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Employment (1)

Indian Institute of Technology Kanpur: Kanpur, Uttar Pradesh, IN

2002-04-30 to present | Professor (Department of Biological Sciences and Bioengineering)
Employment
Source: Self-asserted source
Ramasubbu Sankararamakrishnan

Education and qualifications (1)

Indian Institute of Science: Bangalore, Karnataka, IN

1986-08-01 to 1992-05-12 | Ph.D. (Biological Sciences and Bioengineering)
Education
Source: Self-asserted source
Ramasubbu Sankararamakrishnan

Works (50 of 86)

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Page 1 of 2

Substrate selectivity and unique sequence signatures in SWEET/semiSWEET homologs of four taxonomic groups: Sequence analysis and phylogenetic studies

Proteins: Structure, Function, and Bioinformatics
2025-01 | Journal article
DOI: 10.1002/prot.26670
Contributors: Ankita Gupta; Ramasubbu Sankararamakrishnan
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Self‐contacting Cys, Ser, and Thr residues in high‐resolution protein crystal structures: Tertiary constraints or hydrogen bonds?

Protein Science
2024-12 | Journal article
DOI: 10.1002/pro.5218
Contributors: Prathvi Singh; Venkatnarayanan Ramanathan; Ramasubbu Sankararamakrishnan
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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
2024-06-19 | Journal article
DOI: 10.1021/acsbiomedchemau.3c00073
Contributors: Rajagopalan Muthukumaran; Ramasubbu Sankararamakrishnan
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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
2023-05 | Journal article
DOI: 10.1002/prot.26457
Contributors: C. Narendra Reddy; Ramasubbu Sankararamakrishnan
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dbAQP-SNP: a database of missense single-nucleotide polymorphisms in human aquaporins

Database
2023-03-13 | Journal article
DOI: 10.1093/database/baad012
Contributors: Rachana Dande; Ramasubbu Sankararamakrishnan
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Membrane-binding properties of NS1 proteins from Zika and Dengue viruses: Comparative simulations in explicit bilayers reveal significant differences

2023-01-12 | Preprint
DOI: 10.1101/2023.01.12.523767
Contributors: Rajagopalan Muthukumaran; Ramasubbu Sankararamakrishnan
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Dissociation of CED-4 from CED-9 upon EGL-1 binding: Molecular mechanism of linear apoptotic pathway in Caenorhabditis elegans

2022-06-01 | Preprint
DOI: 10.1101/2022.06.01.494320
Contributors: C. Narendra Reddy; Ramasubbu Sankararamakrishnan
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Designing BH3-Mimetic Peptide Inhibitors for the Viral Bcl-2 Homologues A179L and BHRF1: Importance of Long-Range Electrostatic Interactions

ACS Omega
2021-10-19 | Journal article
DOI: 10.1021/acsomega.1c03385
Contributors: Chinthakunta Narendra Reddy; Ramasubbu Sankararamakrishnan
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Designing BH3-mimetic Peptide Inhibitors for the Viral Bcl-2 Homologs A179L and BHRF1: Importance of long-range electrostatic interactions

2021-06-23 | Other
DOI: 10.1101/2021.06.23.449612
Contributors: C. Narendra Reddy; Ramasubbu Sankararamakrishnan
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Computational Design of BH3-Mimetic Peptide Inhibitors That Can Bind Specifically to Mcl-1 or Bcl-XL: Role of Non-Hot Spot Residues

Biochemistry
2020-11-17 | Journal article
DOI: 10.1021/acs.biochem.0c00661
Contributors: C. Narendra Reddy; Nishat Manzar; Bushra Ateeq; Ramasubbu Sankararamakrishnan
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A novel computational method to design BH3-mimetic peptide inhibitors that can bind specifically to Mcl-1 or Bcl-XL

