Protein Predictive Modeling and Simulation of Mutations of Presenilin-1 Familial Alzheimer’s Disease on the Orthosteric Site

Diffusion Mechanism Modeling of Metformin in Human Organic Cationic Amino Acid Transporter one and Functional Impact of S189L, R206C, and G401S Mutation

(2021) Leydy Cano et al.   Frontiers in Pharmacology

QSAR studies on benzothiophene derivatives as Plasmodium falciparum N‐myristoyltransferase inhibitors: Molecular insights into affinity and selectivity

(2020) Mariana L. Garcia et al.   DRUG DEVELOPMENT RESEARCH

Elucidating Enzymatic Catalysis Using Fast Quantum Chemical Descriptors

(2020) Igor Barden Grillo et al.   Journal of Chemical Information and Modeling

Improving the binding affinity estimations of protein–ligand complexes using machine-learning facilitated force field method

(2020) Anjali Soni et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Successive cleavage of β-amyloid precursor protein by γ-secretase

(2020) Satoru Funamoto et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Mechanisms of γ-Secretase Activation and Substrate Processing

(2020) Apurba Bhattarai et al.   ACS Central Science

Lack of a site-specific phosphorylation of Presenilin 1 disrupts microglial gene networks and progenitors during development

(2020) Jose Henrique Ledo et al.   PLoS One

Recognition of the amyloid precursor protein by human γ-secretase

(2019) Rui Zhou et al.   SCIENCE

γ-Secretase Studied by Atomistic Molecular Dynamics Simulations: Global Dynamics, Enzyme Activation, Water Distribution and Lipid Binding

(2019) Manuel Hitzenberger et al.   Frontiers in Chemistry

Quantifying correlations between mutational sites in the catalytic subunit of γ-secretase

(2019) Cecilia Chávez-García et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Synthesis of new indazole based dual inhibitors of α-glucosidase and α-amylase enzymes, their in vitro, in silico and kinetics studies

(2019) Rafaila Rafique et al.   BIOORGANIC CHEMISTRY

Simulating the γ-secretase enzyme: Recent advances and future directions

(2018) Rodrigo Aguayo-Ortiz et al.   BIOCHIMIE

Synaptic markers of cognitive decline in neurodegenerative diseases: a proteomic approach

(2018) Erika Bereczki et al.   BRAIN

Nanostructural Differentiation and Toxicity of Amyloid-β25-35 Aggregates Ensue from Distinct Secondary Conformation

(2018) Yongxiu Song et al.   Scientific Reports

On the Difference Between Additive and Subtractive QM/MM Calculations

(2018) Lili Cao et al.   Frontiers in Chemistry

Dynamic micellar oligomers of amyloid beta peptides play a crucial role in their aggregation mechanisms

(2018) Bertrand Morel et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Editorial: Quantum Mechanical/Molecular Mechanical Approaches for the Investigation of Chemical Systems – Recent Developments and Advanced Applications

(2018) Thomas S. Hofer et al.   Frontiers in Chemistry

Double-sides sticking mechanism of vinblastine interacting with α,β-tubulin to get activity against cancer cells

(2018) Xiaowen Zhou et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

A Systematic DFT Approach for Studying Mechanisms of Redox Active Enzymes

(2018) Per E. M. Siegbahn et al.   Frontiers in Chemistry

Systematic study of imidazoles inhibiting IDO1 via the integration of molecular mechanics and quantum mechanics calculations

(2017) Yi Zou et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Protein Loop Structure Prediction Using Conformational Space Annealing

(2017) Seungryong Heo et al.   Journal of Chemical Information and Modeling

Genetics of Alzheimer’s disease: From pathogenesis to clinical usage

(2017) Wen Shao et al.   JOURNAL OF CLINICAL NEUROSCIENCE

Phosphorylated Presenilin 1 decreases β-amyloid by facilitating autophagosome–lysosome fusion

(2017) Victor Bustos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterizing the structural ensemble of γ-secretase using a multiscale molecular dynamics approach

(2017) Rodrigo Aguayo-Ortiz et al.   Chemical Science

Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications

(2016) Anders S. Christensen et al.   CHEMICAL REVIEWS

Analysis of 138 pathogenic mutations in presenilin-1 on the in vitro production of Aβ42 and Aβ40 peptides by γ-secretase

