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22 papers · ranked by Valyu relevance

01
PPubMed29 Oct 2023
The Boltzmann distributions of molecular structures predict likely changes through random mutations
Nora S. Martin, Sebastian E. Ahnert
New folded molecular structures can only evolve after arising through mutations. This aspect is modeled using genotype-phenotype maps, which connect sequence changes through mutations to changes in molecular structures. Previous work has shown that the likelihood of appearing through mutations can differ by orders of…
85relevance
02
BbioRxiv22 Feb 2023
The Boltzmann distributions of folded molecular structures predict likely changes through random mutations
Nora S. Martin, Sebastian E. Ahnert
New folded molecular structures can only evolve after arising through mutations. This aspect is modelled using genotype-phenotype (GP) maps, which connect sequence changes through mutations to changes in molecular structures. Previous work has shown that the likelihood of appearing through mutations can differ by…
84relevance
03
PPubMed29 Aug 2007
Spectrum of disease-causing mutations in protein secondary structures
Sofia Khan, Mauno Vihinen
Background Most genetic disorders are linked to missense mutations as even minor changes in the size or properties of an amino acid can alter or prevent the function of the protein. Further, the effect of a mutation is also dependent on the sequence and structure context of the alteration. Results We investigated the…
77relevance
04
PPubMed9 Dec 2016
Alpha Helices Are More Robust to Mutations than Beta Strands Alpha Helices Are More Robust to Mutations than Beta Strands
György Abrusán, Joseph A. Marsh, Christine A. Orengo
The rapidly increasing amount of data on human genetic variation has resulted in a growing demand to identify pathogenic mutations computationally, as their experimental validation is currently beyond reach. Here we show that alpha helices and beta strands differ significantly in their ability to tolerate mutations…
77relevance
05
BbioRxiv9 Feb 2022
Very small spontaneous structural mutation rate in green algae
Matéo Léger-Pigout, Marc Krasovec
Structural mutations are very important in evolution and led to major innovations, but our knowledge of the spontaneous structural mutation rate is very limited. We so cannot have a complete view of the adaptive potential of species and new variant in a population without addressing this lack. Here, we used Illumina…
77relevance
06
AarXiv15 Oct 2015
Quantification of the effect of mutations using a global probability model of natural sequence variation
Thomas A. Hopf, John Ingraham, Frank J. Poelwijk, Michael Springer + 2 more
'Chris Sander' 'Debora S. Marks'] Modern biomedicine is challenged to predict the effects of genetic variation. Systematic functional assays of point mutants of proteins have provided valuable empirical information, but vast regions of sequence space remain unexplored. Fortunately, the mutation-selection process of…
74relevance
07
BbioRxiv14 Apr 2022
AlphaFold2 can predict single-mutation effects
John M. McBride, Konstantin Polev, Amirbek Abdirasulov, Vladimir Reinharz + 2 more
AlphaFold2 (AF) is a promising tool, but is it accurate enough to predict single mutation effects? Here, we report that the localized structural deformation between protein pairs differing by only 1-3 mutations – as measured by the effective strain – is correlated across 3,901 experimental and AF-predicted structures.…
74relevance
08
PPubMed10 Aug 2017
Mass & secondary structure propensity of amino acids explain their mutability and evolutionary replacements
Hugo J. Bohórquez, Carlos F. Suárez, Manuel E. Patarroyo
Why is an amino acid replacement in a protein accepted during evolution? The answer given by bioinformatics relies on the frequency of change of each amino acid by another one and the propensity of each to remain unchanged. We propose that these replacement rules are recoverable from the secondary structural trends of…
73relevance
09
AarXiv14 Apr 2022
AlphaFold2 can predict single-mutation effects
J. Michael McBride, Konstantin Polev, Amirbek Abdirasulov, Vladimir Reinharz + 2 more
'Vladimir Reinharz' 'Bartosz A. Grzybowski' 'Tsvi Tlusty'] AlphaFold2 (AF) is a promising tool, but is it accurate enough to predict single mutation effects? Here, we report that the localized structural deformation between protein pairs differing by only 1-3 mutations – as measured by the effective strain – is…
70relevance
10
PPubMed27 Aug 2009
Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations
Joke Reumers, Joost Schymkowitz, Fréderic Rousseau
Background Linking structural effects of mutations to functional outcomes is a major issue in structural bioinformatics, and many tools and studies have shown that specific structural properties such as stability and residue burial can be used to distinguish neutral variations and disease associated mutations. Results…
70relevance
11
AarXiv13 Oct 2015
Coevolutionary landscape inference and the context-dependence of mutations in beta-lactamase TEM-1
Matteo Figliuzzi, Hervé Jacquier, Alexander Schug, Olivier Tenaillon + 1 more
'Martin Weigt'] The quantitative characterization of mutational landscapes is a task of outstanding importance in evolutionary and medical biology: It is, e.g., of central importance for our understanding of the phenotypic effect of mutations related to disease and antibiotic drug resistance. Here we develop a novel…
