Tertiary alphabet for the observable protein structural universe (Q30394863)

20 August 2017

Tertiary alphabet for the observable protein structural universe (English)

1 reference

20 August 2017

Craig O Mackenzie

1 reference

20 August 2017

Jianfu Zhou

series ordinal

1 reference

20 August 2017

Gevorg Grigoryan

series ordinal

1 reference

20 August 2017

language of work or name

English

0 references

publication date

3 November 2016

1 reference

Proceedings of the National Academy of Sciences of the United States of America

20 August 2017

1 reference

20 August 2017

113

1 reference

20 August 2017

1 reference

20 August 2017

E7438-E7447

1 reference

De Novo Evolutionary Emergence of a Symmetrical Protein Is Shaped by Folding Constraints

20 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

A topological and conformational stability alphabet for multipass membrane proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

A vocabulary of ancient peptides at the origin of folded proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Modularity of Protein Folds as a Tool for Template-Free Modeling of Structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Tertiary structural propensities reveal fundamental sequence/structure relationships.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

The membrane- and soluble-protein helix-helix interactome: similar geometry via different interactions.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Rapid search for tertiary fragments reveals protein sequence-structure relationships

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

CATH: comprehensive structural and functional annotations for genome sequences.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Computational design of water-soluble α-helical barrels

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

High thermodynamic stability of parametrically designed helical bundles

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Protein NMR structures refined with Rosetta have higher accuracy relative to corresponding X-ray crystal structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

SCOP2 prototype: a new approach to protein structure mining

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

β-Propeller blades as ancestral peptides in protein evolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Modeling proteins using a super-secondary structure library and NMR chemical shift information

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Principles for designing ideal protein structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

A modular perspective of protein structures: application to fragment based loop modeling

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Computational protein design with explicit consideration of surface hydrophobic patches

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Protein design with fragment databases

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Computational Design of Virus-Like Protein Assemblies on Carbon Nanotube Surfaces

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Redrawing the Ramachandran plot after inclusion of hydrogen-bonding constraints

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

BriX: a database of protein building blocks for structural analysis, modeling and design

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Probing Designability via a Generalized Model of Helical Bundle Geometry

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Structural characteristics of novel protein folds

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Helix-sheet packing in proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Evolutionary expansion and specialization of the PDZ domains

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Structural specificity in coiled-coil interactions.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Reconstruction of protein backbones from the BriX collection of canonical protein fragments

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Structures and metal-ion-binding properties of the Ca2+-binding helix-loop-helix EF-hand motifs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Assessing computational amino acid beta-turn propensities with a phage-displayed combinatorial library and directed evolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Prediction of EF-hand calcium-binding proteins and analysis of bacterial EF-hand proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

A supersecondary structure library and search algorithm for modeling loops in protein structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Alpha-alpha linking motifs and interhelical orientations.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Hidden Markov model-derived structural alphabet for proteins: the learning of protein local shapes captures sequence specificity.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Global mapping of the protein structure space and application in structure-based inference of protein function.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Small libraries of protein fragments model native protein structures accurately.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Evolution of protein kinase signaling from yeast to man

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Twist and shear in beta-sheets and beta-ribbons.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Protein topology and stability define the space of allowed sequences.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Recurrent oligomers in proteins: an optimal scheme reconciling accurate and concise backbone representations in automated folding and design studies.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

The penultimate rotamer library

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Intrinsic beta-sheet propensities result from van der Waals interactions between side chains and the local backbone

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Correlation of observed fold frequency with the occurrence of local structural motifs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Prediction of local structure in proteins using a library of sequence-structure motifs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Global properties of the mapping between local amino acid sequence and local structure in proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Why are some proteins structures so common?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Elucidating the folding problem of helical peptides using empirical parameters. II. Helix macrodipole effects and rational modification of the helical content of natural peptides.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Structural properties of protein β-sheets

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Improved tools for biological sequence comparison

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Basic local alignment search tool

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Evolution of EF-hand calcium-modulated proteins. II. Domains of several subfamilies have diverse evolutionary histories

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5127300

Protein-peptide complex prediction through fragment interaction patterns

20 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1607178113

Global secondary structure packing angle bias in proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1607178113

A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1607178113

Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: comparison with experimental scales.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1607178113

Protein-peptide interactions adopt the same structural motifs as monomeric protein folds

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1607178113

Emergence of Preferred Structures in a Simple Model of Protein Folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1607178113

Protein fragment clustering and canonical local shapes

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27810958

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The designability of protein structures

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27810958

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.1607178113

1 reference

20 August 2017

1 reference

20 August 2017

PubMed publication ID

27810958

1 reference