Structural insights into the MDP binding and CARD-CARD interaction in zebrafish (Danio rerio) NOD2: a molecular dynamics approach

Activation of Nucleotide-Binding Oligomerization Domain 1 (NOD1) Receptor Signaling in Labeo rohita by iE-DAP and Identification of Ligand-Binding Key Motifs in NOD1 by Molecular Modeling and Docking

(2013) Bikash Ranjan Sahoo et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Latest developments in molecular docking: 2010-2011 in review

(2013) Elizabeth Yuriev et al.   JOURNAL OF MOLECULAR RECOGNITION

Molecular cloning and characterization of nucleotide binding and oligomerization domain-1 (NOD1) receptor in the Indian Major Carp, rohu (Labeo rohita), and analysis of its inductive expression and down-stream signalling molecules following ligands exposure and Gram-negative bacterial infections

(2012) Banikalyan Swain et al.   FISH & SHELLFISH IMMUNOLOGY

Identification of MDP (muramyl dipeptide)-binding key domains in NOD2 (nucleotide-binding and oligomerization domain-2) receptor of Labeo rohita

(2012) Jitendra Maharana et al.   FISH PHYSIOLOGY AND BIOCHEMISTRY

Structural insights of rohu TLR3, its binding site analysis with fish reovirus dsRNA, poly I:C and zebrafish TRIF

(2012) Bikash R. Sahoo et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Pathogen Sensing by Nucleotide-binding Oligomerization Domain-containing Protein 2 (NOD2) Is Mediated by Direct Binding to Muramyl Dipeptide and ATP

(2012) Jinyao Mo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structural prediction of a novel chitinase from the psychrophilic Glaciozyma antarctica PI12 and an analysis of its structural properties and function

(2012) Aizi Nor Mazila Ramli et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

The Tandem CARDs of NOD2: Intramolecular Interactions and Recognition of RIP2

(2012) Veronica Fridh et al.   PLoS One

Exploring PHD Fingers and H3K4me0 Interactions with Molecular Dynamics Simulations and Binding Free Energy Calculations: AIRE-PHD1, a Comparative Study

(2012) Dimitrios Spiliotopoulos et al.   PLoS One

Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates

(2011) Y. Yang et al.   BIOINFORMATICS

Molecular characterization of nucleotide binding and oligomerization domain (NOD)-2, analysis of its inductive expression and down-stream signaling following ligands exposure and bacterial infection in rohu (Labeo rohita)

(2011) B. Swain et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

The inflammatory bowel disease (IBD) susceptibility genes NOD1 and NOD2 have conserved anti-bacterial roles in zebrafish

(2011) S. H. Oehlers et al.   Disease Models & Mechanisms

Regulation of the Antimicrobial Response by NLR Proteins

(2011) Eran Elinav et al.   IMMUNITY

LigPlot+: Multiple Ligand–Protein Interaction Diagrams for Drug Discovery

(2011) Roman A. Laskowski et al.   Journal of Chemical Information and Modeling

An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0

(2011) Alpeshkumar K. Malde et al.   Journal of Chemical Theory and Computation

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

SMART 7: recent updates to the protein domain annotation resource

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

In Silico Approach to Inhibition of Signaling Pathways of Toll-Like Receptors 2 and 4 by ST2L

(2011) Shaherin Basith et al.   PLoS One

Comparative Analysis of Species-Specific Ligand Recognition in Toll-Like Receptor 8 Signaling: A Hypothesis

(2011) Rajiv Gandhi Govindaraj et al.   PLoS One

Synthesis of biologically active biotinylated muramyl dipeptides

(2010) Catherine Leimkuhler Grimes et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Pattern Recognition Receptors and Inflammation

(2010) Osamu Takeuchi et al.   CELL

Cloning of two rainbow trout nucleotide-binding oligomerization domain containing 2 (NOD2) splice variants and functional characterization of the NOD2 effector domains

(2010) Mingxian Chang et al.   FISH & SHELLFISH IMMUNOLOGY

Identification and functions of pattern-recognition receptors

(2010) Yutaro Kumagai et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies

(2010) Justin A. Lemkul et al.   Journal of Chemical Information and Modeling

Challenges and advances in computational docking: 2009 in review

(2010) Elizabeth Yuriev et al.   JOURNAL OF MOLECULAR RECOGNITION

CDD: a Conserved Domain Database for the functional annotation of proteins

(2010) A. Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Molecular Modeling-Based Evaluation of hTLR10 and Identification of Potential Ligands in Toll-Like Receptor Signaling

(2010) Rajiv Gandhi Govindaraj et al.   PLoS One

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

ModLink+: improving fold recognition by using protein–protein interactions

(2009) Oriol Fornes et al.   BIOINFORMATICS

NOD-like subfamily of the nucleotide-binding domain and leucine-rich repeat containing family receptors and their expression in channel catfish

(2009) Zhenxia Sha et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Molecular characterization and expression analysis of nuclear oligomerization domain proteins NOD1 and NOD2 in grass carp Ctenopharyngodon idella

(2009) W.Q. Chen et al.   FISH & SHELLFISH IMMUNOLOGY

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Large-Scale Application of High-Throughput Molecular Mechanics with Poisson−Boltzmann Surface Area for Routine Physics-Based Scoring of Protein−Ligand Complexes

(2009) Scott P. Brown et al.   JOURNAL OF MEDICINAL CHEMISTRY

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Evaluation of Nod-Like Receptor (NLR) Effector Domain Interactions

(2009) Roland N. Wagner et al.   PLoS One

Activating immunity: lessons from the TLRs and NLRs

(2009) Tom P. Monie et al.   TRENDS IN BIOCHEMICAL SCIENCES

Molecular characterization and expression analysis of the IFN-gamma related gene (IFN-γrel) in grass carp Ctenopharyngodon idella

(2009) W.Q. Chen et al.   VETERINARY IMMUNOLOGY AND IMMUNOPATHOLOGY

NOD-Like Receptors: Role in Innate Immunity and Inflammatory Disease

(2008) Grace Chen et al.   Annual Review of Pathology-Mechanisms of Disease

The microbial and danger signals that activate Nod-like receptors

(2008) Szilvia Benko et al.   CYTOKINE

Immunology and zebrafish: Spawning new models of human disease

(2008) Nathan D. Meeker et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Molecular cloning and functional characterization of porcine nucleotide-binding oligomerization domain-2 (NOD2)

(2007) Masanori Tohno et al.   MOLECULAR IMMUNOLOGY