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List of works by Ramasubbu Sankararamakrishnan

A survey of mRNA sequences with a non-AUG start codon in RefSeq database

scientific article published on 01 August 2006

ATCUN-like metal-binding motifs in proteins: identification and characterization by crystal structure and sequence analysis

scientific article published in January 2005

Anion-selective Formate/nitrite transporters: taxonomic distribution, phylogenetic analysis and subfamily-specific conservation pattern in prokaryotes.

scientific article published on 24 July 2017

Anti-apoptotic Bcl-XL protein in complex with BH3 peptides of pro-apoptotic Bak, Bad, and Bim proteins: comparative molecular dynamics simulations.

scientific article published in November 2008

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

scientific article published on 23 November 2013

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

scientific article

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

scientific article published on 9 February 2017

Characterization of proline-containing alpha-helix (helix F model of bacteriorhodopsin) by molecular dynamics studies

scientific article published on 01 January 1993

Characterization of proline-containing right-handed alpha-helix by molecular dynamics studies

scientific article published in April 1991

Comparison of metal-binding strength between methionine and cysteine residues: Implications for the design of metal-binding motifs in proteins.

scientific article published on 18 March 2017

Computational Design of BH3-Mimetic Peptide Inhibitors That Can Bind Specifically to Mcl-1 or Bcl-XL: Role of Non-Hot Spot Residues

scientific article published on 04 November 2020

Conformational studies on peptides with proline in the right-handed alpha-helical region

scientific article published on 01 January 1990

Controlling in Vitro Insulin Amyloidosis with Stable Peptide Conjugates: A Combined Experimental and Computational Study

scientific article published on 08 December 2015

Cooperativity in Plant Plasma Membrane Intrinsic Proteins (PIPs): Mechanism of Increased Water Transport in Maize PIP1 Channels in Hetero-tetramers

scientific article published in Scientific Reports

Dynamics of noncovalent interactions in all-α and all-β class proteins: implications for the stability of amyloid aggregates

scientific article published on 14 November 2011

End-to-end and end-to-middle interhelical interactions: new classes of interacting helix pairs in protein structures.

scientific article published on 16 September 2009

Enforcing solution phase nanoscopic aggregation in a palindromic tripeptide

scientific article published on 28 February 2005

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

scientific article published in January 2010

Hidden coding potential of eukaryotic genomes: nonAUG started ORFs

scientific article published on 18 July 2012

Identification of core structural residues in the sequentially diverse and structurally homologous Bcl-2 family of proteins

scientific article published in March 2010

Imidazole Nitrogens of Two Histidine Residues Participating in N-H…N Hydrogen Bonds in Protein Structures: Structural Bioinformatics Approach Combined with Quantum Chemical Calculations.

scientific article published on 27 December 2017

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

scientific article published on 19 March 2015

Kinked structures of isolated nicotinic receptor M2 helices: a molecular dynamics study

scientific article published on 01 December 1994

Lone pair ... pi interactions between water oxygens and aromatic residues: quantum chemical studies based on high-resolution protein structures and model compounds

scientific article published on March 2009

MIPModDB: a central resource for the superfamily of major intrinsic proteins

scientific article

Major intrinsic protein superfamily: channels with unique structural features and diverse selectivity filters

scientific article

Modelling membrane proteins using structural restraints

scientific article published on 01 August 1995

Modelling packing interactions in parallel helix bundles: pentameric bundles of nicotinic receptor M2 helices

scientific article published on 01 November 1995

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

scientific article published on 01 January 2007

Molecular dynamics simulations of isolated transmembrane helices of potassium channels

scientific article published on 01 October 1996

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)

scientific article published on 27 April 2011

Molecular dynamics simulations on solvated M2 helix bundles of nicotinic receptors

scientific article published on 01 February 1996

Molecular dynamics studies of M2 helices of nicotinic acetylcholine receptors

scientific article published on 01 May 1994

Molecular modelling of Staphylococcal delta-toxin ion channels by restrained molecular dynamics

scientific article published on 01 February 1996

N-H···N Hydrogen Bonds Involving Histidine Imidazole Nitrogen Atoms: A New Structural Role for Histidine Residues in Proteins.

scientific article published on 15 June 2016

New subfamilies of major intrinsic proteins in fungi suggest novel transport properties in fungal channels: implications for the host-fungal interactions

scientific article

Oxygen-aromatic contacts in intra-strand base pairs: analysis of high-resolution DNA crystal structures and quantum chemical calculations

scientific article published on 09 May 2014

Packing interactions of aib-containing helices: Molecular modeling of parallel dimers of simple hydrophobic helices and of alamethicin

article

Parallel helix bundles and ion channels: molecular modeling via simulated annealing and restrained molecular dynamics

scientific article published on October 1994

Prediction of translation initiation sites in human mRNA sequences with AUG start codon in weak Kozak context: A neural network approach

scientific article

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

scientific article published on 23 November 2018

Quantum chemical investigations on intraresidue carbonyl-carbonyl contacts in aspartates of high-resolution protein structures

scientific article published in January 2010

Relationship between helix stability and binding affinities: molecular dynamics simulations of Bfl-1/A1-binding pro-apoptotic BH3 peptide helices in explicit solvent.

scientific article published on 18 July 2012

Self-contacts in Asx and Glx residues of high-resolution protein structures: role of local environment and tertiary interactions

scientific article

Seven-helix bundles: molecular modeling via restrained molecular dynamics.

scientific article published on April 1995

Simplified models of the pore domain of the nicotinic acetylcholine receptor

scientific article published on 01 May 1994

Solvation, water permeation, and ionic selectivity of a putative model for the pore region of the voltage-gated sodium channel.

scientific article

Structural features of isolated M2 helices of nicotinic receptors. Simulated annealing via molecular dynamics studies

scientific article published on 01 August 1995

The pore domain of the nicotinic acetylcholine receptor: molecular modeling, pore dimensions, and electrostatics.

scientific article published on October 1996

Unconventional N-H…N Hydrogen Bonds Involving Proline Backbone Nitrogen in Protein Structures

scientific article

Water dynamics in model transbilayer pores.

scientific article published in February 1996

Water in channel-like cavities: structure and dynamics.

scientific article published on February 1996

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