69relevance
12
AarXiv2023
Analysis of proteins in the light of mutations
Jorge A. Vila
Proteins have evolved through mutations—amino acid substitutions—since life appeared on Earth, some 109 years ago. The study of these phenomena has been of particular significance because of their impact on protein stability, function, and structure. Three of the most recent findings in these areas deserve to be…
66relevance
13
AarXiv1 Apr 2017
The Role of Evolutionary Selection in the Dynamics of Protein Structure Evolution
Amy I. Gilson, Ahmee Marshall-Christensen, Jeong‐Mo Choi, Eugene I. Shakhnovich
'Eugene I. Shakhnovich'] Homology modeling is a powerful tool for predicting a protein's structure. This approach is successful because proteins whose sequences are only 30% identical still adopt the same structure, while structure similarity rapidly deteriorates beyond the 30% threshold. By studying the divergence of…
66relevance
14
CchemRxiv11 Apr 2025
Structure-Based Discovery of a Cryptic Druggable Pocket in TP53 C238Y: Implications for Targeted Therapy
Authors not listed
SIMPLE SUMMARY TP53 gene is really important for keeping our cells healthy. It does this by fixing damaged DNA, managing cell growth, and telling cells to die if they're too damaged to repair. But when TP53 has mutations,these defenses stop working, and cells start growing out of control. One of the big problems in…
64relevance
15
CchemRxiv19 May 2025
Free energy calculations for protein design
Authors not listed
Free energy calculations have become invaluable in protein design, offering a powerful means to rapidly and accurately screen potential variants. Here, we provide a step-by-step protocol that combines molecular dynamics simulations with non-equilibrium alchemical free energy methods to tackle open questions in protein…
63relevance
16
CchemRxiv24 Feb 2022
How do the Mutations in PfK13 Protein Promote Anti-malarial Drug Resistance?
Shikha Sharma, Md. Ehesan Ali
Plasmodium falciparum develops resistance to artemisinin upon exposure to the anti-malarial drug. Various mutations in the Plasmodium falciparum Kelch13 (PfK13) protein such as Y493H, R539T, I543T, and C580Y have been associated with antimalarial drug resistance. (Ariey et al., Nature, 2014, 505, 50-55) These mutations…
63relevance
17
AarXiv2 Jan 2026
Evolutionary and Structural Constraints Define a Mutation-Resistant Catalytic Core in E. coli Serine Hydroxy methyltransferase (SHMT)
D. Surabhi Pandey, Dwipanjan Sanyal, Vladimir N. Uversky, Daniel C. Zielinski + 1 more
Serine hydroxymethyltransferase (SHMT) is an essential enzyme in the Escherichia coli folate pathway, yet it has not been adopted as an antibacterial target, unlike DHFR, DHPS, or thymidylate synthase. To investigate this discrepancy, we applied a multi-scale computational framework that integrates large-scale sequence…
63relevance
18
BbioRxiv6 Feb 2020
Large-scale *in silico* mutagenesis experiments reveal optimization of genetic code and codon usage for protein mutational robustness
Martin Schwersensky, Marianne Rooman, Fabrizio Pucci
The question of how natural evolution acts on DNA and protein sequences to ensure mutational robustness and evolvability has been asked for decades without definitive answer. We tackled this issue through a structurome-scale computational investigation, in which we estimated the change in folding free energy upon all…
62relevance
19
CchemRxiv8 Nov 2022
Tautomerisation Mechanisms in the Adenine-Thymine Nucleobase Pair During DNA Strand Separation
Benjamin King, Max Winokan, Paul Stevenson, Jim Al-Khalili + 2 more
The adenine-thymine tautomer (A-T) has previously been discounted as a spontaneous mutagenesis mechanism due to the energetic instability of the tautomeric configuration. We study the stability of A-T while the nucleobases undergo DNA strand separation. Our calculations indicate an increase in the stability of A-T as…
61relevance
20
BbioRxiv2 Dec 2025
ΦX174 bacteriophage viability predicted by protein biophysical modeling
James T. Van Leuven, Jagdish Suresh Patel, Casey Beard, F. Marty Ytreberg + 9 more
The relationship between genotype and phenotype underlies our ability to understand and predict evolution. Efforts to build genotype-phenotype (GP) maps have revealed several unifying rules: epistasis is pervasive, fitness effects are not normally distributed, and the GP map is non-linear and complicated for high-level…
61relevance
21
BbioRxiv28 Mar 2016
Divergence Model of Protein Evolution
Darrell O. Ricke
Analysis of the evolutionary conservation of amino acids is useful for the analysis of sequence variants detected in individuals with regard to possible impact on protein function. Rapid advances in DNA sequencing technologies are enabling affordable access to SNPs, exome sequencing, and whole genome shotgun…
59relevance
22
CchemRxiv25 Jan 2023
Molecular insights into the Stereospecificity of Arginine in RNA tetraloop folding
Amal Vijay, Arnab Mukherjee
One of the possible hypotheses for the homochirality of amino acids in the context of the origin of life is that only a particular stereoisomer provides preferential stability to RNA folding by acting as a chemical chaperon. This study probes into the molecular understanding of such preferential stability for a small…
50relevance

