Structural Analysis of PfSec62-Autophagy Interacting Motifs (AIM) and PfAtg8 Interactions for Its Implications in RecovER-phagy in Plasmodium falciparum

Evaluation of peptide designing strategy against subunit reassociation in mucin 1: A steered molecular dynamics approach

(2017) J. Lesitha Jeeva Kumari et al.   PLoS One

Improvements to the APBS biomolecular solvation software suite

(2017) Elizabeth Jurrus et al.   PROTEIN SCIENCE

Apicomplexan autophagy and modulation of autophagy in parasite-infected host cells

(2017) Perle Latré de Laté et al.   Biomedical Journal

Fast and accurate determination of the relative binding affinities of small compounds to HIV-1 protease using non-equilibrium work

(2016) Son Tung Ngo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Translocon component Sec62 acts in endoplasmic reticulum turnover during stress recovery

(2016) Fiorenza Fumagalli et al.   NATURE CELL BIOLOGY

Genome-wide association analysis identifies genetic loci associated with resistance to multiple antimalarials in Plasmodium falciparum from China-Myanmar border

(2016) Zenglei Wang et al.   Scientific Reports

Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field

(2015) Michael J. Robertson et al.   Journal of Chemical Theory and Computation

Regulation of endoplasmic reticulum turnover by selective autophagy

(2015) Aliaksandr Khaminets et al.   NATURE

Live to die another way: modes of programmed cell death and the signals emanating from dying cells

(2015) Yaron Fuchs et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

GalaxyPepDock: a protein–peptide docking tool based on interaction similarity and energy optimization

(2015) Hasup Lee et al.   NUCLEIC ACIDS RESEARCH

iLIR

(2014) Ioanna Kalvari et al.   Autophagy

Atomistic Autophagy: The Structures of Cellular Self-Digestion

(2014) James H. Hurley et al.   CELL

Hierarchical sampling for metastable conformers determines biomolecular recognition: the case of malectin and diglucosylated N-glycan interactions

(2014) Ashalatha Sreshty Mamidi et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

g_mmpbsa—A GROMACS Tool for High-Throughput MM-PBSA Calculations

(2014) Rashmi Kumari et al.   Journal of Chemical Information and Modeling

Interactions between Autophagy Receptors and Ubiquitin-like Proteins Form the Molecular Basis for Selective Autophagy

(2014) Vladimir Rogov et al.   MOLECULAR CELL

Cargo recognition and trafficking in selective autophagy

(2014) Alexandra Stolz et al.   NATURE CELL BIOLOGY

The multifunctional autophagy pathway in the human malaria parasite, Plasmodium falciparum

(2013) Serena Cervantes et al.   Autophagy

Autophagy regulation by nutrient signaling

(2013) Ryan C Russell et al.   CELL RESEARCH

Steered Molecular Dynamics Studies of the Potential of Mean Force for Peptide Amphiphile Self-Assembly into Cylindrical Nanofibers

(2013) Tao Yu et al.   JOURNAL OF PHYSICAL CHEMISTRY A

ER exit sites are physical and functional core autophagosome biogenesis components

(2013) Martin Graef et al.   MOLECULAR BIOLOGY OF THE CELL

A Process Similar to Autophagy Is Associated with Cytocidal Chloroquine Resistance in Plasmodium falciparum

(2013) David Gaviria et al.   PLoS One

PepBind: A Comprehensive Database and Computational Tool for Analysis of Protein–peptide Interactions

(2013) Arindam Atanu Das et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Autophagy as a Stress-Response and Quality-Control Mechanism: Implications for Cell Injury and Human Disease

(2012) Lyndsay Murrow et al.   Annual Review of Pathology-Mechanisms of Disease

The pathways of mitophagy for quality control and clearance of mitochondria

(2012) G Ashrafi et al.   CELL DEATH AND DIFFERENTIATION

Stress-induced self-cannibalism: on the regulation of autophagy by endoplasmic reticulum stress

(2012) Shane Deegan et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Structural characterization and inhibition of the Plasmodium Atg8–Atg3 interaction

(2012) Adelaide U.P. Hain et al.   JOURNAL OF STRUCTURAL BIOLOGY

Autophagy modulation as a potential therapeutic target for diverse diseases

(2012) David C. Rubinsztein et al.   NATURE REVIEWS DRUG DISCOVERY

Neuraminidase inhibitor R-125489 – A promising drug for treating influenza virus: Steered molecular dynamics approach

(2011) Binh Khanh Mai et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Microautophagy of Cytosolic Proteins by Late Endosomes

(2011) Ranjit Sahu et al.   DEVELOPMENTAL CELL

Rosetta FlexPepDock web server—high resolution modeling of peptide–protein interactions

(2011) Nir London et al.   NUCLEIC ACIDS RESEARCH

The Unfolded Protein Response: From Stress Pathway to Homeostatic Regulation

(2011) P. Walter et al.   SCIENCE

Atg8-family interacting motif crucial for selective autophagy

(2010) Nobuo N. Noda et al.   FEBS LETTERS

Top Leads for Swine Influenza A/H1N1 Virus Revealed by Steered Molecular Dynamics Approach

(2010) Binh Khanh Mai et al.   Journal of Chemical Information and Modeling

Autophagy and the Integrated Stress Response

(2010) Guido Kroemer et al.   MOLECULAR CELL

Autophagy in mammalian development and differentiation

(2010) Noboru Mizushima et al.   NATURE CELL BIOLOGY

A subdomain of the endoplasmic reticulum forms a cradle for autophagosome formation

(2009) Mitsuko Hayashi-Nishino et al.   NATURE CELL BIOLOGY

Protein-Protein Interaction Investigated by Steered Molecular Dynamics: The TCR-pMHC Complex

(2008) Michel A. Cuendet et al.   BIOPHYSICAL JOURNAL

Ligand Escape Pathways and (Un)Binding Free Energy Calculations for the Hexameric Insulin-Phenol Complex

(2008) Harish Vashisth et al.   BIOPHYSICAL JOURNAL

Autophagosome formation from membrane compartments enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum

(2008) Elizabeth L. Axe et al.   JOURNAL OF CELL BIOLOGY

Mature ribosomes are selectively degraded upon starvation by an autophagy pathway requiring the Ubp3p/Bre5p ubiquitin protease

(2008) Claudine Kraft et al.   NATURE CELL BIOLOGY

FireDock: a web server for fast interaction refinement in molecular docking

(2008) E. Mashiach et al.   NUCLEIC ACIDS RESEARCH