Conformational dynamics of capping protein and interaction partners : simulation studies by Wales, David., Verma, Chandra S., Lukman, Suryani., Robinson, Robert C.

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Ab initio folding of extended α-helix : a theoretical study about the role of electrostatic polarization in the folding of helical structures by Lazim, Raudah, Wei, Caiyi, Sun, Tiedong, Zhang, Dawei

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Computational studies of protein helix kinks by Wilman, H, Henry Wilman

“…<p>Kinks are functionally important structural features found in the alpha-helices of many proteins, particularly membrane proteins. Structurally, they are points at which a helix abruptly changes direction. …”

Novel cation-π interaction revealed by crystal structure of thermoalkalophilic lipase by Matsumura, Hiroyoshi, Yamamoto, Takahiko, Leow, Thean Chor, Mori, Tadashi, Salleh, Abu Bakar, Basri, Mahiran, Inoue, Tsuyoshi, Kai, Yasushi, Raja Abdul Rahman, Raja Noor Zaliha

Multiple sequence analysis in the presence of alignment uncertainty by Herman, J, Joseph Herman

“…In order to extend the range of applicability of this approach, the first chapter of this thesis introduces a probabilistic evolutionary model for protein structures on a phylogenetic tree; since protein structures typically diverge much more slowly than sequences, this allows for more reliable detection of remote homologies, improving the accuracy of the resulting alignments and trees, and reducing sensitivity of the results to the choice of dataset. …”

Microbial enzymes: from earth to space by Raja Abd. Rahman, Raja Noor Zaliha

“…One of the most widely used methods in studying protein structures is crystallography which can provide an insight into the protein structures and functions from global folds to the atomic details of bonding. …”
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Discovering putative protein targets of small molecules : a study of the p53 activator Nutlin by Nguyen, Minh N., Sen, Neeladri, Lin, Meiyin, Joseph, Thomas Leonard, Vaz, Candida, Tanavde, Vivek, Way, Luke, Hupp, Ted, Verma, Chandra Shekhar, Madhusudhan, M. S.

“…We next mined the protein structural database (PDB) for putative binding pockets in other human protein structures that were similar in shape to the Nutlin pocket in MDM2 using our topology-independent structural superimposition tool CLICK. …”
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Molecular mechanisms and design principles for promiscuous inhibitors to avoid drug resistance: Lessons learned from HIV-1 protease inhibition by Shen, Yang, Radhakrishnan, Mala L., Tidor, Bruce

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Interplay between membrane curvature and protein conformational equilibrium investigated by solid-state NMR by Liao, Shu Y., Lee, Myungwoon, Hong, Mei

“…These results highlight the indispensable role of solid-state NMR to simultaneously determine membrane protein structures and characterize the membrane curvature in which these protein structures exist. ©2019…”
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Computational studies of structural motifs and cotranslational folding mechanisms in membrane and soluble proteins by Law, E

“…In this thesis I investigated two aspects of alpha-helical membrane protein structures.</p> <p>Firstly, I investigated kinks in alpha-helices, many of which are thought to have functional roles. …”

Protein modeling, ligand-protein docking, and visualization by Lu, Bai Fang

“…With more and more protein structures being identified, as well as rapid developments in the pharmaceutical industry, computational biology is increasinglyplaying a vital role in biological data retrieval, analysis, and visualization. …”
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Learning feature representation for subgraphs by Zhang, Linghan

“…They are widely used in representing data like social networks, chemical compound, protein structures. Analytical tasks against graph data attracted great attention in many domains. …”
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Molecular dynamics simulations of membrane proteins. by Biggin, P, Bond, P

“…Membrane protein structures are underrepresented in the Protein Data Bank (PDB) because of difficulties associated with expression and crystallization. …”

Data-driven computational protein design by Frappier, Vincent, Keating, Amy E.

“…We present recent creative uses of multiple-sequence alignments, protein structures, and high-throughput functional assays in computational protein design. …”
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Monitoring protein interactions and dynamics with solvatochromic fluorophores by Loving, Galen S., Sainlos, Matthieu, Imperiali, Barbara

“…These dyes have been exploited in applications ranging from the study of protein structural dynamics to the detection of protein-binding interactions. …”
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Towards a Prime Factorization of Proteins by Radev, Simeon

“…The further development of this work could lead to a greater understanding of the organizational complexity of natural phenomena, and in particular, as it relates to the uniquely complex relationship between protein structures and their function.…”
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Protein language models are performant in structure-free virtual screening by Lam, Hilbert Yuen In, Guan, Jia Sheng, Ong, Xing Er, Pincket, Robbe, Mu, Yuguang

“…The implications thereof include highly expedited VS due to the greatly reduced compute required to run this model, and the ability to perform early stages of computer-aided drug design in the complete absence of 3D protein structures.…”
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Stochastic model for protein flexibility analysis by Xia, Kelin, Wei, Guo-Wei

“…The essential idea is to analyze the free induction decay of a perturbed protein structural probability, which satisfies the master equation. …”
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Lipid interaction sites on channels, transporters and receptors: recent insights from molecular dynamics simulations by Sansom, M, Hedger, G

“…Molecular dynamics simulations provide a powerful tool for the identification of these sites, complementing advances in membrane protein structural biology and biophysics. We describe recent notable biomolecular simulation studies which have identified lipid interaction sites on a range of different membrane proteins. …”

Insights into protein kinase regulation and inhibition by large scale structural comparison. by Eswaran, J, Knapp, S

“…Protein structure determination of soluble globular protein domains has developed into an efficient routine technology which can now be applied to generate and analyze structures of entire human protein families. …”