List of works - S Gnanakaran

A data-driven approach to modeling the tripartite structure of multidrug resistance efflux pumps.

scientific article

A mechanistic understanding of allosteric immune escape pathways in the HIV-1 envelope glycoprotein

scientific article

A signature in HIV-1 envelope leader peptide associated with transition from acute to chronic infection impacts envelope processing and infectivity

scientific article

AIDS/HIV. Converging on an HIV vaccine

scientific article

Appreciating HIV type 1 diversity: subtype differences in Env.

scientific article

Assisted peptide folding by surface pattern recognition.

scientific article

Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework

scientific article published on 22 July 2022

Atomic-level description of amyloid beta-dimer formation

scientific article

Broadly targeted CD8⁺ T cell responses restricted by major histocompatibility complex E.

scientific article published on 21 January 2016

Characterization of a disordered protein during micellation: interactions of α-synuclein with sodium dodecyl sulfate.

scientific article

Clade-specific differences between human immunodeficiency virus type 1 clades B and C: diversity and correlations in C3-V4 regions of gp120.

scientific article published on 13 December 2006

Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus

scientific article

Coarse-Grained Model for the Interconversion between Native and Liquid Ammonia-Treated Crystalline Cellulose

article

Computing long time scale biomolecular dynamics using quasi-stationary distribution kinetic Monte Carlo (QSD-KMC)

scientific article published on 01 August 2019

Conformational flexibility of soluble cellulose oligomers: chain length and temperature dependence

scientific article published in October 2009

Conformational study of quaternary epitope region of V1/V2 loop: influence of disulfide bonds and glycosylations

Consistent patterns of change during the divergence of human immunodeficiency virus type 1 envelope from that of the inoculated virus in simian/human immunodeficiency virus-infected macaques

scientific article

Deducing conformational variability of intrinsically disordered proteins from infrared spectroscopy with Bayesian statistics.

scientific article published on August 2013

Emergence of SARS-CoV-2 through recombination and strong purifying selection

scientific article published on 29 May 2020

Escape from autologous neutralizing antibodies in acute/early subtype C HIV-1 infection requires multiple pathways

scientific article published on 18 September 2009

Exploring new strategies for cellulosic biofuels production

article

Genetic signatures in the envelope glycoproteins of HIV-1 that associate with broadly neutralizing antibodies

scientific article

Graph-Directed Approach for Downselecting Toxins for Experimental Structure Determination

scientific article published on 14 May 2020

HIV-1 Neutralizing Antibody Signatures and Application to Epitope-Targeted Vaccine Design

article

HIV-1 Neutralizing Antibody Signatures and Application to Epitope-Targeted Vaccine Design

scientific article published on 01 August 2019

Highly complex neutralization determinants on a monophyletic lineage of newly transmitted subtype C HIV-1 Env clones from India

scientific article published on 23 January 2009

Identification of amino acid substitutions associated with neutralization phenotype in the human immunodeficiency virus type-1 subtype C gp120.

scientific article

Identification of minimally interacting modules in an intrinsically disordered protein.

scientific article

In silico studies of crystalline cellulose and its degradation by enzymes

scientific article

Increased enzyme binding to substrate is not necessary for more efficient cellulose hydrolysis.

scientific article published on 19 June 2013

Insights into Hydrogen Bonding and Stacking Interactions in Cellulose

scientific article published on 16 November 2011

Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) Identifies Immune-Selected HIV Variants

scientific article

MARTINI Coarse-Grained Model for Crystalline Cellulose Microfibers

article

Membrane-mediated regulation of the intrinsically disordered CD3ϵ cytoplasmic tail of the TCR.

scientific article published on May 2015

Nature and kinetic analysis of carbon-carbon bond fragmentation reactions of cation radicals derived from SET-oxidation of lignin model compounds.

scientific article published in October 2010

Perturbation of local solvent structure by a small dication: a theoretical study on structural, vibrational, and reactive properties of beryllium ion in water.

scientific article

Plasma IgG to linear epitopes in the V2 and V3 regions of HIV-1 gp120 correlate with a reduced risk of infection in the RV144 vaccine efficacy trial

scientific article

Probing the Early Events Associated with Liquid Ammonia Pretreatment of Native Crystalline Cellulose

scientific article published on 21 July 2011

Quantifying intramolecular binding in multivalent interactions: a structure-based synergistic study on Grb2-Sos1 complex

scientific article

Quantum Chemical Study of Carbohydrate–Phospholipid Interactions

scientific article published on 17 November 2011

Rapid clearance of bacteria and their toxins: development of therapeutic proteins.

