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Simulating protein evolution in sequence and structure space

scientific article published on April 2004

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Europe PubMed Central

10 August 2017

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Simulating protein evolution in sequence and structure space (English)

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Europe PubMed Central

10 August 2017

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Michael Levitt

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Europe PubMed Central

10 August 2017

Yu Xia

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1 April 2004

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Europe PubMed Central

10 August 2017

Current Opinion in Structural Biology

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Europe PubMed Central

10 August 2017

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Europe PubMed Central

10 August 2017

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Europe PubMed Central

10 August 2017

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Europe PubMed Central

10 August 2017

Principles of protein folding--a perspective from simple exact models.

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Funnel-like organization in sequence space determines the distributions of protein stability and folding rate preferred by evolution

1 reference

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Structure space of model proteins: A principal component analysis

1 reference

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Predictions of gene family distributions in microbial genomes: evolution by gene duplication and modification

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Why are proteins so robust to site mutations?

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Design of a Novel Globular Protein Fold with Atomic-Level Accuracy

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Stability and the evolvability of function in a model protein

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Rational evolutionary design: The theory of in vitro protein evolution

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The frequency distribution of gene family sizes in complete genomes.

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Evolution of the protein repertoire

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Combinatorial and computational challenges for biocatalyst design

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11 October 2022

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Why are proteins marginally stable?

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11 October 2022

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Roles of mutation and recombination in the evolution of protein thermodynamics

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Modeling evolutionary landscapes: mutational stability, topology, and superfunnels in sequence space

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Evolution of digital organisms at high mutation rates leads to survival of the flattest

1 reference

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Evolution of functionality in lattice proteins

1 reference

11 October 2022

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Protein topology and stability define the space of allowed sequences.

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Spin glasses and the statistical mechanics of protein folding

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From structure to sequence and back again.

1 reference

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An in silico Exploration of the Neutral Network in Protein Sequence Space

1 reference

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Correlation between the conformation space and the sequence space of Peptide chain

1 reference

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Energy profile of the space of model protein sequences

1 reference

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Exploring protein sequence space using knowledge-based potentials.

1 reference

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De novo protein design. II. Plasticity in sequence space

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How are model protein structures distributed in sequence space?

1 reference

11 October 2022

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Are protein folds atypical?

1 reference

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The structure of the protein universe and genome evolution

1 reference

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Structurally constrained protein evolution: results from a lattice simulation

1 reference

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Selforganization of matter and the evolution of biological macromolecules

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Identifying proteins of high designability via surface-exposure patterns

1 reference

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Theory of protein folding

1 reference

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Modelling 'evo-devo' with RNA.

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Thoroughly sampling sequence space: large-scale protein design of structural ensembles

1 reference

11 October 2022

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Imprint of evolution on protein structures.

1 reference

11 October 2022

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The distribution of structures in evolving protein populations

1 reference

11 October 2022

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Emergence of highly designable protein-backbone conformations in an off-lattice model.

1 reference

11 October 2022

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Connectivity of Neutral Networks, Overdispersion, and Structural Conservation in Protein Evolution

1 reference

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Designability of alpha-helical proteins

1 reference

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Emergence of Preferred Structures in a Simple Model of Protein Folding

1 reference

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Theoretical studies of protein-folding thermodynamics and kinetics

1 reference

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Sequence optimization for native state stability determines the evolution and folding kinetics of a small protein

1 reference

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Expanding protein universe and its origin from the biological Big Bang

1 reference

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Natural selection of more designable folds: a mechanism for thermophilic adaptation

1 reference

11 October 2022

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Understanding hierarchical protein evolution from first principles 1 1Edited by J. Thornton

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Native protein sequences are close to optimal for their structures

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.SBI.2004.03.001

Lack of self-averaging in neutral evolution of proteins

1 reference

11 October 2022

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Structural determinant of protein designability

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.SBI.2004.03.001

Neutral evolution of model proteins: diffusion in sequence space and overdispersion

1 reference

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How evolution makes proteins fold quickly

1 reference

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Fold change in evolution of protein structures

1 reference

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The evolutionary landscape of functional model proteins

1 reference

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Continuity in evolution: on the nature of transitions

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Protein Evolution within a Structural Space

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Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix

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Exploring folding free energy landscapes using computational protein design.

1 reference

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NMR and temperature-jump measurements of de novo designed proteins demonstrate rapid folding in the absence of explicit selection for kinetics

1 reference

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The designability of protein structures

1 reference

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On the thermodynamic hypothesis of protein folding

1 reference

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Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model

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Recombinatoric exploration of novel folded structures: a heteropolymer-based model of protein evolutionary landscapes

1 reference

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Folding free energy function selects native-like protein sequences in the core but not on the surface

1 reference

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10.1016/J.SBI.2004.03.001

1 reference

stated in

Europe PubMed Central

10 August 2017

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Europe PubMed Central

PubMed ID

15093835

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10 August 2017

ResearchGate publication ID

8609535

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(Q35749505)

Simulating protein evolution in sequence and structure space

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