Results 1 to 10 of about 8,881,036 (200)

Modeling Sequence-Space Exploration and Emergence of Epistatic Signals in Protein Evolution [PDF]

Molecular Biology and Evolution, 2022
During their evolution, proteins explore sequence space via an interplay between random mutations and phenotypic selection. Here we build upon recent progress in reconstructing data-driven fitness landscapes for families of homologous proteins, to ...
Matteo Bisardi, Juan Rodríguez-Rivas, Francesco Zamponi   +2 more
exaly   +4 more sources

Percolation in protein sequence space. [PDF]

PLoS ONE, 2017
The currently known protein sequences are not distributed equally in sequence space, but cluster into families. Analyzing the cluster size distribution gives a glimpse of the large and unknown extant protein sequence space, which has been explored during
Patrick C F Buchholz, Silvia Fademrecht, Jürgen Pleiss   +2 more
doaj   +3 more sources

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. [PDF]

Nucleic Acids Res, 2022
The AlphaFold Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk) is an openly accessible, extensive database of high-accuracy protein-structure predictions.
Varadi M, Anyango S, Deshpande M, Nair S, Natassia C, Yordanova G, Yuan D, Stroe O, Wood G, Laydon A, Žídek A, Green T, Tunyasuvunakool K, Petersen S, Jumper J, Clancy E, Green R, Vora A, Lutfi M, Figurnov M, Cowie A, Hobbs N, Kohli P, Kleywegt G, Birney E, Hassabis D, Velankar S.   +26 more
europepmc   +2 more sources

Individualized VDJ recombination predisposes the available Ig sequence space. [PDF]

Genome Res, 2021
The process of recombination between variable (V), diversity (D), and joining (J) immunoglobulin (Ig) gene segments determines an individual’s naïve Ig repertoire, and consequently (auto)antigen recognition.
Slabodkin A, Chernigovskaya M, Mikocziova I, Akbar R, Scheffer L, Pavlović M, Bashour H, Snapkov I, Mehta BB, Weber CR, Gutierrez-Marcos J, Sollid LM, Haff IH, Sandve GK, Robert PA, Greiff V.   +15 more
europepmc   +2 more sources

Scalable protein design using optimization in a relaxed sequence space. [PDF]

Science
Machine learning (ML)–based design approaches have advanced the field of de novo protein design, with diffusion-based generative methods increasingly dominating protein design pipelines.
Frank C, Khoshouei A, Fuβ L, Schiwietz D, Putz D, Weber L, Zhao Z, Hattori M, Feng S, de Stigter Y, Ovchinnikov S, Dietz H.   +11 more
europepmc   +2 more sources

Multistate and functional protein design using RoseTTAFold sequence space diffusion. [PDF]

Nat Biotechnol
Protein denoising diffusion probabilistic models are used for the de novo generation of protein backbones but are limited in their ability to guide generation of proteins with sequence-specific attributes and functional properties.
Lisanza SL, Gershon JM, Tipps SWK, Sims JN, Arnoldt L, Hendel SJ, Simma MK, Liu G, Yase M, Wu H, Tharp CD, Li X, Kang A, Brackenbrough E, Bera AK, Gerben S, Wittmann BJ, McShan AC, Baker D.   +18 more
europepmc   +2 more sources

Structure-based machine-guided mapping of amyloid sequence space reveals uncharted sequence clusters with higher solubilities. [PDF]

Nat Commun, 2020
The amyloid conformation can be adopted by a variety of sequences, but the precise boundaries of amyloid sequence space are still unclear. The currently charted amyloid sequence space is strongly biased towards hydrophobic, beta-sheet prone sequences ...
Louros N, Orlando G, De Vleeschouwer M, Rousseau F, Schymkowitz J.   +4 more
europepmc   +2 more sources

Engineering orthogonal signalling pathways reveals the sparse occupancy of sequence space. [PDF]

Nature, 2019
Gene duplication is a common and powerful mechanism by which cells create new signalling pathways1,2, but recently duplicated proteins typically must become insulated from each other and from other paralogues to prevent unwanted crosstalk3.
McClune CJ, Alvarez-Buylla A, Voigt CA, Laub MT.   +3 more
europepmc   +2 more sources

The scale-free nature of protein sequence space. [PDF]

PLoS ONE, 2018
The sequence space of five protein superfamilies was investigated by constructing sequence networks. The nodes represent individual sequences, and two nodes are connected by an edge if the global sequence identity of two sequences exceeds a threshold ...
Patrick C F Buchholz, Catharina Zeil, Jürgen Pleiss   +2 more
doaj   +2 more sources

An Infinite System of Fractional Sturm–Liouville Operator with Measure of Noncompactness Technique in Banach Space

Mathematics, 2023
In the current contribution, an appropriate quantity connected to the space of all convergent sequences is provided and shown to be a measure of noncompactness in a Banach space.
Ahmed Salem, Hunida Malaikah, Eid Sayed Kamel   +2 more
doaj   +1 more source