2020-07-10 | Preprint
DOI: 10.1101/2020.07.09.194662
Contributors: C. Narendra Reddy; Nishat Manzar; Bushra Ateeq; Ramasubbu Sankararamakrishnan
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Unraveling the substrate preference of an uncharacterized phylogenetic subgroup in Formate/Nitrite Transporter (FNT) family: Computational studies of anion transport in Escherichia coli FNT homolog

2019-05-13 | Other
DOI: 10.1101/637116
Contributors: Mishtu Mukherjee; Ramasubbu Sankararamakrishnan
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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
2019-02-23 | Journal article
DOI: 10.1007/s00232-018-0054-7
Contributors: Alok Jain; Ravi Kumar Verma; Ramasubbu Sankararamakrishnan
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Cooperativity in Plant Plasma Membrane Intrinsic Proteins (PIPs): Mechanism of Increased Water Transport in Maize PIP1 Channels in Hetero-tetramers

Scientific Reports
2018-08-13 | Journal article
DOI: 10.1038/s41598-018-30257-4
Contributors: Manu Vajpai; Mishtu Mukherjee; Ramasubbu Sankararamakrishnan
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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
2018-01-25 | Journal article
DOI: 10.1021/acs.jpcb.7b11737
Contributors: Abhishek Hariharan Iyer; R. N. V. Krishna Deepak; Ramasubbu Sankararamakrishnan
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Cooperativity in Plant Plasma Membrane Intrinsic Proteins (PIPs): Mechanism of Increased Water Transport in Maize PIP1 Channels in Hetero-tetramers

2017-12-25 | Other
DOI: 10.1101/239780
Contributors: Manu Vajpai; Mishtu Mukherjee; Ramasubbu Sankararamakrishnan
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Anion-selective Formate/nitrite transporters: taxonomic distribution, phylogenetic analysis and subfamily-specific conservation pattern in prokaryotes

BMC Genomics
2017-07 | Journal article
DOI: 10.1186/s12864-017-3947-4
Contributors: Mishtu Mukherjee; Manu Vajpai; Ramasubbu Sankararamakrishnan
Source: Self-asserted source
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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
2017-05 | Journal article
DOI: 10.1016/j.jmgm.2016.12.006
Contributors: Vivek Modi; Ramasubbu Sankararamakrishnan
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Comparison of metal-binding strength between methionine and cysteine residues: Implications for the design of metal-binding motifs in proteins

Biophysical Chemistry
2017-05 | Journal article
DOI: 10.1016/j.bpc.2017.02.007
Contributors: R.N.V. Krishna Deepak; Brijesh Chandrakar; Ramasubbu Sankararamakrishnan
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N–H···N Hydrogen Bonds Involving Histidine Imidazole Nitrogen Atoms: A New Structural Role for Histidine Residues in Proteins

Biochemistry
2016-07 | Journal article
DOI: 10.1021/acs.biochem.6b00253
Contributors: R. N. V. Krishna Deepak; Ramasubbu Sankararamakrishnan
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Unconventional N-H…N Hydrogen Bonds Involving Proline Backbone Nitrogen in Protein Structures

Biophysical Journal
2016-05 | Journal article
DOI: 10.1016/j.bpj.2016.03.034
Contributors: R. N. V. Krishna Deepak; Ramasubbu Sankararamakrishnan
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Functional Diversity within the FNT Superfamily of Anion Channels: Phylogenetics & Molecular Dynamics Studies

Biophysical Journal
2016-02 | Journal article
DOI: 10.1016/j.bpj.2015.11.681
Contributors: Mishtu Mukherjee; Manu Vajpai; Ramasubbbu Sankararamakrishnan
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GPCR Handshake in the Spotlight: Exploring the Dimerization Interface of Dopamine D2 Receptors by Simulations at Multiple Resolutions

Biophysical Journal
2016-02 | Journal article
DOI: 10.1016/j.bpj.2015.11.2305
Contributors: Manu Vajpai; Ramasubbbu Sankararamakrishnan
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Major Intrinsic Protein Superfamily

Membrane Proteins—Engineering, Purification and Crystallization
2015 | Other
DOI: 10.1016/bs.mie.2014.12.006
Contributors: Ravi Kumar Verma; Anjali Bansal Gupta; Ramasubbu Sankararamakrishnan
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Controlling in vitro insulin amyloidosis with stable peptide conjugates: A combined experimental and computational study.

