Bound Protein Backbone and Side-Chain Assignment
Side-Chain to Main-Chain Hydrogen Bonding Controls the Intrinsic Backbone Dynamics of the Amyloid Precursor Protein Transmembrane Helix
... Integrated Protein Science (CIPS M ) at Lehrstuhl Chemie der Biopolymere, Technische Universita¨t Mu¨nchen, Freising, Germany ABSTRACT Many transmembrane helices contain serine and/or threonine residues whose ...
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Protein contacts, inter-residue interactions and side-chain modelling.: protein contacts
... minimize side-chain-backbone clashes and side-chain-side-chain ...the side-chains as graphs and used dead-end elimination step, based on the simple Goldstein ...
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Flat-Bottom Strategy for Improved Accuracy in Protein Side-Chain Placements
... 2. Materials and Methods 2.1 Preparation of Rotamer Libraries Rotamer libraries of various diversities are derived from the complete coordinate rotamer library of Xiang 21 . We added hydrogens to the rotamers, and ...
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Protein side-chain placement: probabilistic inference and integer programming methods
... On the other hand, there exists a pitfall in application of this decomposition; by generating edges as columns, we may end up with a basis for the LP relaxation of the base formulation. To obtain a better lower ...
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The role of the backbone torsion in protein folding
... of protein torsion and twist, which would take into account the geometry of the chemical bonds and energetically favorable conforma- tions within the protein main chain, the effects of chain ...
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Optimization of van der Waals Energy for Protein Side-Chain Placement and Design
... optimal side-chain conformations in protein structures has been a long-standing and challenging ...modeling, protein docking, and for placing small molecule ligands on protein-binding ...
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A protocol for CABS-dock protein–peptide docking driven by side-chain contact information
... representing side chains, D 0 is the distance below which the potential vanishes and s is the slope of the potential ...the side-chain and backbone level, but kept in near native conformation ...
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Strategies for Peptide Backbone Modification in Protein Beta-Sheets
... parent protein 81 and α/β-hybrids proteins 83 and ...with protein 83. Use of a 2:1 substitution shortens the backbone by two atoms, essentially acting as an amide deletion while maintaining the ...
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Prediction of Protein-Protein Interface Sequence Diversity Using Flexible Backbone Computational Protein Design
... advance protein design, here we describe a method employing flexi- ble backbone ensembles to predict sequences toler- ated for a protein-protein ...coupled side ...
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Protein Side Chain Modeling with Orientation-Dependent Atomic Force Fields Derived by Series Expansions
... It takes approximately 15 CPU hours for OSCAR-o or NCN 32 to model the side chain conformations for the 30 test proteins. By comparison, OPUS_Rota 9 or SCWRL4 33 takes 5 CPU minutes only. Both OPUS_Rota and ...
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Automated amino acid side-chain NMR assignment of proteins using 13C- and 15N-resolved 3D [1H,1H]-NOESY
... first assignment phase, only 1 H atoms are assigned for which the resonance frequency of the cova- lently bound heavy atom was present in the ...acid side-chain atoms are being ...covalently ...
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Cyclic peptides bearing a side-chain tail: A tool to model the structure and reactivity of protein zinc sites.
... total protein number) the number of human proteins possessing a tetracysteinate zinc ...the protein chain in a conformation suitable to its binding to ...repair protein Ada [3] and various ...
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Automatic assignment of protein backbone resonances by direct spectrum inspection in targeted acquisition of NMR data
... resonance assignment using pre-recorded and MDD-reconstructed spectra at various percentages of sampled time domain grid (sets 1–13 in ...the protein sample. After a suitable schedule of acquisition and ...
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APSY-NMR with proteins: practical aspects and backbone assignment
... Selection of the number of projections Choosing a minimal number of projections for a given experiment is important whenever it is of overriding interest to collect an informative data set with minimal measurement time. ...
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An Error Bound Based on a Worst Likely Assignment
... The bound process in the previous section rejects assignments a for which E(a, S*) is abnormally high among errors E(a, S) over subsets S of {1, ...each assignment a, the process is equivalent to ranking ...
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Supply-Side Policies and the Zero Lower Bound
... Fortunately, these countries also have a su¢ cient number of “low-hanging fruits”in terms of supply-side reforms. Anyone familiar with the deep inadequacies of the Spanish labor market or with the regulations in ...
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Supply-side policies and the zero lower bound
... Fortunately, these countries also have a su¢ cient number of “low-hanging fruits”in terms of supply-side reforms that can be easily snatched. Anyone even vaguely familiar with the deep inadequacies of the Spanish ...
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Supply-Side Policies and the Zero Lower Bound
... Fortunately, these countries also have a su¢ cient number of “low-hanging fruits”in terms of supply-side reforms that can be easily snatched. Anyone even vaguely familiar with the deep inadequacies of the Spanish ...
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Quantifying and Controlling Semiconducting Polymer Side Chain and Backbone Ordering to Study Charge Transport and Improve Field Effect Transistor Performance.
... the side chains crystallize with the alkyl chain axes oriented predominantly in the out-of-plane direction, though there is some ambiguity about the exact tilt angles due to chain branching and some ...
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Backbone flexibility in protein design theory and experiment
... Coupling Backbone Flexibility and Amino Acid Sequence Selection in Protein Design... Cambridge Univcrsily Press.[r] ...
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