Experimental study and computational modelling of cruzain cysteine protease inhibition by dipeptidyl nitriles

Comparison of QM/MM Methods To Obtain Ligand-Binding Free Energies

(2017) Martin A. Olsson et al.   Journal of Chemical Theory and Computation

Unraveling the Addition–Elimination Mechanism of EPSP Synthase through Computer Modeling

(2017) Alberto M. dos Santos et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Can Relative Binding Free Energy Predict Selectivity of Reversible Covalent Inhibitors?

(2017) Payal Chatterjee et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A limited-memory quasi-Newton algorithm for bound-constrained non-smooth optimization

(2017) N. Keskar et al.   OPTIMIZATION METHODS & SOFTWARE

Catalysis by solvation rather than the desolvation effect: exploring the catalytic efficiency of SAM-dependent chlorinase

(2017) Edson Araújo et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Computational Study of the Catalytic Mechanism of the Cruzain Cysteine Protease

(2017) Kemel Arafet et al.   ACS Catalysis

Enhancing Paradynamics for QM/MM Sampling of Enzymatic Reactions

(2016) Jerônimo Lameira et al.   JOURNAL OF PHYSICAL CHEMISTRY B

First Quantum Mechanics/Molecular Mechanics Studies of the Inhibition Mechanism of Cruzain by Peptidyl Halomethyl Ketones

(2015) Kemel Arafet et al.   BIOCHEMISTRY

Structure-Based Predictions of Activity Cliffs

(2015) Jarmila Husby et al.   Journal of Chemical Information and Modeling

Molecular Design, Synthesis and Trypanocidal Activity of Dipeptidyl Nitriles as Cruzain Inhibitors

(2015) Leandro A. A. Avelar et al.   PLoS Neglected Tropical Diseases

Reaction Pathway and Free Energy Profile for Papain-Catalyzed Hydrolysis of N-Acetyl-Phe-Gly 4-Nitroanilide

(2013) Donghui Wei et al.   BIOCHEMISTRY

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

(2013) Jing Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The catalytic mechanism of glyceraldehyde 3-phosphate dehydrogenase from Trypanosoma cruzi elucidated via the QM/MM approach

(2013) Mauro Reis et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Cysteine protease inhibition by nitrile-based inhibitors: a computational study

(2013) Matthew G. Quesne et al.   Frontiers in Chemistry

(1R,2R)-N-(1-Cyanocyclopropyl)-2-(6-methoxy-1,3,4,5-tetrahydropyrido[4,3-b]indole-2-carbonyl)cyclohexanecarboxamide (AZD4996): A Potent and Highly Selective Cathepsin K Inhibitor for the Treatment of Osteoarthritis

(2012) Alexander G. Dossetter et al.   JOURNAL OF MEDICINAL CHEMISTRY

Exploring, Refining, and Validating the Paradynamics QM/MM Sampling

(2012) Nikolay V. Plotnikov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKaValues

(2011) Chresten R. Søndergaard et al.   Journal of Chemical Theory and Computation

Enzyme Molecular Mechanism as a Starting Point to Design New Inhibitors: A Theoretical Study ofO-GlcNAcase

(2011) Jerônimo Lameira et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Cathepsin K: its skeletal actions and role as a therapeutic target in osteoporosis

(2011) Aline G. Costa et al.   Nature Reviews Rheumatology

Multiscale modeling of biological functions

(2011) Shina Caroline Lynn Kamerlin et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Nitrile-Containing Pharmaceuticals: Efficacious Roles of the Nitrile Pharmacophore

(2010) Fraser F. Fleming et al.   JOURNAL OF MEDICINAL CHEMISTRY

Dipeptidyl nitrile inhibitors of Cathepsin L

(2009) Nabil Asaad et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Current epidemiological trends for Chagas disease in Latin America and future challenges in epidemiology, surveillance and health policy

(2009) Álvaro Moncayo et al.   MEMORIAS DO INSTITUTO OSWALDO CRUZ

The discovery of odanacatib (MK-0822), a selective inhibitor of cathepsin K

(2008) Jacques Yves Gauthier et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

The pDynamo Program for Molecular Simulations using Hybrid Quantum Chemical and Molecular Mechanical Potentials

(2008) Martin J. Field   Journal of Chemical Theory and Computation

Atomistic Insights into the Inhibition of Cysteine Proteases: First QM/MM Calculations Clarifying the Stereoselectivity of Epoxide-Based Inhibitors

(2008) Milena Mladenovic et al.   JOURNAL OF PHYSICAL CHEMISTRY B