Homology Modeling and Molecular Dynamics Simulations of Trypanosoma cruzi Phosphodiesterase b1

Lead Optimization of Phthalazinone Phosphodiesterase Inhibitors as Novel Antitrypanosomal Compounds

(2020) Irene G. Salado et al.   JOURNAL OF MEDICINAL CHEMISTRY

In Vitro and in Vivo Activity of mTOR Kinase and PI3K Inhibitors Against Leishmania donovani and Trypanosoma brucei

(2020) Trong-Nhat Phan et al.   MOLECULES

Application of target repositioning and in silico screening to exploit fatty acid binding proteins (FABPs) from Echinococcus multilocularis as possible drug targets

(2020) Julián A. Bélgamo et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

(2020) A. Acharya et al.   Journal of Chemical Information and Modeling

Predicting cryptic ligand binding sites based on normal modes guided conformational sampling

(2020) Wenjun Zheng   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Ensemble Docking in Drug Discovery: How Many Protein Configurations from Molecular Dynamics Simulations are Needed To Reproduce Known Ligand Binding?

(2019) Wilfredo Evangelista Falcon et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Alkynamide phthalazinones as a new class of TbrPDEB1 inhibitors (Part 2)

(2019) Erik de Heuvel et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Alkynamide phthalazinones as a new class of TbrPDEB1 inhibitors

(2019) Erik de Heuvel et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Phenyldihydropyrazolones as Novel Lead Compounds Against Trypanosoma cruzi

(2019) Maarten Sijm et al.   ACS Omega

Chagas Disease: From Discovery to a Worldwide Health Problem

(2019) Kárita Cláudia Freitas Lidani et al.   Frontiers in Public Health

QMEANDisCo – Distance Constraints Applied on Model Quality Estimation

(2019) Gabriel Studer et al.   BIOINFORMATICS

A structure-based approach towards the identification of novel antichagasic compounds: Trypanosoma cruzi carbonic anhydrase inhibitors

(2019) Manuel A. Llanos et al.   JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY

Ensemble Docking in Drug Discovery

(2018) Rommie E. Amaro et al.   BIOPHYSICAL JOURNAL

Cryptic binding sites on proteins: definition, detection, and druggability

(2018) Sandor Vajda et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Protein structure-based drug design: from docking to molecular dynamics

(2018) Paweł Śledź et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Targeting a Subpocket in Trypanosoma brucei Phosphodiesterase B1 (TbrPDEB1) Enables the Structure-Based Discovery of Selective Inhibitors with Trypanocidal Activity

(2018) Antoni R. Blaazer et al.   JOURNAL OF MEDICINAL CHEMISTRY

Experimental accuracy in protein structure refinement via molecular dynamics simulations

(2018) Lim Heo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

What makes it difficult to refine protein models further via molecular dynamics simulations?

(2017) Lim Heo et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Synthesis and evaluation of analogs of the phenylpyridazinone NPD-001 as potent trypanosomal TbrPDEB1 phosphodiesterase inhibitors and in vitro trypanocidals

(2016) Johan Veerman et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Repurposing strategies for tropical disease drug discovery

(2016) Dana M. Klug et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Assessment of the Sampling Performance of Multiple-Copy Dynamics versus a Unique Trajectory

(2016) Juan J. Perez et al.   Journal of Chemical Information and Modeling

Accelerated structure-based design of chemically diverse allosteric modulators of a muscarinic G protein-coupled receptor

(2016) Yinglong Miao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparing structural fingerprints using a literature-based similarity benchmark

(2016) Noel M. O’Boyle et al.   Journal of Cheminformatics

Fast, accurate, and reliable molecular docking with QuickVina 2

(2015) Amr Alhossary et al.   BIOINFORMATICS

Estimating Error in Diffusion Coefficients Derived from Molecular Dynamics Simulations

(2015) Gaurav Pranami et al.   Journal of Chemical Theory and Computation

Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning

(2015) Chad W. Hopkins et al.   Journal of Chemical Theory and Computation

Randomized Trial of Benznidazole for Chronic Chagas’ Cardiomyopathy

(2015) Carlos A. Morillo et al.   NEW ENGLAND JOURNAL OF MEDICINE

Evaluation of pyrrolidine and pyrazolone derivatives as inhibitors of trypanosomal phosphodiesterase B1 (TbrPDEB1)

(2015) Emanuele Amata et al.   TETRAHEDRON LETTERS

Repurposing human PDE4 inhibitors for neglected tropical diseases: Design, synthesis and evaluation of cilomilast analogues as Trypanosoma brucei PDEB1 inhibitors

(2014) Emanuele Amata et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Repurposing Human PDE4 Inhibitors for Neglected Tropical Diseases. Evaluation of Analogs of the Human PDE4 Inhibitor GSK-256066 as Inhibitors of PDEB1 ofTrypanosoma brucei

(2014) Stefan O. Ochiana et al.   Chemical Biology & Drug Design

Parameterization of Highly Charged Metal Ions Using the 12-6-4 LJ-Type Nonbonded Model in Explicit Water

(2014) Pengfei Li et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Synthesis and assessment of catechol diether compounds as inhibitors of trypanosomal phosphodiesterase B1 (TbrPDEB1)

(2013) Jennifer L. Woodring et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise

(2013) David Ryan Koes et al.   Journal of Chemical Information and Modeling

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Discovery of Novel Trypanosoma brucei Phosphodiesterase B1 Inhibitors by Virtual Screening against the Unliganded TbrPDEB1 Crystal Structure

(2013) Chimed Jansen et al.   JOURNAL OF MEDICINAL CHEMISTRY

Synthesis and evaluation of human phosphodiesterases (PDE) 5 inhibitor analogs as trypanosomal PDE inhibitors. Part 2. Tadalafil analogs

(2012) Stefan O. Ochiana et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Catechol Pyrazolinones as Trypanocidals: Fragment-Based Design, Synthesis, and Pharmacological Evaluation of Nanomolar Inhibitors of Trypanosomal Phosphodiesterase B1

(2012) Kristina M. Orrling et al.   JOURNAL OF MEDICINAL CHEMISTRY

Refinement of protein structure homology models via long, all-atom molecular dynamics simulations

(2012) Alpan Raval et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Target repurposing for neglected diseases

(2011) Michael P Pollastri et al.   Future Medicinal Chemistry

Pharmacological Validation of Trypanosoma brucei Phosphodiesterases B1 and B2 as Druggable Targets for African Sleeping Sickness

(2011) Nicholas D. Bland et al.   JOURNAL OF MEDICINAL CHEMISTRY

Chemical Validation of Phosphodiesterase C as a Chemotherapeutic Target in Trypanosoma cruzi, the Etiological Agent of Chagas' Disease

(2010) S. King-Keller et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

(2009) Oleg Trott et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

NCBI BLAST: a better web interface

(2008) M. Johnson et al.   NUCLEIC ACIDS RESEARCH

How well can the accuracy of comparative protein structure models be predicted?

(2008) David Eramian et al.   PROTEIN SCIENCE