scientific article published on January 2007

Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections

scientific article

Restructuring the Crystalline Cellulose Hydrogen Bond Network Enhances Its Depolymerization Rate

scientific article published on 05 July 2011

Sequential exposure to specific antibody escape mutations may program neutralization breadth during subtype A HIV-1 infection

scientific article published on 13 September 2012

Snails In Silico: A Review of Computational Studies on the Conopeptides.

scientific article

Sodium ion interactions with aqueous glucose: insights from quantum mechanics, molecular dynamics, and experiment.

scientific article

Special section dedicated to The Sixth q-bio Conference: meeting report and preface

scientific article published on 4 June 2013

Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2

scientific article published on 01 May 2020

Subtype-specific conservation of isoleucine 309 in the envelope V3 domain is linked to immune evasion in subtype C HIV-1 infection

scientific article published on 21 May 2010

Taste of sugar at the membrane: thermodynamics and kinetics of the interaction of a disaccharide with lipid bilayers

scientific article published on February 2013

Temperature dependence of water interactions with the amide carbonyls of α-helices

scientific article

The B cell response is redundant and highly focused on V1V2 during early subtype C infection in a Zambian seroconverter

scientific article

The SARS-CoV-2 Spike Variant D614G Favors an Open Conformational State

scientific article published on 26 July 2020

The Seventh q-bio Conference: meeting report and preface

scientific article published on 30 July 2014

The eighth q-bio conference: meeting report and special issue preface

scientific article published on 30 December 2015

The implications of patterns in HIV diversity for neutralizing antibody induction and susceptibility.

scientific article published on September 2009

The solvent-dependent shift of the amide I band of a fully solvated peptide as a local probe for the solvent composition in the peptide/solvent interface.

scientific article published in December 2008

The stability of cellulose: a statistical perspective from a coarse-grained model of hydrogen-bond networks

scientific article (publication date: 22 April 2009)

Theoretical Study of the Remarkably Diverse Linkages in Lignin

Uncovering a membrane-distal conformation of KRAS available to recruit RAF to the plasma membrane

scientific article published on 10 September 2020

Understanding the interaction of Lipoarabinomannan with membrane mimetic architectures

scientific article published on 26 October 2011

Unique mutational patterns in the envelope alpha 2 amphipathic helix and acquisition of length in gp120 hypervariable domains are associated with resistance to autologous neutralization of subtype C human immunodeficiency virus type 1.

scientific article published on 14 March 2007

Viral Escape from Neutralizing Antibodies in Early Subtype A HIV-1 Infection Drives an Increase in Autologous Neutralization Breadth

scientific article

Visualization of the HIV-1 Env Glycan Shield Across Scales

scientific article published on 12 November 2019

Visualization of the HIV-1 Env glycan shield across scales

scientific article published on 22 October 2020

epitopes immediately below the base of the V3 loop of gp120 as targets for the initial autologous neutralizing antibody response in two HIV-1 subtype B-infected individuals

scientific article

List of works by S Gnanakaran

A data-driven approach to modeling the tripartite structure of multidrug resistance efflux pumps.

A mechanistic understanding of allosteric immune escape pathways in the HIV-1 envelope glycoprotein

A signature in HIV-1 envelope leader peptide associated with transition from acute to chronic infection impacts envelope processing and infectivity

AIDS/HIV. Converging on an HIV vaccine

Appreciating HIV type 1 diversity: subtype differences in Env.

Assisted peptide folding by surface pattern recognition.

Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework

Atomic-level description of amyloid beta-dimer formation

Broadly targeted CD8⁺ T cell responses restricted by major histocompatibility complex E.

Characterization of a disordered protein during micellation: interactions of α-synuclein with sodium dodecyl sulfate.

Clade-specific differences between human immunodeficiency virus type 1 clades B and C: diversity and correlations in C3-V4 regions of gp120.

Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus

Coarse-Grained Model for the Interconversion between Native and Liquid Ammonia-Treated Crystalline Cellulose

Computing long time scale biomolecular dynamics using quasi-stationary distribution kinetic Monte Carlo (QSD-KMC)

Conformational flexibility of soluble cellulose oligomers: chain length and temperature dependence

Conformational study of quaternary epitope region of V1/V2 loop: influence of disulfide bonds and glycosylations

Consistent patterns of change during the divergence of human immunodeficiency virus type 1 envelope from that of the inoculated virus in simian/human immunodeficiency virus-infected macaques

Deducing conformational variability of intrinsically disordered proteins from infrared spectroscopy with Bayesian statistics.

