Polar Desolvation and Position 226 of Pancreatic and Neutrophil Elastases Are Crucial to their Affinity for the Kunitz-Type Inhibitors ShPI-1 and ShPI-1/K13L

Three-dimensional Structure of a Kunitz-type Inhibitor in Complex with an Elastase-like Enzyme

(2015) Rossana García-Fernández et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Insights into the Interactions of Fasciola hepatica Cathepsin L3 with a Substrate and Potential Novel Inhibitors through In Silico Approaches

(2015) Lilian Hernández Alvarez et al.   PLoS Neglected Tropical Diseases

Molecular Determinants of Binding to the Plasmodium Subtilisin-like Protease 1

(2013) Simone Fulle et al.   Journal of Chemical Information and Modeling

Improved Generalized Born Solvent Model Parameters for Protein Simulations

(2013) Hai Nguyen et al.   Journal of Chemical Theory and Computation

Neutrophil Elastase as a Target in Lung Cancer

(2012) Gautier Moroy et al.   Anti-Cancer Agents in Medicinal Chemistry

Develop and Test a Solvent Accessible Surface Area-Based Model in Conformational Entropy Calculations

(2012) Junmei Wang et al.   Journal of Chemical Information and Modeling

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

(2012) Bill R. Miller et al.   Journal of Chemical Theory and Computation

Effect of atomic charge, solvation, entropy, and ligand protonation state on MM-PB(GB)SA binding energies of HIV protease

(2012) Daniel P. Oehme et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Impact of Ligand and Protein Desolvation on Ligand Binding to the S1 Pocket of Thrombin

(2012) A. Biela et al.   JOURNAL OF MOLECULAR BIOLOGY

A strategy for reducing gross errors in the generalized Born models of implicit solvation

(2011) Alexey V. Onufriev et al.   JOURNAL OF CHEMICAL PHYSICS

Comparison of the Efficiency of the LIE and MM/GBSA Methods to Calculate Ligand-Binding Energies

(2011) Samuel Genheden et al.   Journal of Chemical Theory and Computation

MEROPS: the database of proteolytic enzymes, their substrates and inhibitors

(2011) N. D. Rawlings et al.   NUCLEIC ACIDS RESEARCH

Virtual screening using molecular simulations

(2011) Tianyi Yang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking

(2010) Tingjun Hou et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

A Medicinal Chemist’s Guide to Molecular Interactions

(2010) Caterina Bissantz et al.   JOURNAL OF MEDICINAL CHEMISTRY

Neutrophil Elastase, Proteinase 3, and Cathepsin G as Therapeutic Targets in Human Diseases

(2010) B. Korkmaz et al.   PHARMACOLOGICAL REVIEWS

Structural basis of substrate specificity in the serine proteases

(2010) John J. Perona et al.   PROTEIN SCIENCE

Prediction of Protein-Protein Interface Sequence Diversity Using Flexible Backbone Computational Protein Design

(2008) Elisabeth L. Humphris et al.   STRUCTURE