Problem of Domain/Building Block Preservation in the Evolution of Biological Macromolecules and Evolutionary Computation

Authors: Spirov, A.V., Myasnikova, E.M.

Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics IEEE/ACM Trans. Comput. Biol. and Bioinf. Computational Biology and Bioinformatics, IEEE/ACM Transactions on. 20(2):1345-1362 Apr, 2023

Extensions of Royal Road Functions for Use in SELEX in silico

Authors: Myasnikova, Ekaterina, Spirov, Alexander

Source: 2021 17th International Asian School-Seminar "Optimization Problems of Complex Systems (OPCS) School-Seminar "Optimization Problems of Complex Systems (OPCS), 2021 17th International Asian. :60-64 Sep, 2021

Relation: 2021 17th International Asian School-Seminar "Optimization Problems of Complex Systems (OPCS)

Transfer of Genetic Algorithms to Directed Evolution of Macromolecules: Tests in Silico

Authors: Myasnikova, Ekaterina, Spirov, Alexander

Source: 2020 Cognitive Sciences, Genomics and Bioinformatics (CSGB) Cognitive Sciences, Genomics and Bioinformatics (CSGB), 2020. :297-300 Jul, 2020

Relation: 2020 Cognitive Sciences, Genomics and Bioinformatics (CSGB)

Creation of sequence-regulating polyhydroxyalkanoate (PHA) synthases with improved thermostability using a full consensus design for the biosynthesis of 2-hydroxyalkanoate-based PHA block copolymers

Authors: Furukawa, Shoko ^a, Nakagawa, Naoya ^a, Hachisuka, Shin-ichi ^b, Nakano, Shogo ^{c, ⁎}, Tomita, Hiroya ^{b, 1}, Kikukawa, Hiroshi ^b, Matsumoto, Ken'ichiro ^{b, ⁎}

Source: In Polymer Degradation and Stability June 2025 236

Evolution of chemistry and selection technology for DNA-encoded library

Authors: Peixiang Ma, Shuning Zhang, Qianping Huang, Yuang Gu, Zhi Zhou, Wei Hou, Wei Yi, Hongtao Xu

Source: Acta Pharmaceutica Sinica B, Vol 14, Iss 2, Pp 492-516 (2024)

Subject Terms: DNA-encoded library, Drug discovery, High-throughput selection, DNA-compatible synthesis, In vitro evolution, Chemical central dogma, Therapeutics. Pharmacology, RM1-950

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211383523003842; https://doaj.org/toc/2211-3835

Access URL: https://doaj.org/article/a774b54beb824f15ac80634d4103ed28

Predicting Plasmodium drug resistance through in vitro evolution

Authors: Cui, Liwang ^{1, ⁎}

Source: In Trends in Parasitology March 2025 41(3):170-171

Genotype-to-Protein Map and Collective Adaptation in a Viral Population

Authors: Ariadna Villanueva, Henry Secaira-Morocho, Luis F. Seoane, Ester Lázaro, Susanna Manrubia

Source: Biophysica, Vol 2, Iss 4, Pp 381-399 (2022)

Subject Terms: genotype–phenotype map, viral quasispecies, deep sequencing, phenotypic bias, non-silent mutations, in vitro evolution, Biology (General), QH301-705.5

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Relation: https://www.mdpi.com/2673-4125/2/4/34; https://doaj.org/toc/2673-4125

Access URL: https://doaj.org/article/fc7b7520f13946bbbe643fd3f8bd77c0

Bacillus thuringiensis Toxins: Functional Characterization and Mechanism of Action

Contributors: Bel, Yolanda, Ferré, Juan, Hernández-Martínez, Patricia

Subject Terms: Bacillus thuringiensis, Plutella xylostella, Cry1Ac resistance, trypsin-like midgut protease, protoxin activation, Spodoptera spp., Helicoverpa armigera, Mamestra brassicae, Anticarsia gemmatalis, Ostrinia furnacalis, Cry2Ab toxin, Bombyx mori, ATP-binding cassette subfamily a member 2 (ABCA2), genome editing, transcription activator-like effector-nucleases (TALENs), HEK293T cell, functional receptor, Vip3Aa, lysosome, mitochondria, apoptosis, Sf9 cells, Cry1Ab, oligomer formation, Sf21 cell line, Ostrinia nubilalis, Lobesia botrana, Leptinotarsa decemlineata, bioassay, Cyt2Aa2 toxin, protein-lipid binding, erythrocyte membrane, AFM, QCM-D, Asian corn borer, ABCC2, CRISPR/Cas9, Cry1Fa, resistance, chitin-binding protein, adhesion, peritrophic matrix, Vip3A, Spodoptera litura, site-directed mutagenesis, Cry, Cyt, parasporins, S-layer proteins, Vip, Sip, membrane receptors, insecticidal activity, anticancer activity, Aedes aegypti, minor proteins, synergy, mosquito control, Bti, Spodoptera frugiperda, cadherin, mode of action of Cry toxin, insecticidal proteins, insect resistance, tobacco budworm, Bacillus thuringiensis proteins, coleopteran pests, structure, mode of action, 3D-structure, biological control, antimicrobial peptide, gut microbiota, vegetative insecticidal proteins, pyramids, 3D-Cry toxins, in vitro evolution, rational design, toxin enhancement, Research and information: general

