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Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.
We present an updated and integrated version of our widely used protein-protein docking and binding affinity benchmarks. The benchmarks consist of non-redundant, high-quality structures ofExpand
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Contacts-based prediction of binding affinity in protein–protein complexes
Almost all critical functions in cells rely on specific protein–protein interactions. Understanding these is therefore crucial in the investigation of biological systems. Despite all past efforts, weExpand
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PRODIGY: a web server for predicting the binding affinity of protein-protein complexes
Gaining insights into the structural determinants of protein-protein interactions holds the key for a deeper understanding of biological functions, diseases and development of therapeutics. AnExpand
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On the binding affinity of macromolecular interactions: daring to ask why proteins interact
Interactions between proteins are orchestrated in a precise and time-dependent manner, underlying cellular function. The binding affinity, defined as the strength of these interactions, is translatedExpand
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The DisVis and PowerFit Web Servers: Explorative and Integrative Modeling of Biomolecular Complexes.
Structure determination of complex molecular machines requires a combination of an increasing number of experimental methods with highly specialized software geared toward each data source toExpand
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Building Macromolecular Assemblies by Information-driven Docking
Over the last years, large scale proteomics studies have generated a wealth of information of biomolecular complexes. Adding the structural dimension to the resulting interactomes represents a majorExpand
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Time- and ensemble-averaged direct NOE restraints
SummaryNMR data are collected as time- and ensemble-averaged quantities. Yet, in commonly used methods for structure determination of biomolecules, structures are required to satisfy simultaneously aExpand
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Solvated docking: introducing water into the modelling of biomolecular complexes
MOTIVATION Interfacial water, which plays an important role in mediating biomolecular interactions, has been neglected in the modelling of biomolecular complexes. METHODS We present a solvatedExpand
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Crystal structure and catalytic mechanism of the LPS 3-O-deacylase PagL from Pseudomonas aeruginosa.
Pathogenic gram-negative bacteria can modify the lipid A portion of their lipopolysaccharide in response to environmental stimuli. 3-O-deacylation of lipid A by the outer membrane enzyme PagLExpand
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SAMPLEX: Automatic mapping of perturbed and unperturbed regions of proteins and complexes
BackgroundThe activity of proteins within the cell is characterized by their motions, flexibility, interactions or even the particularly intriguing case of partially unfolded states. In the last twoExpand
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