Uncovering allosteric pathways in caspase-1 with Markov transient analysis and multiscale community detection [PDF]
Mol Biosyst. 2014 Aug;10(8):2247-58, 2014 Allosteric regulation at distant sites is central to many cellular processes. In particular, allosteric sites in proteins are a major target to increase the range and selectivity of new drugs, and there is a need for methods capable of identifying intra-molecular signalling pathways leading to allosteric effects.
arxiv +1 more source
The Speed of Allosteric Signaling Within a Single-Domain Protein [PDF]
arXiv, 2021 While much is known about different allosteric regulation mechanisms, the nature of the "allosteric signal", and the timescale on which it propagates, remains elusive. The PDZ3 domain from postsynaptic density-95 protein is a small protein domain with a terminal third alpha helix -- the $\alpha$3-helix, which is known to be allosterically active.
arxiv
PASSerRank: Prediction of Allosteric Sites with Learning to Rank [PDF]
arXiv, 2023 Allostery plays a crucial role in regulating protein activity, making it a highly sought-after target in drug development. One of the major challenges in allosteric drug research is the identification of allosteric sites. In recent years, many computational models have been developed for accurate allosteric site prediction.
arxiv
Prediction of protein allosteric signalling pathways and functional residues through paths of optimised propensity [PDF]
arXiv, 2022 Allostery commonly refers to the mechanism that regulates protein activity through the binding of a molecule at a different, usually distal, site from the orthosteric site. The omnipresence of allosteric regulation in nature and its potential for drug design and screening render the study of allostery invaluable.
arxiv
Molecular Characterization of Ebselen Binding Activity to SARS-CoV-2 Main Protease [PDF]
arXiv, 2020 The Coronavirus Disease (COVID-19) pandemic caused by the SARS-coronavirus 2 (SARS-CoV-2) urgently calls for the design of drugs directed against this new virus. Given its essential role in proteolytic processing, the main protease Mpro has been identified as an attractive candidate for drugs against SARS-CoV-2 and similar coronaviruses.
arxiv
Information propagation in time through allosteric signaling [PDF]
Phys. Rev. Research 2, 023367 (2020), 2019 Naively, one expects the information communicated by an enzyme downstream within a signaling network, in which the enzyme is embedded, to grow monotonically with the enzyme's rate of product formation. However, here we observe that this does not necessarily hold true for allosterically regulated enzymes, often observed in signaling networks.
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Medium dependence of asphaltene agglomeration inhibitor efficiency [PDF]
Energy & Fuels vol.22, 2008, pp 1917 - 1922;, 2007 Applying chemical additives (molecule inhibitors or dispersants) is one of the common ways to control asphaltene agglomeration and precipitation. However, it is not clear why at some conditions the synthetic flocculation inhibitors as well as resins not only do not inhibit the asphaltene agglomeration,, they may also promote it, and why the increasing ...
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Biological and structural analysis of new potent Integrase-LEDGF allosteric HIV-1 inhibitors [PDF]
, 2023 Erwann Le Rouzic +11 more
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Combining Alchemical Transformation with Physical Pathway to Accurately Compute Absolute Binding Free Energy [PDF]
arXiv, 2018 We present a new method that combines alchemical transformation with physical pathway to accurately and efficiently compute the absolute binding free energy of receptor-ligand complex. Currently, the double decoupling method (DDM) and the potential of mean force approach (PMF) methods are widely used to compute the absolute binding free energy of ...
arxiv
Ligand Binding, Protein Fluctuations, and Allosteric Free Energy [PDF]
, 2006 Although the importance of protein dynamics in protein function is generally recognized, the role of protein fluctuations in allosteric effects scarcely has been considered. To address this gap, the Kullback-Leibler divergence (Dx) between protein conformational distributions before and after ligand binding was proposed as a means of quantifying ...
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