Results for structural mutation probability

The Boltzmann distributions of molecular structures predict likely changes through random mutations

The Boltzmann distributions of folded molecular structures predict likely changes through random mutations

Spectrum of disease-causing mutations in protein secondary structures

Alpha Helices Are More Robust to Mutations than Beta Strands Alpha Helices Are More Robust to Mutations than Beta Strands

Very small spontaneous structural mutation rate in green algae

Quantification of the effect of mutations using a global probability model of natural sequence variation

AlphaFold2 can predict single-mutation effects

Mass & secondary structure propensity of amino acids explain their mutability and evolutionary replacements

AlphaFold2 can predict single-mutation effects

Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations

Coevolutionary landscape inference and the context-dependence of mutations in beta-lactamase TEM-1

Analysis of proteins in the light of mutations

The Role of Evolutionary Selection in the Dynamics of Protein Structure Evolution

Structure-Based Discovery of a Cryptic Druggable Pocket in TP53 C238Y: Implications for Targeted Therapy

Free energy calculations for protein design

How do the Mutations in PfK13 Protein Promote Anti-malarial Drug Resistance?

Evolutionary and Structural Constraints Define a Mutation-Resistant Catalytic Core in E. coli Serine Hydroxy methyltransferase (SHMT)

Large-scale *in silico* mutagenesis experiments reveal optimization of genetic code and codon usage for protein mutational robustness

Tautomerisation Mechanisms in the Adenine-Thymine Nucleobase Pair During DNA Strand Separation

ΦX174 bacteriophage viability predicted by protein biophysical modeling

Divergence Model of Protein Evolution

Molecular insights into the Stereospecificity of Arginine in RNA tetraloop folding

The Boltzmann distributions of molecular structures predict likely changes through random mutations

The Boltzmann distributions of folded molecular structures predict likely changes through random mutations

Spectrum of disease-causing mutations in protein secondary structures

Alpha Helices Are More Robust to Mutations than Beta Strands Alpha Helices Are More Robust to Mutations than Beta Strands

Very small spontaneous structural mutation rate in green algae

Quantification of the effect of mutations using a global probability model of natural sequence variation

AlphaFold2 can predict single-mutation effects

Mass & secondary structure propensity of amino acids explain their mutability and evolutionary replacements

AlphaFold2 can predict single-mutation effects

Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations

Coevolutionary landscape inference and the context-dependence of mutations in beta-lactamase TEM-1

Analysis of proteins in the light of mutations

The Role of Evolutionary Selection in the Dynamics of Protein Structure Evolution

Structure-Based Discovery of a Cryptic Druggable Pocket in TP53 C238Y: Implications for Targeted Therapy

Free energy calculations for protein design

How do the Mutations in PfK13 Protein Promote Anti-malarial Drug Resistance?

Evolutionary and Structural Constraints Define a Mutation-Resistant Catalytic Core in E. coli Serine Hydroxy methyltransferase (SHMT)

Large-scale *in silico* mutagenesis experiments reveal optimization of genetic code and codon usage for protein mutational robustness

Tautomerisation Mechanisms in the Adenine-Thymine Nucleobase Pair During DNA Strand Separation

ΦX174 bacteriophage viability predicted by protein biophysical modeling

Divergence Model of Protein Evolution

Molecular insights into the Stereospecificity of Arginine in RNA tetraloop folding

Large-scale in silico mutagenesis experiments reveal optimization of genetic code and codon usage for protein mutational robustness

Large-scale in silico mutagenesis experiments reveal optimization of genetic code and codon usage for protein mutational robustness