID, Sansom MS. Molecular dynamics simulations of water within models of ion channels. Biophysical Journal. 70: 1643-61. PMID 8785323 DOI: 10.1016/S0006-3495(96)79727-8 |
0.575 |
|
| 1996 |
Sansom MSP, Breed J, Sankararamakrishnan R, Kerr ID. Water dynamics in model transbilayer pores. Biochemical Society Transactions. 24. PMID 8674629 DOI: 10.1042/Bst024139S |
0.349 |
|
| 1996 |
Sankararamakrishnan R, Sansom MS. Molecular dynamics simulations on solvated M2 helix bundles of nicotinic receptors. Biochemical Society Transactions. 24: 138S. PMID 8674628 DOI: 10.1042/Bst024138S |
0.576 |
|
| 1996 |
Sankararamakrishnan R, Sansom MS. Water-mediated conformational transitions in nicotinic receptor M2 helix bundles: a molecular dynamics study. Febs Letters. 377: 377-82. PMID 8549759 DOI: 10.1016/0014-5793(95)01376-8 |
0.594 |
|
| 1996 |
Sankararamakrishnan R, Sansom MS. Modelling packing interactions in parallel helix bundles: pentameric bundles of nicotinic receptor M2 helices. Biochimica Et Biophysica Acta. 1239: 122-32. PMID 7488617 DOI: 10.1016/0005-2736(95)00165-Y |
0.58 |
|
| 1995 |
Sansom MS, Son HS, Sankararamakrishnan R, Kerr ID, Breed J. Seven-helix bundles: molecular modeling via restrained molecular dynamics. Biophysical Journal. 68: 1295-1310. PMID 7787019 DOI: 10.1016/S0006-3495(95)80303-6 |
0.437 |
|
| 1995 |
Breed J, Kerr ID, Sankararamakrishnan R, Sansom MS. Packing interactions of Aib-containing helices: molecular modeling of parallel dimers of simple hydrophobic helices and of alamethicin. Biopolymers. 35: 639-55. PMID 7766829 DOI: 10.1002/Bip.360350610 |
0.576 |
|
| 1995 |
Sankararamakrishnan R, Sansom MS. Structural features of isolated M2 helices of nicotinic receptors. Simulated annealing via molecular dynamics studies. Biophysical Chemistry. 55: 215-30. PMID 7626742 DOI: 10.1016/0301-4622(95)00006-J |
0.591 |
|
| 1995 |
Sansom MSP, Sankararamakrishnan R, Kerr ID. Modelling membrane proteins using structural restraints Nature Structural & Molecular Biology. 2: 624-631. PMID 7552722 DOI: 10.1038/Nsb0895-624 |
0.477 |
|
| 1994 |
Kerr ID, Sankararamakrishnan R, Sansom MS. Simplified models of the pore domain of the nicotinic acetylcholine receptor. Biochemical Society Transactions. 22: 158S. PMID 7958226 DOI: 10.1042/Bst022158S |
0.48 |
|
| 1994 |
Sankararamakrishnan R, Sansom MS. Molecular dynamics studies of M2 helices of nicotinic acetylcholine receptors. Biochemical Society Transactions. 22: 156S. PMID 7958224 DOI: 10.1042/Bst022156S |
0.518 |
|
| 1994 |
Sankararamakrishnan R, Sansom MSP. Kinked structures of isolated nicotinic receptor M2 helices: a molecular dynamics study. Biopolymers. 34: 1647-1657. PMID 7849226 DOI: 10.1002/Bip.360341209 |
0.501 |
|
| 1994 |
Kerr ID, Sankararamakrishnan R, Smart OS, Sansom MS. Parallel helix bundles and ion channels: molecular modeling via simulated annealing and restrained molecular dynamics. Biophysical Journal. 67: 1501-15. PMID 7529585 DOI: 10.1016/S0006-3495(94)80624-1 |
0.58 |
|
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