Eigenvector Centrality Distribution for Characterization of Protein Allosteric Pathways [PDF]
, 2017 Determining the principal energy pathways for allosteric communication in biomolecules, that occur as a result of thermal motion, remains challenging due to the intrinsic complexity of the systems involved. Graph theory provides an approach for making sense of such complexity, where allosteric proteins can be represented as networks of amino acids.
arxiv +1 more source
Automatic Retrosynthetic Pathway Planning Using Template-free Models [PDF]
arXiv, 2019 We present an attention-based Transformer model for automatic retrosynthesis route planning. Our approach starts from reactants prediction of single-step organic reactions for given products, followed by Monte Carlo tree search-based automatic retrosynthetic pathway prediction.
arxiv
Design of elastic networks with evolutionary optimised long-range communication as mechanical models of allosteric proteins [PDF]
arXiv, 2017 Allosteric effects are often underlying the activity of proteins and elucidating generic design aspects and functional principles which are unique to allosteric phenomena represents a major challenge. Here an approach which consists in the in silico design of synthetic structures which, as the principal element of allostery, encode dynamical long-range
arxiv
Symmetry, Rigidity, and Allosteric Signaling: From Monomeric Proteins to Molecular Machines [PDF]
Chem. Rev. (2019) 119, 6788-6821, 2018 Allosteric signaling in biological molecules, which may be viewed as specific action at a distance due to localized perturbation upon binding of ligands or changes in environmental cues, is pervasive in biology. Phenomenological MWC and KNF models galvanized research for over five decades, and these models continue to be the basis for describing the ...
arxiv
Classification of Tangle Solutions for Integrases, A Protein Family that Changes DNA Topology [PDF]
arXiv, 2005 Integrase proteins acting on circular double-stranded DNA often change its topology by transforming unknotted circles into torus knots and links. Two systems of tangle equations--corresponding to the two initial DNA sequences--arise when modelling this transformation: direct and inverted.
arxiv
Allosteric Communication Pathways and Thermal Rectification in PDZ-2 Protein: A Computational Study [PDF]
arXiv, 2014 Allosteric communication in proteins is a central and yet unsolved problem of structural biochemistry. Previous findings, from computational biology (Ota and Agard, 2005), have proposed that heat diffuses in a protein through cognate protein allosteric pathways.
arxiv
Topological characterization of the continuum of allosteric response [PDF]
arXivAllosteric regulation in proteins is often accompanied by conformational changes that facilitate transmission of mechanical signals between distant ligand binding sites. Typically, these deformations are classified in terms of specific archetypes, including various types of hinge mechanisms or allosteric pathways localized to sequences of amino acids ...
arxiv
Allosteric HIV-1 integrase inhibitors promote aberrant protein multimerization by directly mediating inter-subunit interactions: Structural and thermodynamic modeling studies [PDF]
, 2016 Nanjie Deng +7 more
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Designing complex behaviors using transition-based allosteric self-assembly [PDF]
arXivAllosteric interactions occur when binding at one part of a complex affects the interactions at another part. Allostery offers a high degree of control in multi-species processes, and these interactions play a crucial role in many biological and synthetic contexts.
arxiv
The Competitive Interplay between Allosteric HIV-1 Integrase Inhibitor BI/D and LEDGF/p75 during the Early Stage of HIV-1 Replication Adversely Affects Inhibitor Potency [PDF]
, 2016 Lei Feng +13 more
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