Results 41 to 50 of about 83,323 (258)

Pairwise alignment incorporating dipeptide covariation

, 2005
Motivation: Standard algorithms for pairwise protein sequence alignment make the simplifying assumption that amino acid substitutions at neighboring sites are uncorrelated.
Altschul, Altschul, Altschul, Altschul, Bailey, Bishop, Brenner, Cline, Crooks, DOOLITTLE, Frith, Fukami-Kobayashi, G. E. Crooks, Goldman, Gonnet, Henikoff, Henikoff, Jung, Karplus, Lin, Muller, Murzin, Park, Pearson, R. E. Green, RODIONOV, S. E. Brenner, Sander, Smith, Thorne, Thorne, Thorne, Topham, Weiss, Zachariah   +34 more
core   +1 more source

Estimation of the infinitesimal generator by square-root approximation [PDF]

, 2017
For the analysis of molecular processes, the estimation of time-scales, i.e., transition rates, is very important. Estimating the transition rates between molecular conformations is -- from a mathematical point of view -- an invariant subspace projection
Donati, Luca, Heida, Martin, Keller, Bettina G., Weber, Marcus   +3 more
core   +3 more sources

Sequence‐Modulated Active Tripeptide Condensates for Tandem Catalysis

Angewandte Chemie, EarlyView.
Sequence‐modulated tripeptide coacervates mimic biomolecular condensates with controllable, enzyme‐regulated phase separation. They co‐sequester hydrophobic active species and hydrophilic enzymes, enabling tandem catalysis in aqueous media. Incorporated into artificial cells, they function as adaptive sub‐organelles, orchestrating compartmentalized ...
Hao Han, Siyu Song, Jianqiang Wang, Tsvetomir Ivanov, Dongdong Zhou, Hao Su, Katharina Landfester, Shoupeng Cao   +7 more
wiley   +2 more sources

Proteogenic Dipeptides Are Characterized by Diel Fluctuations and Target of Rapamycin Complex-Signaling Dependency in the Model Plant Arabidopsis thaliana

Frontiers in Plant Science, 2021
As autotrophic organisms, plants capture light energy to convert carbon dioxide into ATP, nicotinamide adenine dinucleotide phosphate (NADPH), and sugars, which are essential for the biosynthesis of building blocks, storage, and growth.
Maria Juliana Calderan-Rodrigues, Marcin Luzarowski, Carolina Cassano Monte-Bello, Romina I. Minen, Boris M. Zühlke, Boris M. Zühlke, Zoran Nikoloski, Zoran Nikoloski, Aleksandra Skirycz, Aleksandra Skirycz, Camila Caldana   +10 more
doaj   +1 more source

Enhanced sampling of multidimensional free-energy landscapes using adaptive biasing forces

, 2010
We propose an adaptive biasing algorithm aimed at enhancing the sampling of multimodal measures by Langevin dynamics. The underlying idea consists in generalizing the standard adaptive biasing force method commonly used in conjunction with molecular ...
Chipot, Chris, Lelièvre, Tony
core   +3 more sources

The Role of Chemistry Across Disciplines From Humanities to Life Sciences in Understanding Complexity and Emergence

Angewandte Chemie, EarlyView.
This study explores the origins of life by linking prebiotic chemistry, the emergence of information‐carrying molecules such as RNA and proteins, and philosophical questions about consciousness. The study emphasizes the role of molecular evolution in the Central Dogma and provides insights into the chemical origins of biology and the basis of life's ...
Harald Schwalbe, Josef Wachtveitl, Alexander Heckel, Florian Buhr, Sabrina Toews, Thomas M. Schimmer   +5 more
wiley   +2 more sources

Surfactant-Assisted Assembly of Dipeptide Forming a Broom-like Structure

Molecules, 2022
Understanding the influence of surfactants on the assembly of peptides has a considerable practical motivation. In this paper, we systematically study the anionic surfactant-assisted assembly of diphenylalanine (FF).
Yunping Wei, Jie Zhang, Xingcen Liu
doaj   +1 more source

Unfolding Hidden Barriers by Active Enhanced Sampling

, 2017
Collective variable (CV) or order parameter based enhanced sampling algorithms have achieved great success due to their ability to efficiently explore the rough potential energy landscapes of complex systems.
Chen, Ming, Zhang, Jing
core   +1 more source

The early expansion and evolutionary dynamics of POU class genes. [PDF]

, 2014
The POU genes represent a diverse class of animal-specific transcription factors that play important roles in neurogenesis, pluripotency, and cell-type specification. Although previous attempts have been made to reconstruct the evolution of the POU class,
Gates, Ruth D, Gold, David A, Jacobs, David K   +2 more
core   +1 more source

Redefining Therapies for Drug‐Resistant Tuberculosis: Synergistic Effects of Antimicrobial Peptides, Nanotechnology, and Computational Design

Advanced Healthcare Materials, EarlyView.
Antimicrobial peptide (AMP)‐loaded nanocarriers provide a multifunctional strategy to combat drug‐resistant Mycobacterium tuberculosis. By enhancing intracellular delivery, bypassing efflux pumps, and disrupting bacterial membranes, this platform restores phagolysosome fusion and macrophage function.
Christian S. Carnero Canales, Jessica Ingrid Marquez Cazorla, Renzo Marianito Marquez Cazorla, Aline Martins dos Santos, Jonatas Lobato Duarte, Letícia Oliveira Catarin Nunes, Túlio Custódio Reis, Lara Cerazi Salvador, Norival Alves Santos‐Filho, Rafael Miguel Sábio, Hélder A. Santos, Fernando Rogério Pavan   +11 more
wiley   +1 more source