A new parameter‐rich structure‐aware mechanistic model for amino acid substitution during evolution-Reference-Cited by-同舟云学术

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A new parameter‐rich structure‐aware mechanistic model for amino acid substitution during evolution

Published:2017-12-12 Issue:2 Volume:86 Page:218-228
ISSN:0887-3585
Container-title:Proteins: Structure, Function, and Bioinformatics
language:en
Short-container-title:Proteins

Author:

Chi Peter B.¹²,Kim Dohyup³,Lai Jason K.³,Bykova Nadia³⁴,Weber Claudia C.¹,Kubelka Jan⁵,Liberles David A.¹³^ORCID

Affiliation:

1. Department of Biology and Center for Computational Genetics and GenomicsTemple UniversityPhiladelphia Pennsylvania19122

2. Department of Mathematics and Computer ScienceUrsinus CollegeCollegeville Pennsylvania19426

3. Department of Molecular BiologyUniversity of WyomingLaramie Wyoming82071

4. Faculty of Bioengineering and BioinformaticsMoscow State UniversityMoscow119234 Russia

5. Department of ChemistryUniversity of WyomingLaramie Wyoming82071

Funder

Division of Biological Infrastructure

Publisher

Wiley

Subject

Molecular Biology,Biochemistry,Structural Biology

Link

https://onlinelibrary.wiley.com/doi/pdf/10.1002/prot.25429

Reference40 articles.

1. State-of the art methodologies dictate new standards for phylogenetic analysis

2. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods

3. Amino acid coevolution induces an evolutionary Stokes shift

4. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation

5. A statistical mechanical method to optimize energy functions for protein folding

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1. Artificial intelligence for template-free protein structure prediction: a comprehensive review;Artificial Intelligence Review;2022-12-17

2. A review of visualisations of protein fold networks and their relationship with sequence and function;Biological Reviews;2022-10-09

3. Unattained geometric configurations of secondary structure elements in protein structural space;Journal of Structural Biology;2022-09

4. Ancestral Sequence Reconstruction: From Chemical Paleogenetics to Maximum Likelihood Algorithms and Beyond;Journal of Molecular Evolution;2021-01-24

5. Detecting Signatures of Positive Selection against a Backdrop of Compensatory Processes;Molecular Biology and Evolution;2020-07-06

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