Drug Design

Predicting the duration of action of β2-adrenergic receptor agonists: Ligand and structure-based approaches.

Agonists of the β2 adrenergic receptor (ADRB2) are an important class of medications used for the treatment of respiratory diseases.

Chiesa, L.

Target-Focused Library Design by Pocket-Applied Computer Vision and Fragment Deep Generative Linking.

We here describe a computational approach (POEM: Pocket Oriented Elaboration of Molecules) to drive the generation of target-focused libraries while taking advantage of all …

Eguida, M.

Estimating the Similarity between Protein Pockets.

With the exponential increase in publicly available protein structures, the comparison of protein binding sites naturally emerged as a scientific topic to explain observations or …

Eguida, M.

Design, Synthesis and Biological Evaluation of Arylpyridin-2-yl Guanidine Derivatives and Cyclic Mimetics as Novel MSK1 Inhibitors. An Application in an Asthma Model.

Mitogen- and Stress-Activated Kinase 1 (MSK1) is a nuclear kinase, taking part in the activation pathway of the pro-inflammatory transcription factor NF-kB and is demonstrating a …

Bollenbach, M.

A Computer Vision Approach to Align and Compare Protein Cavities: Application to Fragment-Based Drug Design.

Identifying local similarities in binding sites from distant proteins is a major hurdle to rational drug design.

Eguida, M.

IChem: A Versatile Toolkit for Detecting, Comparing, and Predicting Protein–Ligand Interactions

Abstract Structure-based ligand design requires an exact description of the topology of molecular entities under scrutiny.

Da Silva, F.

Structure-Based Detection of Orthosteric and Allosteric Pockets at Protein-Protein Interfaces

Protein-protein interfaces represent challenging but very promising targets to discover novel drugs with exquisite specificity profiles.

Da Silva, F.

Multi-target Fragments Display Versatile Binding Modes

Promiscuity is an interesting concept in fragment-based drug design as fragments with low specificity can be advantageous for finding many screening hits.

Drwal, M. N.

Customizing G Protein-coupled receptor models for structure-based virtual screening.

This review will focus on the construction, refinement, and validation of G Protein-coupled receptor models for the purpose of structure-based virtual screening.

De Graaf, C.

Comparative evaluation of eight docking tools for docking and virtual screening accuracy

Eight docking programs (DOCK, FLEXX, FRED, GLIDE, GOLD, SLIDE, SURFLEX, and QXP) that can be used for either single-ligand docking or database screening have been compared for …

Kellenberger, E.