A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). (Q43181588)

15 November 2017

A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). (English)

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15 November 2017

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2

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15 November 2017

4

Ruben Abagyan

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author name string

Giovanni Bottegoni

series ordinal

1

1 reference

PMC publication ID

2641994

15 November 2017

Maxim Totrov

series ordinal

3

1 reference

15 November 2017

14 February 2008

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Journal of Computer - Aided Molecular Design

15 November 2017

1 reference

15 November 2017

22

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15 November 2017

5

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15 November 2017

311-325

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Exploring experimental sources of multiple protein conformations in structure-based drug design.

15 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

Novel procedure for modeling ligand/receptor induced fit effects.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

METLIN: a metabolite mass spectral database

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

Side-chain flexibility in protein-ligand binding: the minimal rotation hypothesis

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

Pocketome via comprehensive identification and classification of ligand binding envelopes.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

Flexible docking in solution using metadynamics

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

Docking and scoring in virtual screening for drug discovery: methods and applications

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

Cholesterol depletion suppresses the translational diffusion of class II major histocompatibility complex proteins in the plasma membrane

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

Comparative study of several algorithms for flexible ligand docking

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

Implications of protein flexibility for drug discovery

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

FlexE: efficient molecular docking considering protein structure variations.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

Flexible protein-ligand docking by global energy optimization in internal coordinates.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

Molecular docking to ensembles of protein structures

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

"Soft docking": matching of molecular surface cubes

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

FLIPDock: docking flexible ligands into flexible receptors.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

Diverse, high-quality test set for the validation of protein-ligand docking performance.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

Representing receptor flexibility in ligand docking through relevant normal modes.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

Protein flexibility in ligand docking and virtual screening to protein kinases.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

Accurate and efficient generalized born model based on solvent accessibility: derivation and application for LogP octanol/water prediction and flexible peptide docking

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

Computational drug design accommodating receptor flexibility: the relaxed complex scheme

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

Ligand docking to proteins with discrete side-chain flexibility.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2641994

Recognition of distantly related proteins through energy calculations

15 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18273556

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A method to configure protein side-chains from the main-chain trace in homology modelling

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18273556

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/18273556

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1007/S10822-008-9188-5

1 reference

journals/jcamd/BottegoniKTA08

15 November 2017

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

PMC publication ID

2641994

15 November 2017

PubMed publication ID

18273556

1 reference

PMC publication ID

2641994