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Concept

Scoring functions for docking

Related publications (13)

SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions

Jaume Bonet Martinez

BackgroundStatistical potentials, also named knowledge-based potentials, are scoring functions derived from empirical data that can be used to evaluate the quality of protein folds and protein-protein interaction (PPI) structures. In previous works we deco ...

2021

Progressive Correspondence Pruning by Consensus Learning

Mathieu Salzmann, Chen Zhao, Chenxu Zhao

Correspondence pruning aims to correctly remove false matches (outliers) from an initial set of putative correspondences. The pruning process is challenging since putative matches are typically extremely unbalanced, largely dominated by outliers, and the r ...

IEEE2021

Toward a unified scoring function for native state discrimination and drug-binding pocket recognition

Stefano Zamuner

Protein folding and receptor–ligand recognition are fundamental processes for any living organism. Although folding and ligand recognition are based on the same chemistry, the existing empirical scoring functions target just one problem: predicting the cor ...

2018

Constrained optimization applied to multiscale integrative modeling

Giorgio Elikem Tamo

Multiscale integrative modeling stands at the intersection between experimental and computational techniques to predict the atomistic structures of important macromolecules. In the integrative modeling process, the experimental information is often integra ...

EPFL2018

Guidance, Navigation and Control for Autonomous Rendezvous and Docking of Nano-Satellites

Camille Sébastien Pirat

Is it possible to dock CubeSats in Low Earth Orbit? Challenges are associated with the level of miniaturisation: the docking accuracy is driven by the docking mechanism dimensions. The achievable docking performance with the Guidance, Navigation and Contro ...

EPFL2018

Computational design of environmental sensors for the potent opioid fentanyl

Kai Johnsson, Luc Reymond

We describe the computational design of proteins that bind the potent analgesic fentanyl. Our approach employs a fast docking algorithm to find shape complementary ligand placement in protein scaffolds, followed by design of the surrounding residues to opt ...

Elife Sciences Publications Ltd2017

Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses

Bruno Emanuel Ferreira De Sousa Correia, Stefano Zamuner

The prediction of protein-protein interactions and their structural configuration remains a largely unsolved problem. Most of the algorithms aimed at finding the native conformation of a protein complex starting from the structure of its monomers are based ...

Wiley-Blackwell2016

First-principles Hubbard U approach for small molecule binding in metal-organic frameworks

Berend Smit, Matteo Cococcioni

We apply first-principles approaches with Hubbard U corrections for calculation of small molecule binding energetics to open-shell transition metal atoms in metal-organic frameworks (MOFs). Using density functional theory with van derWaals dispersion-corre ...

American Institute of Physics2016

Fe N-Heterocyclic Carbene Complexes as Promising Photosensitizers

Yizhu Liu

The photophysics and photochemistry of transition metal complexes (TMCs) has long been a hot field of interdisciplinary research. Rich metal-based redox processes, together with a high variety in electronic configurations and excited-state dynamics, have r ...

American Chemical Society2016

Rational Design of 4-Aryl-1,2,3-Triazoles for Indoleamine 2,3-Dioxygenase 1 Inhibition

Pierre Vogel, Somi Reddy Majjigapu

Indoleamine 2,3-dioxygenase 1 (IDO1) is an important therapeutic target treatment of diseases such as cancer that involve pathological immune escape. Starting from the scaffold of our previously discovered IDO1 inhibitor 4-phenyl-1,2,3-triazole, we used co ...

2012

Revised self-consistent continuum solvation in electronic-structure calculations

Nicola Marzari, Oliviero Andreussi

The solvation model proposed by Fattebert and Gygi [J. Comput. Chem. 23, 662 (2002)] and Scherlis et al. [J. Chem. Phys. 124, 074103 (2006)] is reformulated, overcoming some of the numerical limitations encountered and extending its range of applicability. ...

2012

Probing Odorant-Mediated Receptor Activation

Olivia Baud

Molecular interactions of odorants with their olfactory receptors (ORs) are of central importance for the mammalian olfactory system to detect and discriminate a large variety of odors with a limited set of receptors. How a particular OR binds and distingu ...

EPFL2012

Synthesis, Biological Evaluation and Docking Studies of Casuarine Analogues: Effects of Structural Modifications at Ring B on Inhibitory Activity Towards Glucoamylase

Pierre Vogel

We report the total synthesis of a series of pyrrolizidine analogues of casuarine (1) and their 6-O-alpha-glucoside derivatives. The synthetic strategy is based on a totally regio- and stereoselective 1,3-dipolar cycloaddition of suitably substituted alken ...

2010