Docking into Several Individual Protein Conformations
Scoring docking conformations using predicted protein interfaces
... An alternative research line has exploited the fact that structurally similar proteins (or structural neighbours) share similar interaction sites even if they are unrelated [10,29,30]. PredUs extracts structural ...
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Optimal Clustering for Detecting Near-Native Conformations in Protein Docking
... from several in- teracting proteins as obtained by the default options of the server ClusPro that includes the program DOT (19) for screening surface ...docked conformations are within 5–10 A ˚ RMSD than ...
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Comparative Docking to Distinct G Protein–Coupled Receptor Conformations Exclusively Yields Ligands with Agonist Efficacy
... each docking calculation in the present work, we can evaluate each strategy in terms of the number of agonists ...in docking calculations against the β 2 AR active than the β 2 AR inactive ...the ...
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The Performance of Several Docking Programs at Reproducing Protein-Macrolide-Like Crystal Structures
... five docking programs were initially examined using their standard ...rings docking” with the program AD ...different docking programs to reproduce a set of complexes that contain poly-functional ...
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Protein Docking mit weichen Volumenmodellen
... based Protein-Protein Docking One of the existing docking systems is the docking suite 3D-D OCK by Sternberg et ...the docking hypotheses are scored with a statistical residue- ...
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Protein-protein and peptide-protein docking and refinement using ATTRACT in CAPRI
... the docking partners could orient towards each ...multiple conformations were available for the association partners, these conformations were docked separately (ensemble ...the docking models ...
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Sequence homology based protein-protein interacting residue predictions and the applications in ranking docked conformations
... for docking programs to generate detectable numbers of near native con- formations, and it is challenging to make reliable interface predictions for the interface predictor used by the scoring ...of docking ...
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Protein ligand interactions: docking, design and protein conformational change
... computational protein design that, although quite distinct from one another, are significantly ...by several groups in this field shows that improvements in design techniques have been made possible through ...
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Sampling the Conformation of Protein Surface Residues for Flexible Protein Docking
... possible conformations. Taking just the lowest-energy conformations in this set would not provide a good sampling of the confor- mational space accessible by the ...exhaustive conformations, we ...
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Using Ion Mobility Spectrometry to Study Protein Conformations in the Gas Phase
... analyte conformations. Several methods have been developed for predicting Ω values of model structures, but these methods yield results that can differ by 30% or ...
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Structural and energy determinants in protein-RNA docking
... two protein-RNA docking benchmarks [19], which provided the opportunity for a more exhaustive evaluation and optimization of existing protein-RNA docking protocols, and constituted a good ...
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Structural Prediction of Protein–Protein Interactions by Docking: Application to Biomedical Problems
... for Protein Structure Prediction ) (Kryshtafovych, Fidelis, & Moult, 2014) aims to assess how accurate is the prediction of current modeling programs in blind ...the protein sequences, considering the ...
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Graphics processing unit accelerated coarse-grained protein-protein docking
... We have implemented all of these options for lookup table storage and the performance of each one analysed in Chapter 7. Choosing the particular memory to use for the lookup table is determined at compile time using C ...
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Modeling of flexible side chains for protein-ligand docking
... crete conformations that can be built with the rigid backbone and a xed set of rotamers per side ...later docking, this results in about three side chains on average pointing in the wrong ...the ...
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Predicting the accuracy of protein-ligand docking on homology models
... the conformations of the active siteside chains plays an important role in docking into homology models, as shown by the dRMSD-s ...in protein binding sites upon ligand binding is becoming a central ...
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High throughput simulation methods for protein ligand docking
... the docking studies without the co-factor, the affinity of the ligands which have direct interactions with those residues which are blocked if the co-factor is present should be re- ...aside. Several ...
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Optimization and machine learning methods for Computational Protein Docking
... of protein conformations is ...the conformations from the global sam- pling stage and the goal is to generate an ensemble of refined conformations closer to the native ...input ...
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Potential cellular conformations of the CCN3(NOV) protein
... Discussion In this study we exploited the range of binding affinities present in polyclonal antibodies raised against the C-ter- minal peptide of CCN3 and analyzed with different immunoaffinity methods to ask whether ...
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Enhancing protein-protein docking by new approaches to protein flexibility and scoring of docking hypotheses
... The probabilities for the side chain conformations are calculated using a so called language model, a statistical approach used within the field of speech recognition, enabling precise e[r] ...
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Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins
... Traditional Protein-Protein Interaction (PPI) networks, which use a node and edge representation, lack some valuable information about the mechanistic details of biological ...Mapping protein ...
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