List of works - Hammad Naveed

An integrated structure- and system-based framework to identify new targets of metabolites and known drugs.

scientific article published on 18 August 2015

CoCiter: an efficient tool to infer gene function by assessing the significance of literature co-citation

scientific article

Computational studies of membrane proteins: models and predictions for biological understanding

scientific article published on 12 October 2011

Dynamic mechanical finite element model of biological cells for studying cellular pattern formation

scientific article published on January 2013

Effects of mechanical properties on tumor invasion: insights from a cellular model

scientific article published on January 2014

Efficient computation of transfer free energies of amino acids in beta-barrel membrane proteins

scientific article

Engineered oligomerization state of OmpF protein through computational design decouples oligomer dissociation from unfolding

scientific article

Finding optimal interaction interface alignments between biological complexes

scientific article published on June 2015

GOntoSim: a semantic similarity measure based on LCA and common descendants

scientific article published on 09 March 2022

GeTFEP: A general transfer free energy profile of transmembrane proteins

scientific article published on 11 November 2019

GeTFEP: a general transfer free energy profile for transmembrane proteins

Geometric order in proliferating epithelia: impact of rearrangements and cleavage plane orientation

scientific article published on January 2010

HECNet: a hierarchical approach to Enzyme Function Classification using a Siamese Triplet Network

scientific article published on 25 May 2020

High-resolution structure prediction of β-barrel membrane proteins

scientific article

Identification of destabilizing SNPs in SARS-CoV2-ACE2 protein and spike glycoprotein: implications for virus entry mechanisms

scientific article published on 23 September 2020

Identification of potential inhibitors of three key enzymes of SARS-CoV2 using computational approach

scientific article published on 09 June 2020

Improving the resistance of a eukaryotic β-barrel protein to thermal and chemical perturbations

scientific article

Lipid-binding surfaces of membrane proteins: evidence from evolutionary and structural analysis

scientific article

Lymphopenia in treatment-naive relapsing multiple sclerosis

scientific article published on 12 August 2016

Mechanical forces mediate localized topological change in epithelia

scientific article published on January 2011

Mechanical model of geometric cell and topological algorithm for cell dynamics from single-cell to formation of monolayered tissues with pattern

scientific article (publication date: 2015)

Mechanisms of regulating cell topology in proliferating epithelia: impact of division plane, mechanical forces, and cell memory

scientific article

Mechanisms of regulating tissue elongation in Drosophila wing: impact of oriented cell divisions, oriented mechanical forces, and reduced cell size

scientific article

Modeling spatial population dynamics of stem cell lineage in tissue growth

scientific article published on January 2012

Modeling spatial population dynamics of stem cell lineage in wound healing and cancerogenesis

scientific article published on January 2013

ModuleAlign: module-based global alignment of protein-protein interaction networks

scientific article

Multiscale Modeling of Cellular Epigenetic States: Stochasticity in Molecular Networks, Chromatin Folding in Cell Nuclei, and Tissue Pattern Formation of Cells

scientific article published on January 2015

Outer Membrane Protein Folding and Topology from a Computational Transfer Free Energy Scale.

scientific article

Predicting the pathogenicity of protein coding mutations using Natural Language Processing

scientific article published on 01 July 2020

Predicting three-dimensional structures of transmembrane domains of β-barrel membrane proteins

scientific article

Predicting weakly stable regions, oligomerization state, and protein-protein interfaces in transmembrane domains of outer membrane proteins

scientific article

SAlign-a structure aware method for global PPI network alignment

scientific article published on 04 November 2020

Structure-based analysis of VDAC1 protein: defining oligomer contact sites

scientific article published on 23 November 2011

The effect of systemic inflammation on human brain barrier function

scientific article published on 31 October 2016

The structure of the TOM core complex in the mitochondrial outer membrane

scientific article published on 01 April 2020

Weakly stable regions and protein-protein interactions in beta-barrel membrane proteins

scientific article

List of works by Hammad Naveed

An integrated structure- and system-based framework to identify new targets of metabolites and known drugs.

CoCiter: an efficient tool to infer gene function by assessing the significance of literature co-citation

Computational studies of membrane proteins: models and predictions for biological understanding

Dynamic mechanical finite element model of biological cells for studying cellular pattern formation

Effects of mechanical properties on tumor invasion: insights from a cellular model

Efficient computation of transfer free energies of amino acids in beta-barrel membrane proteins

Engineered oligomerization state of OmpF protein through computational design decouples oligomer dissociation from unfolding

Finding optimal interaction interface alignments between biological complexes

GOntoSim: a semantic similarity measure based on LCA and common descendants

GeTFEP: A general transfer free energy profile of transmembrane proteins

GeTFEP: a general transfer free energy profile for transmembrane proteins

Geometric order in proliferating epithelia: impact of rearrangements and cleavage plane orientation

HECNet: a hierarchical approach to Enzyme Function Classification using a Siamese Triplet Network

High-resolution structure prediction of β-barrel membrane proteins

Identification of destabilizing SNPs in SARS-CoV2-ACE2 protein and spike glycoprotein: implications for virus entry mechanisms

Identification of potential inhibitors of three key enzymes of SARS-CoV2 using computational approach

Improving the resistance of a eukaryotic β-barrel protein to thermal and chemical perturbations

Lipid-binding surfaces of membrane proteins: evidence from evolutionary and structural analysis

Lymphopenia in treatment-naive relapsing multiple sclerosis

Mechanical forces mediate localized topological change in epithelia

Mechanical model of geometric cell and topological algorithm for cell dynamics from single-cell to formation of monolayered tissues with pattern

Mechanisms of regulating cell topology in proliferating epithelia: impact of division plane, mechanical forces, and cell memory

Mechanisms of regulating tissue elongation in Drosophila wing: impact of oriented cell divisions, oriented mechanical forces, and reduced cell size

Modeling spatial population dynamics of stem cell lineage in tissue growth

Modeling spatial population dynamics of stem cell lineage in wound healing and cancerogenesis

ModuleAlign: module-based global alignment of protein-protein interaction networks

Multiscale Modeling of Cellular Epigenetic States: Stochasticity in Molecular Networks, Chromatin Folding in Cell Nuclei, and Tissue Pattern Formation of Cells

Outer Membrane Protein Folding and Topology from a Computational Transfer Free Energy Scale.

Predicting the pathogenicity of protein coding mutations using Natural Language Processing

Predicting three-dimensional structures of transmembrane domains of β-barrel membrane proteins

Predicting weakly stable regions, oligomerization state, and protein-protein interfaces in transmembrane domains of outer membrane proteins

SAlign-a structure aware method for global PPI network alignment

Structure-based analysis of VDAC1 protein: defining oligomer contact sites

The effect of systemic inflammation on human brain barrier function

The structure of the TOM core complex in the mitochondrial outer membrane

Weakly stable regions and protein-protein interactions in beta-barrel membrane proteins