VoroMQA: Assessment of protein structure quality using interatomic contact areas

2017 ◽  
Vol 85 (6) ◽  
pp. 1131-1145 ◽  
Author(s):  
Kliment Olechnovič ◽  
Česlovas Venclovas
Keyword(s):  
Protein Structure ◽  
Structure Quality ◽  
Contact Areas ◽  
Interatomic Contact

scholarly journals Improving NMR protein structure quality by Rosetta refinement: A molecular replacement study

2008 ◽  
Vol 75 (1) ◽  
pp. 147-167 ◽  
Author(s):  
Theresa A. Ramelot ◽  
Srivatsan Raman ◽  
Alexandre P. Kuzin ◽  
Rong Xiao ◽  
Li-Chung Ma ◽  
...  
Keyword(s):  
Protein Structure ◽  
Molecular Replacement ◽  
Structure Quality ◽  
Replacement Study

scholarly journals Is too `creative' language acceptable in crystallography?

2010 ◽  
Vol 66 (9) ◽  
pp. 1041-1042 ◽  
Author(s):  
Alexander Wlodawer ◽  
Jacek Lubkowski ◽  
Wladek Minor ◽  
Mariusz Jaskolski
Keyword(s):  
Protein Structure ◽  
Super Resolution ◽  
Structure Quality ◽  
Figures Of Speech ◽  
Creative Language

While figures of speech are often useful and even educational, flashy titles combined with hyperbole and imprecise language can mislead or deceive non-specialist readers and should therefore be avoided. The possibility of such confusion exists when poorly defined terms like `structure quality' or `super-resolution' are used to describe a protein structure.

scholarly journals LAHMA: structure analysis through local annotation of homology-matched amino acids

2021 ◽  
Vol 77 (1) ◽  
pp. 28-40
Author(s):  
Bart van Beusekom ◽  
George Damaskos ◽  
Maarten L. Hekkelman ◽  
Fernando Salgado-Polo ◽  
Yoshitaka Hiruma ◽  
...  
Keyword(s):  
Amino Acids ◽  
Protein Structure ◽  
3D Models ◽  
Structural Features ◽  
Structure Model ◽  
Ramachandran Plot ◽  
Structure Quality ◽  
Structural Superposition ◽  
Homologous Structure ◽  
Selection Of

Comparison of homologous structure models is a key step in analyzing protein structure. With a wealth of homologous structures, comparison becomes a tedious process, and often only a small (user-biased) selection of data is used. A multitude of structural superposition algorithms are then typically used to visualize the structures together in 3D and to compare them. Here, the Local Annotation of Homology-Matched Amino acids (LAHMA) website (https://lahma.pdb-redo.eu) is presented, which compares any structure model with all of its close homologs from the PDB-REDO databank. LAHMA displays structural features in sequence space, allowing users to uncover differences between homologous structure models that can be analyzed for their relevance to chemistry or biology. LAHMA visualizes numerous structural features, also allowing one-click comparison of structure-quality plots (for example the Ramachandran plot) and `in-browser' structural visualization of 3D models.

scholarly journals Modeling of protein complexes in CASP14 with emphasis on the interaction interface prediction

2021 ◽  
Author(s):  
Justas Dapkunas ◽  
Kliment Olechnovič ◽  
Česlovas Venclovas
Keyword(s):  
Protein Structure ◽  
Structure Prediction ◽  
Protein Complexes ◽  
Assessment Method ◽  
Protein Assemblies ◽  
Structure Quality ◽  
Interaction Interface ◽  
Quality Assessment Method ◽  
Interface Prediction ◽  
Antigen Interaction

The goal of CASP experiments is to monitor the progress in the protein structure prediction field. During the 14th CASP edition we aimed to test our capabilities of predicting structures of protein complexes. Our protocol for modeling protein assemblies included both template-based modeling and free docking. Structural templates were identified using sensitive sequence-based searches. If sequence-based searches failed, we performed structure-based template searches using selected CASP server models. In the absence of reliable templates we applied free docking starting from monomers generated by CASP servers. We evaluated and ranked models of protein complexes using an improved version of protein structure quality assessment method, VoroMQA, taking into account both interaction interface and global structure scores. If reliable templates could be identified, generally accurate models of protein assemblies were generated with the exception of an antibody-antigen interaction. The success of free docking mainly depended on the accuracy of initial subunit models and on the scoring of docking solutions. To put our overall results in perspective, we analyzed our performance in the context of other CASP groups. Although the subunits in our assembly models often were not of the top quality, these models had, overall, the best predicted interfaces according to several protein-protein interface accuracy measures. Since we did not use co-evolution-based prediction of inter-chain contacts, we attribute our relative success in predicting interfaces primarily to the emphasis on the interaction interface when modeling and scoring.

Membrane protein structure quality in molecular dynamics simulation

2005 ◽  
Vol 24 (2) ◽  
pp. 157-165 ◽  
Author(s):  
Richard J. Law ◽  
Charlotte Capener ◽  
Marc Baaden ◽  
Peter J. Bond ◽  
Jeff Campbell ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Protein Structure ◽  
Molecular Dynamics Simulation ◽  
Membrane Protein ◽  
Dynamics Simulation ◽  
Membrane Protein Structure ◽  
Structure Quality
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