File Description: image/jpeg

Access URL: https://directory.doabooks.org/handle/20.500.12854/77019
https://mdpi.com/books/pdfview/book/4629

Editorial: Molecular evolution: You learn from your mistakes

Authors: Marco Fantini, Edoardo Sarti, Gian Gaetano Tartaglia, Annalisa Pastore

Source: Frontiers in Molecular Biosciences, Vol 9 (2022)

Subject Terms: molecular evolution, mutagenesis, in vitro evolution, evolutionary biology, structural biology, mutational data analysis, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmolb.2022.985289/full; https://doaj.org/toc/2296-889X

Access URL: https://doaj.org/article/7854a09bbb8f4fbaa6b0af99ad26b3c2

Chapter 3 - Monoclonal antibody generation by phage display: history, state-of-the-art, and future

Authors: Hentrich, Christian, Ylera, Francisco, Frisch, Christian, Knappik, Achim

Source: In Handbook of Immunoassay Technologies Edition: Second Edition. 2025:45-82

Emergence and diversification of a host-parasite RNA ecosystem through Darwinian evolution

Authors: Taro Furubayashi, Kensuke Ueda, Yohsuke Bansho, Daisuke Motooka, Shota Nakamura, Ryo Mizuuchi, Norikazu Ichihashi

Source: eLife, Vol 9 (2020)

Subject Terms: artificial cell, RNA replication system, self-replication system, in vitro evolution, coevolution, molecular parasite, Medicine, Science, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://elifesciences.org/articles/56038; https://doaj.org/toc/2050-084X

Access URL: https://doaj.org/article/5567fa67fd06459c808be83faa1739d7

Creation of the First Anomeric D/L-Sugar Kinase by Means of Directed Evolution

Authors: Hoffmeister, Dirk, Yang, Jie, Liu, Lesley, Thorson, Jon S.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2003 Nov 01. 100(23), 13184-13189.

Access URL: https://www.jstor.org/stable/3148114

Two inhibitors of yeast plasma membrane ATPase 1 (ScPma1p): toward the development of novel antifungal therapies

Authors: Sabine Ottilie, Gregory M. Goldgof, Andrea L. Cheung, Jennifer L. Walker, Edgar Vigil, Kenneth E. Allen, Yevgeniya Antonova-Koch, Carolyn W. Slayman, Yo Suzuki, Jacob D. Durrant

Source: Journal of Cheminformatics, Vol 10, Iss 1, Pp 1-9 (2018)

Subject Terms: Antifungal, PMA1, P-type ATPase, Computer modeling, Saccharomyces cerevisiae, In vitro evolution, Information technology, T58.5-58.64, Chemistry, QD1-999

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s13321-018-0261-3; https://doaj.org/toc/1758-2946

Access URL: https://doaj.org/article/fd41685e74f3424eaaeab6152fd0de81

Functional and Nonfunctional Mutations Distinguished by Random Recombination of Homologous Genes

Authors: Zhao, Huimin, Arnold, Frances H.

Source: Proceedings of the National Academy of Sciences of the United States of America, 1997 Jul . 94(15), 7997-8000.

Access URL: https://www.jstor.org/stable/42795

Can Principles of Evolution and Ecology be Applied to the Problem of HIV Infection/AIDS?

Authors: Powell, Paul D.

Source: Biodiversity Letters, 1996 Jan 01. 3(1), 14-17.

Access URL: https://www.jstor.org/stable/2999705

Low-stringency selection of TEM1 for BLIP shows interface plasticity and selection for faster binders

Authors: Cohen-Khait, Ruth, Schreiber, Gideon

Source: Proceedings of the National Academy of Sciences of the United States of America, 2016 Dec . 113(52), 14982-14987.

Access URL: https://www.jstor.org/stable/26473015

Amplification of RNA by an RNA polymerase ribozyme

Authors: Horning, David P., Joyce, Gerald F.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2016 Aug . 113(35), 9786-9791.

Access URL: https://www.jstor.org/stable/26471704

Making 3D-Cry Toxin Mutants: Much More Than a Tool of Understanding Toxins Mechanism of Action

Authors: Susana Vílchez

Source: Toxins, Vol 12, Iss 9, p 600 (2020)

Subject Terms: 3D-Cry toxins, in vitro evolution, rational design, Bacillus thuringiensis, toxin enhancement, Medicine

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Relation: https://www.mdpi.com/2072-6651/12/9/600; https://doaj.org/toc/2072-6651

Access URL: https://doaj.org/article/098aff8d90ca485583fad281686000a9

Drugs Based on de novo-developed Peptides are Coming of Age

Authors: Kaycie Deyle, Christian Heinis

Source: CHIMIA, Vol 72, Iss 6 (2018)

Subject Terms: Cyclic peptide, Drug development, In vitro evolution, Peptide, Phage display, Protein epitope mimetics, Chemistry, QD1-999

File Description: electronic resource

Relation: https://www.chimia.ch/chimia/article/view/1456; https://doaj.org/toc/0009-4293; https://doaj.org/toc/2673-2424

Access URL: https://doaj.org/article/5bbcd6b7adeb4d05a73aab361cebc462

Nucleic Acid Enzymes: Playing with a Fuller Deck

Authors: Joyce, Gerald F.

Source: Proceedings of the National Academy of Sciences of the United States of America, 1998 May . 95(11), 5845-5847.

Access URL: https://www.jstor.org/stable/45295