Journal of Physical Chemistry B
2015-11-16 | Journal article
DOI: 10.1021/acs.jpcb.5b08215
Source: Self-asserted source
Ramasubbu 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.

BBA Biomembranes
2015-06 | Journal article
DOI: 10.1016/j.bbamem.2015.03.013
Source: Self-asserted source
Ramasubbu Sankararamakrishnan

Molecular Dynamics Simulations of Wild-Type and Mutant AQP6 Channels: Investigation of Anion Transport in Human AQP6

Biophysical Journal
2015-01 | Journal article
DOI: 10.1016/j.bpj.2014.11.2049
Contributors: Ravi Kumar Verma; Ramasubbu Sankararamakrishnan
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New subfamilies of major intrinsic proteins in fungi suggest novel transport properties in fungal channels: implications for the host-fungal interactions

BMC Evolutionary Biology
2014-08 | Journal article
DOI: 10.1186/s12862-014-0173-4
Contributors: Ravi Kumar Verma; Neel Duti Prabh; Ramasubbu Sankararamakrishnan
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Oxygen–aromatic contacts in intra-strand base pairs: Analysis of high-resolution DNA crystal structures and quantum chemical calculations

Journal of Structural Biology
2014-07 | Journal article
DOI: 10.1016/j.jsb.2014.04.008
Contributors: Alok Jain; R.N.V. Krishna Deepak; Ramasubbu Sankararamakrishnan
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Affinities of Selective-Serotonin Reuptake Inhibitor (SSRI) for Human Transporters: Molecular Modeling and Quantum Chemical Studies

Biophysical Journal
2014-01 | Journal article
DOI: 10.1016/j.bpj.2013.11.1499
Contributors: Krishna Deepak; Alok Jain; Ramasubbu Sankararamakrishnan
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Antiapoptotic Bcl-2 homolog CED-9 inCaenorhabditis elegans: Dynamics of BH3 and CED-4 binding regions and comparison with mammalian antiapoptotic Bcl-2 proteins

Proteins: Structure, Function, and Bioinformatics
2013-11 | Journal article
DOI: 10.1002/prot.24476
Contributors: Vivek Modi; Ramasubbu Sankararamakrishnan
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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
2013-02 | Journal article
DOI: 10.1371/journal.pone.0054397
Contributors: Dilraj Lama; Vivek Modi; Ramasubbu Sankararamakrishnan; Narayanaswamy Srinivasan
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PLASTICITY OF BH3 DOMAIN-BINDING HYDROPHOBIC GROOVES IN THE ANTI-APOPTOTIC MCL-1 AND A1 PROTEINS

Biomolecular Forms and Functions
2013-02 | Other
DOI: 10.1142/9789814449144_0036
Contributors: VIVEK MODI; DILRAJ LAMA; RAMASUBBU SANKARARAMAKRISHNAN
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Hidden coding potential of eukaryotic genomes: nonAUG started ORFs

Journal of Biomolecular Structure and Dynamics
2013-01 | Journal article
DOI: 10.1080/07391102.2012.691367
Contributors: Alex V. Kochetov; Phani Deep Prayaga; Oxana A. Volkova; Ramasubbu Sankararamakrishnan
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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 and Dynamics
2013-01 | Journal article
DOI: 10.1080/07391102.2012.691363
Contributors: Vivek Modi; Dilraj Lama; Ramasubbu Sankararamakrishnan
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Distinguishing Features of Aquaglyceroporin in Plasmodium Falciparum: Comparative Molecular Dynamics Simulations of Three Aquaporins

