Quantifying the evolutionary divergence of protein structures: The role of function change and function conservation

No abstract is available for this paper.

• Publication year

  2010

• Venue

  Proteins: Structure, Function, and Bioinformatics

• Publication date

  2010-01-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1002/prot.22616PMID 19830831
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Cross-Over between Discrete and Continuous Protein Structure Space: Insights into Automatic Classification and Networks of Protein Structures

  2009cited by this paper
• On the application of statistical physics to evolutionary biology.

  2009cited by this paper
• Molecular Evolution and Phylogenetics

  2008cited by this paper
• SSMap: A new UniProt-PDB mapping resource for the curation of structural-related information in the UniProt/Swiss-Prot Knowledgebase

  2008cited by this paper
• Protein Meta-Functional Signatures from Combining Sequence, Structure, Evolution, and Amino Acid Property Information

  2008cited by this paper
• InterPro: the integrative protein signature database

  2008cited by this paper
• Quantitative sequence-function relationships in proteins based on gene ontology

  2007cited by this paper
• Assessment of the probabilities for evolutionary structural changes in protein folds

  2007cited by this paper
• A new method to measure the semantic similarity of GO terms

  2007cited by this paper
• Emergence of Protein Fold Families through Rational Design

  2006cited by this paper
• Automated protein function predictionçthe genomic challenge

  2006cited by this paper
• Correction: Improving the Precision of the Structure–Function Relationship by Considering Phylogenetic Context

  2005cited by this paper
• Structure of oxidized alpha-haemoglobin bound to AHSP reveals a protective mechanism for haem.

  2005cited by this paper
• Improving the Precision of the Structure–Function Relationship by Considering Phylogenetic Context

  2005cited by this paper
• The application of statistical physics to evolutionary biology.

  2005cited by this paper
• Structural divergence and distant relationships in proteins: evolution of the globins.

  2005cited by this paper
• Assigning new GO annotations to protein data bank sequences by combining structure and sequence homology

  2005cited by this paper
• Data and text mining

  2005cited by this paper
• A new progressive-iterative algorithm for multiple structure alignment

  2005cited by this paper
• On the constancy of the evolutionary rate of cistrons

  2005cited by this paper
• Quantifying structure-function uncertainty: a graph theoretical exploration into the origins and limitations of protein annotation.

  2004cited by this paper
• Genomic determinants of protein folding thermodynamics in prokaryotic organisms.

  2004cited by this paper
• Scoring function for automated assessment of protein structure template quality

  2004cited by this paper
• Probability models for DNA sequence evolution

  2004cited by this paper
• Prediction of protein function from protein sequence and structure

  2003cited by this paper
• Functional fingerprints of folds: evidence for correlated structure-function evolution.

  2003cited by this paper
• The modern molecular clock

  2003cited by this paper
• Structural Elucidation of the Specificity of the Antibacterial Agent Triclosan for Malarial Enoyl Acyl Carrier Protein Reductase*

  2002cited by this paper
• MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison

  2002cited by this paper
• Statistical Properties of Neutral Evolution

  2002cited by this paper
• Fold change in evolution of protein structures.

  2001cited by this paper
• Evolution of function in protein superfamilies, from a structural perspective.

  2001cited by this paper
• Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores.

  2000cited by this paper
• Practical limits of function prediction

  2000cited by this paper
• Gene Ontology: tool for the unification of biology

  2000cited by this paper
• CATH--a hierarchic classification of protein domain structures.

  1997cited by this paper
• The multiple functions of hemoglobin.

  1995cited by this paper
• SCOP: a structural classification of proteins database for the investigation of sequences and structures.

  1995cited by this paper
• Involvement of Tyr24 and Trp108 in substrate binding and substrate specificity of glycolate oxidase.

  1995cited by this paper
• Crystallographic studies on p21(H-ras) using the synchrotron Laue method: improvement of crystal quality and monitoring of the GTPase reaction at different time points.

  1994cited by this paper
• Protein structure comparison by alignment of distance matrices.

  1993cited by this paper
• The rapid generation of mutation data matrices from protein sequences

  1992cited by this paper
• The causes of molecular evolution

  1991cited by this paper
• Fundamentals of molecular evolution

  1991cited by this paper
• The relation between the divergence of sequence and structure in proteins.

  1986cited by this paper
• Ultrametricity for physicists

  1986cited by this paper
• The neutral theory of molecular evolution.

  1983cited by this paper
• Structure of the zeta chain of human embryonic hemoglobin.

  1981cited by this paper
• Role of very slightly deleterious mutations in molecular evolution and polymorphism.

  1976cited by this paper
• Non-Darwinian evolution.

  1969cited by this paper
• Evolutionary Rate at the Molecular Level

  1968influential reference
• Weighted kappa: nominal scale agreement with provision for scaled disagreement or partial credit.

  1968cited by this paper
• Weighted kappa: Nominal scale agreement provision for scaled disagreement or partial credit.

