(Q35948872)

11 August 2017

Comparative modeling and protein-like features of hydrophobic-polar models on a two-dimensional lattice (English)

1 reference

11 August 2017

1 reference

2

Michael Levitt

1 reference

11 August 2017

Sergio Moreno-Hernández

series ordinal

1

1 reference

PMC publication ID

3348970

11 August 2017

language of work or name

English

0 references

publication date

13 April 2012

1 reference

11 August 2017

1 reference

11 August 2017

80

1 reference

11 August 2017

6

1 reference

11 August 2017

1683-1693

1 reference

Cooperativity, local-nonlocal coupling, and nonnative interactions: principles of protein folding from coarse-grained models

11 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Atomic-Level Characterization of the Structural Dynamics of Proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Trade-off between positive and negative design of protein stability: from lattice models to real proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Evaluation of template-based models in CASP8 with standard measures

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Coupling between properties of the protein shape and the rate of protein folding.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Nature of the protein universe

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Analysing the origin of long-range interactions in proteins using lattice models

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Side-chain recognition and gating in the ribosome exit tunnel.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Perspectives on protein evolution from simple exact models.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Simulating protein evolution in sequence and structure space

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Imprint of evolution on protein structures.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Assessment of RAPTOR's linear programming approach in CAFASP3

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

TOUCHSTONE II: a new approach to ab initio protein structure prediction

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Small libraries of protein fragments model native protein structures accurately.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Roles of mutation and recombination in the evolution of protein thermodynamics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

The CATH protein family database: a resource for structural and functional annotation of genomes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Multiple protein folding nuclei and the transition state ensemble in two-state proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

On hydrophobicity correlations in protein chains

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Folding pathway of a lattice model for proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Lattice models for proteins reveal multiple folding nuclei for nucleation-collapse mechanism

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Are protein folds atypical?

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

How evolution makes proteins fold quickly

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

On the origin of the cooperativity of protein folding: implications from model simulations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

The FSSP database: fold classification based on structure-structure alignment of proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Kinetics and thermodynamics of folding in model proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Protein superfamilies and domain superfolds

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Exploring conformational space with a simple lattice model for protein structure

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

A test of lattice protein folding algorithms

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Forces of tertiary structural organization in globular proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

The complexity and accuracy of discrete state models of protein structure

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

SCOP: a structural classification of proteins database for the investigation of sequences and structures

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

2 October 2017

How does a protein fold?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Cooperativity in protein-folding kinetics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

A 3D building blocks approach to analyzing and predicting structure of proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Dynamic Monte Carlo simulations of globular protein folding/unfolding pathways. I. Six-member, Greek key beta-barrel proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Dominant forces in protein folding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

One thousand families for the molecular biologist

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

A simplified representation of protein conformations for rapid simulation of protein folding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Enumerating Designing Sequences in the HP Model

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Population statistics of protein structures: lessons from structural classifications

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Comparing folding codes for proteins and polymers

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348970

Simulations of the folding of a globular protein

11 July 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24067

Emergence of Preferred Structures in a Simple Model of Protein Folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24067

Genetic algorithms for protein folding simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24067

Specific nucleus as the transition state for protein folding: evidence from the lattice model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24067

Local interactions dominate folding in a simple protein model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24067

Scaling law in sizes of protein sequence families: from super-families to orphan genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24067

Protein folding funnels: the nature of the transition state ensemble

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24067

Cooperativity, smooth energy landscapes and the origins of topology-dependent protein folding rates

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24067

Population dynamics simulations of functional model proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24067

Conformations of folded proteins in restricted spaces

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24067

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

21 January 2018

1 reference

12 December 2020

Factors governing the foldability of proteins

1 reference

12 December 2020

The distribution of structures in evolving protein populations

1 reference

12 December 2020

Scaling behavior of some molecular shape descriptors of polymer chains and protein backbones

1 reference

12 December 2020

Cooperativity in protein folding: from lattice models with sidechains to real proteins

1 reference

12 December 2020

Physical origins of protein superfamilies

1 reference

12 December 2020

Modeling protein density of states: additive hydrophobic effects are insufficient for calorimetric two-state cooperativity

1 reference

12 December 2020

A lattice statistical mechanics model of the conformational and sequence spaces of proteins

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PROT.24067

Identifiers

DOI

10.1002/PROT.24067

1 reference

11 August 2017

1 reference

PMC publication ID

3348970

11 August 2017

PubMed publication ID

22411636

1 reference

PMC publication ID

3348970