Journal ArticleDOI
LigPlot+: multiple ligand-protein interaction diagrams for drug discovery.
TLDR
A graphical system for automatically generating multiple 2D diagrams of ligand-protein interactions from 3D coordinates that facilitates popular research tasks, such as analyzing a series of small molecules binding to the same protein target, a single ligand binding to homologous proteins, or the completely general case where both protein and ligand change.Abstract:
We describe a graphical system for automatically generating multiple 2D diagrams of ligand–protein interactions from 3D coordinates. The diagrams portray the hydrogen-bond interaction patterns and hydrophobic contacts between the ligand(s) and the main-chain or side-chain elements of the protein. The system is able to plot, in the same orientation, related sets of ligand–protein interactions. This facilitates popular research tasks, such as analyzing a series of small molecules binding to the same protein target, a single ligand binding to homologous proteins, or the completely general case where both protein and ligand change.read more
Citations
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Journal ArticleDOI
PLIP: fully automated protein–ligand interaction profiler
TL;DR: The protein-ligand interaction profiler (PLIP) is presented, a novel web service for fully automated detection and visualization of relevant non-covalent protein–ligand contacts in 3D structures, freely available at projects.tu-dresden.de/plip-web.
Journal ArticleDOI
Cyclic GMP-AMP Containing Mixed Phosphodiester Linkages Is An Endogenous High-Affinity Ligand for STING.
TL;DR: The crystal structure of STING bound to 2'3'-cGAMP revealed the structural basis of this high-affinity binding and a ligand-induced conformational change in STING that may underlie its activation, and showed that endogenous cGAMP in mammalian cells contains two distinct phosphodiester linkages.
Journal ArticleDOI
Structural basis of PROTAC cooperative recognition for selective protein degradation.
M.S. Gadd,Andrea Testa,Xavier Lucas,Kwok-Ho Chan,Wenzhang Chen,Douglas J. Lamont,Michael Zengerle,Alessio Ciulli +7 more
TL;DR: The results elucidate how PROTAC-induced de novo contacts dictate preferential recruitment of a target protein into a stable and cooperative complex with an E3 ligase for selective degradation.
Journal ArticleDOI
Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2.
J. Huo,J. Huo,A. Le Bas,A. Le Bas,Reinis R. Ruza,Duyvesteyn Hme.,H. Mikolajek,Tomas Malinauskas,Tiong Kit Tan,Pramila Rijal,Pramila Rijal,Maud Dumoux,Philip N. Ward,Philip N. Ward,Jingshan Ren,D. Zhou,Peter J. Harrison,Peter J. Harrison,Miriam Weckener,Daniel K. Clare,V K Vogirala,Julika Radecke,Lucile Moynié,Yuguang Zhao,Javier Gilbert-Jaramillo,Michael L. Knight,Julia A. Tree,Karen R. Buttigieg,Naomi Coombes,Michael J. Elmore,Miles W. Carroll,Loic Carrique,Shah Pnm.,William James,Alain Townsend,Alain Townsend,David I. Stuart,Raymond J. Owens,Raymond J. Owens,James H. Naismith,James H. Naismith +40 more
TL;DR: Two nanobodies that bind SARS-CoV-2 spike RBD are shown to block interaction with receptor ACE2 and thus neutralize the virus, and have an additive effect with antibody CR3022.
Journal ArticleDOI
PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA.
Melissa F. Adasme,Katja L Linnemann,Sarah Naomi Bolz,Florian Kaiser,Sebastian Salentin,V. Joachim Haupt,Michael Schroeder +6 more
TL;DR: PLIP as discussed by the authors is a profiler for protein-ligand interaction profilers that detects and visualises these interactions and provides data in formats suitable for further processing, including DNA and RNA.
References
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Journal ArticleDOI
The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Journal ArticleDOI
A general method applicable to the search for similarities in the amino acid sequence of two proteins
TL;DR: A computer adaptable method for finding similarities in the amino acid sequences of two proteins has been developed and it is possible to determine whether significant homology exists between the proteins to trace their possible evolutionary development.
Journal ArticleDOI
LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions
TL;DR: The LIGPLOT program automatically generates schematic 2-D representations of protein-ligand complexes from standard Protein Data Bank file input giving a simple and informative representation of the intermolecular interactions and their strengths, including hydrogen bonds, hydrophobic interactions and atom accessibilities.
Journal ArticleDOI
A Fast Flexible Docking Method using an Incremental Construction Algorithm
TL;DR: This work presents an automatic method for docking organic ligands into protein binding sites that combines an appropriate model of the physico-chemical properties of the docked molecules with efficient methods for sampling the conformational space of the ligand.
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