  1968cited by this paper
• Horizons in Biochemistry

  1962influential reference
• Materials and Methods Som Text Figs. S1 and S2 Table S1 References Abad Directly Links A␤ to Mitochondrial Toxicity in Alzheimer's Disease

  year unknowncited by this paper
• Bioinformatics Discovery Note Structural Drift: a Possible Path to Protein Fold Change

  year unknowncited by this paper

• Identification and Antimicrobial Characterization of Galectin-2 in Miichthys miiuy.

  2026cites this paper
• Forecasting protein evolution by integrating birth-death population models with structurally constrained substitution models

  2025cites this paper
• Ion-Channel Proteins in the Prepubertal Bitch Reproductive System: The Immunolocalization of ASIC2, ASIC4, and PIEZO2

  2025cites this paper
• Site-specific structure and stability constrained substitution models improve phylogenetic inference.

  2025cites this paper
• Exploring the Structural Diversity and Evolution of the D1 Subunit of Photosystem II Using AlphaFold and Foldtree

  2025cites this paper
• Trends in substitution models of protein evolution for phylogenetic inference.

  2025cites this paper
• Facilitating the enzymatic hydrolysis of polysaccharides by carbohydrate active enzymes and enhanced humification process with microbial consortium revealed by metagenomics analysis during cow manure-straw composting

  2025cites this paper
• Quantifying microbial guilds

  2024cites this paper
• Site-specific structure and stability constrained substitution models improve phylogenetic inference

  2024cites this paper
• PC_ali: a tool for improved multiple alignments and evolutionary inference based on a hybrid protein sequence and structure similarity score

  2023influential citation
• PC_sim: An integrated measure of protein sequence and structure similarity for improved alignments and evolutionary inference

  2023influential citation
• Combining Protein Conformational Diversity and Phylogenetic Information Using CoDNaS and CoDNaS‐Q

  2023cites this paper
• Influence of substitution model selection on protein phylogenetic tree reconstruction.

  2023cites this paper
• Carbohydrate-binding modules facilitate the enzymatic hydrolysis of lignocellulosic biomass: Releasing reducing sugars and dissociative lignin available for producing biofuels and chemicals.

  2023cites this paper
• The evolution of the HIV-1 protease folding stability

  2022cites this paper
• ProteinEvolverABC: coestimation of recombination and substitution rates in protein sequences by approximate Bayesian computation

  2021cites this paper
• ProtASR2: Ancestral reconstruction of protein sequences accounting for folding stability

  2020cites this paper
• The Molecular Clock in the Evolution of Protein Structures.

  2019cites this paper
• Comparison of dopamine D2 receptor (homology model and X-ray structure) and virtual screening protocol validation for the antagonism mechanism

  2019cites this paper
• Substitution Rates Predicted by Stability‐Constrained Models of Protein Evolution Are Not Consistent with Empirical Data

  2018influential citation
• Algoritmos en bioinformática estructural

  2018influential citation
• A method for partitioning the information contained in a protein sequence between its structure and function

  2018cites this paper
• Contributions of substitutions and indels to the structural variations in ancient protein superfamilies

  2018cites this paper
• Evolution of Single-Domain Globins in Hydrothermal Vent Scale-Worms

  2017cites this paper
• ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability.

  2017cites this paper
• A neural network learning approach for improving the prediction of residue depth based on sequence-derived features

  2016cites this paper
• Learning structural bioinformatics and evolution with a snake puzzle

  2016cites this paper
• Evolution of off-lattice model proteins under ligand binding constraints.

  2016cites this paper
• Learning protein folding and evolution with a snake puzzle

  2016cites this paper
• Biomedical ontologies—A review

  2015cites this paper
• Anomalous diffusion in neutral evolution of model proteins.

  2015cites this paper
• A new method to improve network topological similarity search: applied to fold recognition

  2015cites this paper
• Normal Mode Dynamics Comparison of Proteins

  2014cites this paper
• Smooth functional transition along a mutational pathway with an abrupt protein fold switch.

  2014cites this paper
• Evaluating the Significance of Protein Functional Similarity Based on Gene Ontology

  2014cites this paper
• Long indels are disordered: a study of disorder and indels in homologous eukaryotic proteins.

  2013cites this paper
• Solution structure of the factor VIII binding region on von Willebrand factor

  2013cites this paper
• The Dynasome as the Missing Link Between Protein Structure and Function

  2012cites this paper
• Modeling Structural and Genomic Constraints in the Evolution of Proteins

  2012cites this paper
• Quality assessment of protein model-structures based on structural and functional similarities

  2012cites this paper
• Exploring Protein Dynamics Space: The Dynasome as the Missing Link between Protein Structure and Function

  2012cites this paper
• The Significance of the ProtDeform Score for Structure Prediction and Alignment

  2011cites this paper
• Moonlighting enzymes in parasitic protozoa

  2010cites this paper
• Tracing the Origin of the Fungal α1 Domain Places Its Ancestor in the HMG-Box Superfamily: Implication for Fungal Mating-Type Evolution

  2010cites this paper
• Kinetic and binding effects in peptide substrate selectivity of matrix metalloproteinase‐2: Molecular dynamics and QM/MM calculations

  2010cites this paper
• How significant is a protein structure similarity with TM-score = 0.5?

  2010cites this paper