Emergence of SARS-CoV-2 through recombination and strong purifying selection

Escape from autologous neutralizing antibodies in acute/early subtype C HIV-1 infection requires multiple pathways

Exploring new strategies for cellulosic biofuels production

Genetic signatures in the envelope glycoproteins of HIV-1 that associate with broadly neutralizing antibodies

Graph-Directed Approach for Downselecting Toxins for Experimental Structure Determination

HIV-1 Neutralizing Antibody Signatures and Application to Epitope-Targeted Vaccine Design

HIV-1 Neutralizing Antibody Signatures and Application to Epitope-Targeted Vaccine Design

Highly complex neutralization determinants on a monophyletic lineage of newly transmitted subtype C HIV-1 Env clones from India

Identification of amino acid substitutions associated with neutralization phenotype in the human immunodeficiency virus type-1 subtype C gp120.

Identification of minimally interacting modules in an intrinsically disordered protein.

In silico studies of crystalline cellulose and its degradation by enzymes

Increased enzyme binding to substrate is not necessary for more efficient cellulose hydrolysis.

Insights into Hydrogen Bonding and Stacking Interactions in Cellulose

Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) Identifies Immune-Selected HIV Variants

MARTINI Coarse-Grained Model for Crystalline Cellulose Microfibers

Membrane-mediated regulation of the intrinsically disordered CD3ϵ cytoplasmic tail of the TCR.

Nature and kinetic analysis of carbon-carbon bond fragmentation reactions of cation radicals derived from SET-oxidation of lignin model compounds.

Perturbation of local solvent structure by a small dication: a theoretical study on structural, vibrational, and reactive properties of beryllium ion in water.

Plasma IgG to linear epitopes in the V2 and V3 regions of HIV-1 gp120 correlate with a reduced risk of infection in the RV144 vaccine efficacy trial

Probing the Early Events Associated with Liquid Ammonia Pretreatment of Native Crystalline Cellulose

Quantifying intramolecular binding in multivalent interactions: a structure-based synergistic study on Grb2-Sos1 complex

Quantum Chemical Study of Carbohydrate–Phospholipid Interactions

Rapid clearance of bacteria and their toxins: development of therapeutic proteins.

Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections

Restructuring the Crystalline Cellulose Hydrogen Bond Network Enhances Its Depolymerization Rate

Sequential exposure to specific antibody escape mutations may program neutralization breadth during subtype A HIV-1 infection

Snails In Silico: A Review of Computational Studies on the Conopeptides.

Sodium ion interactions with aqueous glucose: insights from quantum mechanics, molecular dynamics, and experiment.

Special section dedicated to The Sixth q-bio Conference: meeting report and preface

Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2

Subtype-specific conservation of isoleucine 309 in the envelope V3 domain is linked to immune evasion in subtype C HIV-1 infection

Taste of sugar at the membrane: thermodynamics and kinetics of the interaction of a disaccharide with lipid bilayers

Temperature dependence of water interactions with the amide carbonyls of α-helices

The B cell response is redundant and highly focused on V1V2 during early subtype C infection in a Zambian seroconverter

The SARS-CoV-2 Spike Variant D614G Favors an Open Conformational State

The Seventh q-bio Conference: meeting report and preface

The eighth q-bio conference: meeting report and special issue preface

The implications of patterns in HIV diversity for neutralizing antibody induction and susceptibility.

The solvent-dependent shift of the amide I band of a fully solvated peptide as a local probe for the solvent composition in the peptide/solvent interface.

The stability of cellulose: a statistical perspective from a coarse-grained model of hydrogen-bond networks

Theoretical Study of the Remarkably Diverse Linkages in Lignin

Uncovering a membrane-distal conformation of KRAS available to recruit RAF to the plasma membrane

Understanding the interaction of Lipoarabinomannan with membrane mimetic architectures

Unique mutational patterns in the envelope alpha 2 amphipathic helix and acquisition of length in gp120 hypervariable domains are associated with resistance to autologous neutralization of subtype C human immunodeficiency virus type 1.

Viral Escape from Neutralizing Antibodies in Early Subtype A HIV-1 Infection Drives an Increase in Autologous Neutralization Breadth

Visualization of the HIV-1 Env Glycan Shield Across Scales

Visualization of the HIV-1 Env glycan shield across scales

epitopes immediately below the base of the V3 loop of gp120 as targets for the initial autologous neutralizing antibody response in two HIV-1 subtype B-infected individuals