SAM and protein side chain orientation
Protein Side Chain Modeling with Orientation-Dependent Atomic Force Fields Derived by Series Expansions
... a protein, can be decomposed as a mathematical ...relative orientation of two residues and increased the discrimination power in fold ...non-native side-chain conformations and by minimizing ...
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Protein contacts, inter-residue interactions and side-chain modelling.: protein contacts
... of side-chain positioning also shows strong divergences; SCWRL prediction gives only 55% of contacts in common with SC 4 ...with side chains repositioned by SCWRL could be done to know if these ...
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Flat-Bottom Strategy for Improved Accuracy in Protein Side-Chain Placements
... 3.2 Effects of Buried vs. Exposed Residues The percentage of exposed residues considered in section 3.1 is only 25% because crystallographic waters and solvents were included in the calculation. We consider this as the ...
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Protein side-chain placement: probabilistic inference and integer programming methods
... A.1 Side-chain placement The initial protein test set for the side-chain placement is presented in Table ...of side-chain torsion angles, and therefore have a larger num- ...
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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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SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures
... complete protein structure in order to identify or annotate functional sites that have been documented in other ...entire Protein Data Bank (18) for occurrences of a specific small amino acid ...
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A protocol for CABS-dock protein–peptide docking driven by side-chain contact information
... of protein–peptide complexes with the CABS-dock ...expected protein–pep- tide contacts into soft restraints, which enable extensive sampling of the peptide con- formational space in a large area around the ...
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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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IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank
... Nadzirin, N, Willett, P, Artymiuk, PJ and Firdaus-Raih, M (2013) IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank.[r] ...
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Side Chain Packing below the Fusion Peptide Strongly Modulates Triggering of the Hendra Virus F Protein
... (F) protein is required to initiate the conformational changes which drive membrane fusion, but the factors which control triggering remain poorly ...that side chain packing beneath the fusion ...
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Cyclic peptides bearing a side-chain tail: A tool to model the structure and reactivity of protein zinc sites.
... To cite this version: Olivier S´ en` eque, Emilie Bourl` es, Vincent Lebrun, Estelle Bonnet, Pascal Dumy, et al.. Cyclic peptides bearing a side-chain tail: A tool to model the structure and reactivity of ...
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Protein structure prediction with the 3D-HP side-chain model using a master–slave parallel genetic algorithm
... César Manuel Vargas Benítez · Heitor Silvério Lopes Received: 29 September 2009 / Accepted: 23 February 2010 / Published online: 24 April 2010 © The Brazilian Computer Society 2010 Abstract This work presents a ...
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Detection of Side Chain Rearrangements Mediating the Motions of Transmembrane Helices in Molecular Dynamics Simulations of G Protein-Coupled Receptors.
... of protein function. Protein structure is constantly fluctuating and undergoing conformational changes, which are captured by molecular dynamics (MD) ...how protein me- chanics emerge from side ...
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Recurring side-chain triads in monomeric enzymatic structures
... a protein chain for the recurrences of larger side-chain arrangements to take into account enzymatic structures with active sites of 4 and 5 ...the protein surface, rather than in the ...
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Recurring side-chain triads in monomeric enzymatic structures
... a protein chain for the recurrences of larger side-chain arrangements to take into account enzymatic structures with active sites of 4 and 5 ...the protein surface, rather than in the ...
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Optimization methods for side-chain positioning and macromolecular docking
... and side-chain conformations for ...the side-chains in the interface region between two proteins in the process of ...incorporating side- chain flexibility in docking provides ...
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Vibrational spectroscopy of deprotonated peptides containing an acidic side chain
... deprotonated side chain carboxylate receiving hydrogen bonds from the C-terminus acid, the N-terminus amine and one of the peptidic ...relative orientation of these two groups which creates intensity ...
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A Monte Carlo Method for Generating Side Chain Structural Ensembles
... Carlo side chain entropy (MC-SCE) method that uses a physical energy function inclusive of long-range electrostatics and hydrophobic poten- tial of mean force, coupled with both backbone varia- tions and a ...
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Side Chain Modifications To Improve Peptide Structure–Activity Relations
... the side-chain carboxylate of glutamic acid, rendering it prone to ...and protein sequencing with a broad substrate scope, including cleavage of bioactive peptides and mutated peptides with unnatural ...
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THE SIDE-CHAIN THEORY OF THE STRUCTURE OF THE GENE
... I n “quantitative” series of multiple allelomorphs which are interpreted to be due to varying numbers of one kind of episome, the mutation rates indicate that like episomes unite [r] ...
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