Protein-protein docking using region-based 3D Zernike descriptors (Q33517871)

27 July 2017

title

Protein-protein docking using region-based 3D Zernike descriptors (English)

1 reference

27 July 2017

Daisuke Kihara

4

0 references

Lee Sael

object named as

Lee Sael

series ordinal

3

0 references

author name string

Vishwesh Venkatraman

series ordinal

1

1 reference

27 July 2017

Yifeng D Yang

series ordinal

2

1 reference

27 July 2017

publication date

9 December 2009

1 reference

27 July 2017

1 reference

27 July 2017

volume

10

1 reference

27 July 2017

page(s)

407

1 reference

3D-SURFER: software for high-throughput protein surface comparison and analysis

27 July 2017

cites work

1 reference

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Potential for protein surface shape analysis using spherical harmonics and 3D Zernike descriptors

21 June 2018

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21 June 2018

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Predicting protein function and binding profile via matching of local evolutionary and geometric surface patterns

21 June 2018

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Shape complementarity of protein-protein complexes at multiple resolutions

21 June 2018

1 reference

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Principles of flexible protein-protein docking

21 June 2018

1 reference

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Rapid comparison of properties on protein surface

21 June 2018

1 reference

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Benchmarking of TASSER_2.0: an improved protein structure prediction algorithm with more accurate predicted contact restraints

21 June 2018

1 reference

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21 June 2018

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Fast protein tertiary structure retrieval based on global surface shape similarity.

21 June 2018

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Recent Progress and Future Directions in Protein-Protein Docking

21 June 2018

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Using self-organizing maps to learn geometric hash functions for model-based object recognition

21 June 2018

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Characterization of local geometry of protein surfaces with the visibility criterion.

21 June 2018

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Docking and scoring protein complexes: CAPRI 3rd Edition

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

Shape variation in protein binding pockets and their ligands

21 June 2018

1 reference

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Multipolar representation of protein structure.

21 June 2018

1 reference

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Flexible protein-protein docking

21 June 2018

1 reference

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Prediction of physical protein-protein interactions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

Protein-Protein Docking Benchmark 2.0: an update

21 June 2018

1 reference

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ProFunc: a server for predicting protein function from 3D structure

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

PatchDock and SymmDock: servers for rigid and symmetric docking

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

Progress and challenges in high-resolution refinement of protein structure models.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

Assessing predictions of protein-protein interaction: the CAPRI experiment

21 June 2018

1 reference

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Protein modeling and structure prediction with a reduced representation.

21 June 2018

1 reference

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A structural perspective on protein-protein interactions.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

Computational methods of analysis of protein-protein interactions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

Docking of protein models

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

Principles of docking: An overview of search algorithms and a guide to scoring functions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints.

21 June 2018

1 reference

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Modelling protein docking using shape complementarity, electrostatics and biochemical information

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

Shape complementarity at protein/protein interfaces

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

"Soft docking": matching of molecular surface cubes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

Shape distributions of protein topography

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

3D-Garden: a system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

An extension of spherical harmonics to region-based rotationally invariant descriptors for molecular shape description and comparison.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

Context shapes: Efficient complementary shape matching for protein-protein docking.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

Implicit flexibility in protein docking: cross-docking and local refinement.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

Protein docking using surface matching and supervised machine learning.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

Evaluating virtual screening methods: good and bad metrics for the "early recognition" problem.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

A new protein-protein docking scoring function based on interface residue properties

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

ATTRACT: protein-protein docking in CAPRI using a reduced protein model.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

A protein-protein docking benchmark.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

ZDOCK: an initial-stage protein-docking algorithm.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

A novel shape complementarity scoring function for protein‐protein docking

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

Docking unbound proteins using shape complementarity, desolvation, and electrostatics.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

Protein docking using a genetic algorithm.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

BiGGER: a new (soft) docking algorithm for predicting protein interactions.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

Protein docking using spherical polar Fourier correlations.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

Automated docking of peptides and proteins by using a genetic algorithm combined with a tabu search.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

A geometry-based suite of molecular docking processes

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

Complementarity of Structure Ensembles in Protein-Protein Binding

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

Ten thousand interactions for the molecular biologist

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800122

The effect of resolution-dependent global shape modifications on rigid-body protein-protein docking

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20003235

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Shape complementarity at the hemoglobin alpha 1 beta 1 subunit interface

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20003235

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Principles of docking: An overview of search algorithms and a guide to scoring functions

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20003235

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2105-10-407

1 reference

journals/bmcbi/VenkatramanYSK09

27 July 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

27 July 2017

1 reference