Biophysical Journal
2012-01 | Journal article
DOI: 10.1016/j.bpj.2011.11.2478
Contributors: Ravi Kumar Verma; Alok Jain; Ramasubbu Sankararamakrishnan
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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
2011 | Journal article
DOI: 10.1021/ci200302q
Contributors: Alok Jain; Ramasubbu Sankararamakrishnan
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MIPModDB: a central resource for the superfamily of major intrinsic proteins

Nucleic Acids Research
2011-11 | Journal article
DOI: 10.1093/nar/gkr914
Contributors: A. B. Gupta; R. K. Verma; V. Agarwal; M. Vajpai; V. Bansal; R. Sankararamakrishnan
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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-XL

Journal of Computer-Aided Molecular Design
2011-04 | Journal article
DOI: 10.1007/s10822-011-9428-y
Contributors: Dilraj Lama; Ramasubbu Sankararamakrishnan
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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
2011-02 | Journal article
DOI: 10.1016/j.bpj.2010.12.2351
Contributors: Vivek Modi; Dilraj Lama; Ramasubbu Sankararamakrishnan
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Identification of Core Structural Residues in the Sequentially Diverse and Structurally Homologous Bcl-2 Family of Proteins

Biochemistry
2010-03 | Journal article
DOI: 10.1021/bi100029k
Contributors: Dilraj Lama; Ramasubbu Sankararamakrishnan
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Non-Covalent Interactions Involving Aromatic Residues in Protein Structures: Stability and Dynamics in Membrane and Globular Proteins using Molecular Dynamics Simulations

Biophysical Journal
2010-01 | Journal article
DOI: 10.1016/j.bpj.2009.12.3480
Contributors: Alok Jain; Ramasubbu Sankararamakrishnan
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Quantum Chemical Investigations on Intraresidue Carbonyl−Carbonyl Contacts in Aspartates of High-Resolution Protein Structures

The Journal of Physical Chemistry B
2010-01 | Journal article
DOI: 10.1021/jp909339r
Contributors: Tuhin Kumar Pal; Ramasubbu Sankararamakrishnan
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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
2009 | Journal article
DOI: 10.1186/1471-2229-9-134
Contributors: Anjali Gupta; Ramasubbu Sankararamakrishnan
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Lone pair ···π interactions between water oxygens and aromatic residues: Quantum chemical studies based on high-resolution protein structures and model compounds

Protein Science
2009 | Journal article
DOI: 10.1002/pro.67
Contributors: Alok Jain; Venkatnarayan Ramanathan; Ramasubbu Sankararamakrishnan
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End-to-end and end-to-middle inter-helical interactions: New classes of interacting helix pairs in protein structures.

Acta Crystallographica D Biological Crystallography
2009-10 | Journal article
DOI: 10.1107/S0907444909027012
Source: Self-asserted source
Ramasubbu Sankararamakrishnan

Force field dependence of phospholipid headgroup and acyl chain properties: Comparative molecular dynamics simulations of DMPC bilayers

Journal of Computational Chemistry
2009-05 | Journal article
DOI: 10.1002/jcc.21313
Contributors: Priyanka Prakash; Ramasubbu Sankararamakrishnan
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Geometry of proline-containing alpha-helices in proteins

International Journal of Peptide and Protein Research
2009-01 | Journal article
DOI: 10.1111/j.1399-3011.1992.tb01595.x
Contributors: R. SANKARARAMAKRISHNAN; SARASWATHI VISHVESHWARA
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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
2008-08 | Journal article
DOI: 10.1016/j.jmgm.2008.02.001
Contributors: Tuhin Kumar Pal; Ramasubbu Sankararamakrishnan
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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
2008-05 | Journal article
DOI: 10.1016/j.bbrc.2008.03.008
Contributors: Suhas Tikole; Ramasubbu Sankararamakrishnan
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Peer review (6 reviews for 3 publications/grants)

Review activity for Biochemistry. (3)
Review activity for Biophysical journal. (1)
Review activity for Journal of chemical information and modeling. (2)
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