(2016) Linfeng Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A QM/MM Free Energy Study of the Oxidation Mechanism of Dihydroorotate Dehydrogenase (Class 1A) from Lactococcus lactis

(2015) José Rogério A. Silva et al.   JOURNAL OF PHYSICAL CHEMISTRY B

An atomic structure of human γ-secretase

(2015) Xiao-chen Bai et al.   NATURE

The I-TASSER Suite: protein structure and function prediction

(2015) Jianyi Yang et al.   NATURE METHODS

Nicastrin functions to sterically hinder γ-secretase–substrate interactions driven by substrate transmembrane domain

(2015) David M. Bolduc et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sampling the conformational space of the catalytic subunit of human γ-secretase

(2015) Xiao-chen Bai et al.   eLife

Birth and Future of Multiscale Modeling for Macromolecular Systems (Nobel Lecture)

(2014) Michael Levitt   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Challenges in computational studies of enzyme structure, function and dynamics

(2014) Alexandra T.P. Carvalho et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Three-dimensional structure of human γ-secretase

(2014) Peilong Lu et al.   NATURE

Genetics of Alzheimer’s Disease

(2014) Rita Guerreiro et al.   Neurotherapeutics

Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods in Computational Enzymology

(2013) Marc W. van der Kamp et al.   BIOCHEMISTRY

Self-propagation of pathogenic protein aggregates in neurodegenerative diseases

(2013) Mathias Jucker et al.   NATURE

Alpha-Secretase Cleavage of the Amyloid Precursor Protein: Proteolysis Regulated by Signaling Pathways and Protein Trafficking

(2012) Stefan F. Lichtenthaler   Current Alzheimer Research

The mechanism of γ-Secretase dysfunction in familial Alzheimer disease

(2012) Lucía Chávez-Gutiérrez et al.   EMBO JOURNAL

ExPASy: SIB bioinformatics resource portal

(2012) P. Artimo et al.   NUCLEIC ACIDS RESEARCH

Alzheimer's Disease-Linked Mutations in Presenilin-1 Result in a Drastic Loss of Activity in Purified γ-Secretase Complexes

(2012) Matthias Cacquevel et al.   PLoS One

Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field

(2012) Dong Xu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improving the Physical Realism and Structural Accuracy of Protein Models by a Two-Step Atomic-Level Energy Minimization

(2011) Dong Xu et al.   BIOPHYSICAL JOURNAL

Cognitive Impairment in Huntington Disease: Diagnosis and Treatment

(2011) Jane S. Paulsen   Current Neurology and Neuroscience Reports

Cholesterol Promotes the Interaction of Alzheimer β-Amyloid Monomer with Lipid Bilayer

(2011) Xiang Yu et al.   JOURNAL OF MOLECULAR BIOLOGY

Alzheimer's disease

(2011) Clive Ballard et al.   LANCET

Atomic-Level Protein Structure Refinement Using Fragment-Guided Molecular Dynamics Conformation Sampling

(2011) Jian Zhang et al.   STRUCTURE

Three-Amino Acid Spacing of Presenilin Endoproteolysis Suggests a General Stepwise Cleavage of  -Secretase-Mediated Intramembrane Proteolysis

(2010) A. Fukumori et al.   JOURNAL OF NEUROSCIENCE

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

Advances in Quantum and Molecular Mechanical (QM/MM) Simulations for Organic and Enzymatic Reactions

(2009) Orlando Acevedo et al.   ACCOUNTS OF CHEMICAL RESEARCH

Protein structure prediction on the Web: a case study using the Phyre server

(2009) Lawrence A Kelley et al.   Nature Protocols

I-TASSER server for protein 3D structure prediction

(2008) Yang Zhang   BMC BIOINFORMATICS

Beta-Secretase: Structure, Function, and Evolution

(2008) Chitra Venugopal et al.   CNS & Neurological Disorders-Drug Targets

Parenchymal and vascular Aβ-deposition and its effects on the degeneration of neurons and cognition in Alzheimer's disease

(2008) Dietmar Rudolf Thal et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE