An atomic environment potential for use in protein structure prediction. (Q30351317)

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English	An atomic environment potential for use in protein structure prediction.	scientific article

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Europe PubMed Central

20 June 2017

An atomic environment potential for use in protein structure prediction. (English)

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Europe PubMed Central

20 June 2017

protein structure prediction

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2

Michael Levitt

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Europe PubMed Central

20 June 2017

Christopher M Summa

1

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Europe PubMed Central

PubMed ID

16126228

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20 June 2017

William F Degrado

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3

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Europe PubMed Central

PubMed ID

16126228

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20 June 2017

language of work or name

English

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publication date

1 September 2005

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Europe PubMed Central

20 June 2017

16

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published in

Journal of Molecular Biology

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Europe PubMed Central

20 June 2017

352

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Europe PubMed Central

20 June 2017

4

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Europe PubMed Central

20 June 2017

986-1001

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stated in

Europe PubMed Central

20 June 2017

Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction

1 reference

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Verification of protein structures: patterns of nonbonded atomic interactions

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A graph-theoretic algorithm for comparative modeling of protein structure

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An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction

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Atom density in protein structures

1 reference

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Some factors in the interpretation of protein denaturation

1 reference

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Computational design of protein-protein interactions

1 reference

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Characterizing the microenvironment surrounding protein sites

1 reference

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Ab initio construction of protein tertiary structures using a hierarchical approach

1 reference

11 October 2022

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Combinatorial protein design

1 reference

11 October 2022

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Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

1 reference

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PQS: a protein quaternary structure file server

1 reference

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Learning about protein folding via potential functions

1 reference

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Ab initio protein structure prediction: progress and prospects.

1 reference

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Energy functions that discriminate X-ray and near native folds from well-constructed decoys

1 reference

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Contact potential that recognizes the correct folding of globular proteins

1 reference

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Easily searched protein folding potentials.

1 reference

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Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation

1 reference

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Statistical potentials extracted from protein structures: how accurate are they?

1 reference

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Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.

1 reference

11 October 2022

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Enhanced dead-end elimination in the search for the global minimum energy conformation of a collection of protein side chains

1 reference

11 October 2022

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A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional Structure

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.JMB.2005.07.054

Protein folding theory: from lattice to all-atom models

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.JMB.2005.07.054

Branch-and-terminate: a combinatorial optimization algorithm for protein design

1 reference

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Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds

1 reference

11 October 2022

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Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment

1 reference

11 October 2022

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Identification of side-chain clusters in protein structures by a graph spectral method.

1 reference

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De novo design and structural characterization of proteins and metalloproteins

1 reference

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De novo design of biocatalysts

1 reference

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Quantifying the effect of burial of amino acid residues on protein stability

1 reference

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A new force field for molecular mechanical simulation of nucleic acids and proteins

1 reference

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A Novel Approach to Decoy Set Generation: Designing a Physical Energy Function Having Local Minima with Native Structure Characteristics

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.JMB.2005.07.054

Protein folding: the endgame

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.JMB.2005.07.054

Polar and nonpolar atomic environments in the protein core: implications for folding and binding

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.JMB.2005.07.054

Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics.

1 reference

11 October 2022

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Computational design of a biologically active enzyme

1 reference

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CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.JMB.2005.07.054

The dead-end elimination theorem and its use in protein side-chain positioning

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.JMB.2005.07.054

Dead-end based modeling tools to explore the sequence space that is compatible with a given scaffold

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.JMB.2005.07.054

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

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.JMB.2005.07.054

PISCES: a protein sequence culling server

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.JMB.2005.07.054

Profile analysis: detection of distantly related proteins

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.JMB.2005.07.054

Effective energy functions for protein structure prediction.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.JMB.2005.07.054

Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular dynamics simulations

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.JMB.2005.07.054

Atomic environment energies in proteins defined from statistics of accessible and contact surface areas

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.JMB.2005.07.054

Novel knowledge-based mean force potential at atomic level

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.JMB.2005.07.054

How to derive a protein folding potential? A new approach to an old problem

1 reference

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Raster3D: photorealistic molecular graphics

1 reference

11 October 2022

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MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures

1 reference

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https://opencitations.net/index/coci/api/v1/references/10.1016/J.JMB.2005.07.054

Solvation energy in protein folding and binding

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.JMB.2005.07.054

Characterizations of diverse residue clusters in protein three-dimensional structures

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.JMB.2005.07.054

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DOI

10.1016/J.JMB.2005.07.054

1 reference

stated in

Europe PubMed Central

20 June 2017

1 reference

Europe PubMed Central

PubMed ID

16126228

retrieved

20 June 2017

ResearchGate publication ID

7635019

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An atomic environment potential for use in protein structure prediction. (Q30351317)

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An atomic environment potential for use in protein structure prediction. (Q30351317)

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