HAAD: A quick algorithm for accurate prediction of hydrogen atoms in protein structures. (Q30379961)

13 November 2017

HAAD: A quick algorithm for accurate prediction of hydrogen atoms in protein structures. (English)

1 reference

protein structure prediction

13 November 2017

0 references

author name string

Yunqi Li

series ordinal

1

1 reference

13 November 2017

Ambrish Roy

series ordinal

2

1 reference

13 November 2017

Yang Zhang

series ordinal

3

1 reference

13 November 2017

language of work or name

English

0 references

publication date

20 August 2009

1 reference

13 November 2017

1 reference

13 November 2017

4

1 reference

13 November 2017

8

1 reference

13 November 2017

e6701

1 reference

Creative Commons Attribution 4.0 International

13 November 2017

start time

20 August 2009

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

All-atom empirical potential for molecular modeling and dynamics studies of proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724740

Protein structure prediction: when is it useful?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724740

REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724740

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724740

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724740

Assessment of CASP7 predictions in the high accuracy template-based modeling category

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724740

Can molecular dynamics simulations provide high-resolution refinement of protein structure?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724740

Protein structure prediction by all-atom free-energy refinement.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724740

A backbone-based theory of protein folding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724740

Virtual ligand screening: strategies, perspectives and limitations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724740

An assessment of the accuracy of methods for predicting hydrogen positions 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=2724740

The process of structure-based drug 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=2724740

Hydrogen atoms in proteins: positions and dynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724740

A graph-theory algorithm for rapid protein side-chain prediction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724740

Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724740

Hyperconjugation not steric repulsion leads to the staggered structure of ethane

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724740

Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent 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=2724740

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724740

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724740

Ambiguous distance data in the calculation of NMR 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=2724740

Principles of protein-protein 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=2724740

Crystal structure of hydrophobic protein from soybean; a member of a new cysteine-rich family

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724740

Comparative protein modelling by satisfaction of spatial restraints

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724740

Satisfying hydrogen bonding potential 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=2724740

Protein structure refinement based on paramagnetic NMR shifts: applications to wild-type and mutant forms of cytochrome c.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724740

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724740

Neutron protein crystallography: advances in methods and applications

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724740

WHAT IF: a molecular modeling and drug design program

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724740

Expanding GPCR homology model binding sites via a balloon potential: A molecular dynamics refinement approach

20 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0006701

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0006701

THE NATURE OF THE CHEMICAL BOND. APPLICATION OF RESULTS OBTAINED FROM THE QUANTUM MECHANICS AND FROM A THEORY OF PARAMAGNETIC SUSCEPTIBILITY TO THE STRUCTURE OF MOLECULES

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0006701

The Case for Steric Repulsion Causing the Staggered Conformation of Ethane

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0006701

Protein dynamics investigated by the neutron diffraction-hydrogen exchange technique.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0006701

A discussion of the solution for the best rotation to relate two sets of vectors

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0006701

Intermolecular Nonbonded Contact Distances in Organic Crystal Structures: Comparison with Distances Expected from van der Waals Radii

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0006701

Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0006701

GROMACS 3.0: a package for molecular simulation and trajectory analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0006701

Effects of pH on the interactions and conformation of bovine serum albumin: comparison between chemical force microscopy and small-angle neutron scattering

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19693270

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Atomic contacts in protein structures. A detailed analysis of atomic radii, packing, and overlaps

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19693270

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0006701

1 reference

13 November 2017

0 references

1 reference

13 November 2017

1 reference