Results 91 to 100 of about 6,883,088 (299)

Prospecting the protein design landscape

FEBS Letters, EarlyView.
This review outlines the current state of various protein design approaches. We discuss the current possibilities enabled by recently released tools, highlight future avenues to pursue in protein design, and underscore the crucial role of key databases and resources for successful protein design workflows.
Jakob R. Riccabona, Katharina T. Stonig, Jens Meiler, Clara T. Schoeder, Monica L. Fernández‐Quintero   +4 more
wiley   +1 more source

Accurate Reconstruction of Molecular Phylogenies for Proteins Using Codon and Amino Acid Unified Sequence Alignments (CAUSA) [PDF]

, 2011
Based on molecular clock hypothesis, and neutral theory of molecular evolution, molecular phylogenies have been widely used for inferring evolutionary history of organisms and individual genes.
Jingjie Hu, Yu Fu, Yue Zhao, Chandra Sekhar Pedamallu, Yingbo Niu, Shuang-yong Xu, Xiaolong Wang, Qi Wang   +7 more
core  

Objective Functions

, 2013
Multiple sequence alignment involves alignment of more than two sequences and is an NP-complete problem. Therefore, heuristic algorithms that use different criteria to find an approximation to the optimal solution are employed.
Haluk Doğan, Hasan H. Otu, Dogan, Haluk, Otu, Hasan H.   +3 more
core   +1 more source

OrthoSelect: a protocol for selecting orthologous groups in phylogenomics [PDF]

, 2009
Background: Phylogenetic studies using expressed sequence tags (EST) are becoming a standard approach to answer evolutionary questions. Such studies are usually based on large sets of newly generated, unannotated, and error-prone EST sequences from ...
Schreiber Fabian, Fabian Schreiber, Morgenstern Burkhard, Erpenbeck Dirk, Pik, Kerstin, Pick, Kerstin, Morgenstern, Burkhard, Kerstin Pick, Schreiber, Fabian, Wörheide, Gert, Erpenbeck, Dirk, Burkhard Morgenstern, Wörheide Gert, Gert Wörheide, Dirk Erpenbeck, Woerheide, Gert, Pick Kerstin   +16 more
core   +1 more source

The heterodimeric amino acid transporters (HAT) of the SLC7/SLC3 family: A structure−function relationships and relevance to human pathology

FEBS Letters, EarlyView.
Heterodimeric amino acid transporters consist of SLC7 and SLC3 family proteins arranged in a conserved structural organization. They regulate nutrient transport across cell membranes, supporting essential cellular functions. These transporters also contribute to xenobiotic/drug uptake and distribution.
Mariafrancesca Scalise, Tiziano Mazza, Raffaella Scanga, Lara Console, Michele Galluccio, Cesare Indiveri   +5 more
wiley   +1 more source

Numerical Encodings of Amino Acids in Multivariate Gaussian Modeling of Protein Multiple Sequence Alignments

Molecules, 2018
Residues in proteins that are in close spatial proximity are more prone to covariate as their interactions are likely to be preserved due to structural and evolutionary constraints.
Patrice Koehl, Henri Orland, Marc Delarue   +2 more
doaj   +1 more source

Leucine‐rich glioma inactivated 1 (LGI1) is a ganglioside‐binding protein

FEBS Letters, EarlyView.
Neuronal hyperexcitability associated with a decrease/absence of the extracellular protein LGI1 has been suggested to be primarily due to the downregulation of Kv1 channel expression. The molecular mechanisms underlying this decrease have not yet been elucidated.
Kévin Debreux, Christian Lévêque, Fodil Azzaz, Marion Sangiardi, Sarosh R Irani, Michael Seagar, Jacques Fantini, Oussama El Far   +7 more
wiley   +1 more source

Smaller is better: nanobodies meet NMR

FEBS Letters, EarlyView.
Nanobodies are single‐domain antigen‐binding fragments derived from camelid heavy chain antibodies. Their small size, high stability, and exceptional specificity make nanobodies uniquely useful probes for NMR studies of protein dynamics, transient conformational states, and protein–protein interactions.
Oleg Y. Dmitriev
wiley   +1 more source

A statistical score for assessing the quality of multiple sequence alignments

BMC Bioinformatics, 2006
Background Multiple sequence alignment is the foundation of many important applications in bioinformatics that aim at detecting functionally important regions, predicting protein structures, building phylogenetic trees etc.
Aittokallio Tero, Ahola Virpi, Vihinen Mauno, Uusipaikka Esa   +3 more
doaj   +1 more source

Membrane composition and thermodynamic identity as boundaries of life for synthetic cell research

FEBS Letters, EarlyView.
What makes a cell a cell? The boundary of a living cell is not just a wall. Read as a Markov blanket, the membrane separates internal from external states, generating identity and non‐equilibrium order. Can this identity be rebuilt from scratch in a synthetic cell?
Caterina Presutti, Bert Poolman
wiley   +1 more source