(Q30358437)

20 June 2017

title

Exhaustive docking and solvated interaction energy scoring: lessons learned from the SAMPL4 challenge. (English)

1 reference

20 June 2017

1 reference

Hervé Hogues

1

1 reference

20 June 2017

Traian Sulea

series ordinal

2

1 reference

20 June 2017

Enrico O Purisima

series ordinal

3

1 reference

20 June 2017

publication date

29 January 2014

1 reference

Journal of Computer - Aided Molecular Design

20 June 2017

published in

1 reference

20 June 2017

volume

28

1 reference

20 June 2017

issue

4

1 reference

20 June 2017

page(s)

417-427

1 reference

Alchemical free energy methods for drug discovery: progress and challenges

20 June 2017

cites work

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

Calculation of protein-ligand binding affinities.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

Assessing scoring functions for protein-ligand interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

A critical assessment of docking programs and scoring functions

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

Docking ligands into flexible and solvated macromolecules. 4. Are popular scoring functions accurate for this class of proteins?

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

Protein-ligand binding free energies from exhaustive docking.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

Modeling Protein-Ligand Binding by Mining Minima

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

Large-scale application of high-throughput molecular mechanics with Poisson-Boltzmann surface area for routine physics-based scoring of protein-ligand complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 1. Exploring the parameter space.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

Molecular dynamics-solvated interaction energy studies of protein-protein interactions: the MP1-p14 scaffolding complex

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

CSAR benchmark exercise of 2010: selection of the protein-ligand complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

The Amber biomolecular simulation programs

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

Development and testing of a general amber force field

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

Molecular surface generation using a variable-radius solvent probe.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

Free energy, entropy, and induced fit in host-guest recognition: calculations with the second-generation mining minima algorithm

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

Calculation of cyclodextrin binding affinities: energy, entropy, and implications for drug design

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

Rapid Prediction of Solvation Free Energy. 2. The First-Shell Hydration (FiSH) Continuum Model

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

Rapid prediction of solvation free energy. 3. Application to the SAMPL2 challenge

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

Acyclic cucurbit[n]uril congeners are high affinity hosts

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

New ultrahigh affinity host-guest complexes of cucurbit[7]uril with bicyclo[2.2.2]octane and adamantane guests: thermodynamic analysis and evaluation of M2 affinity calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

Host-guest complexes with protein-ligand-like affinities: computational analysis and design

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

Symmetry numbers for rigid, flexible, and fluxional molecules: theory and applications

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

Small Molecule Inhibitors of the LEDGF Site of Human Immunodeficiency Virus Integrase Identified by Fragment Screening and Structure Based Design

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

Structural basis for a new mechanism of inhibition of HIV-1 integrase identified by fragment screening and structure-based design

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

The SAMPL4 host-guest blind prediction challenge: an overview.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

The solvated interaction energy method for scoring binding affinities

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 2. Benchmark in the CSAR-2010 scoring exercise

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9715-5

Exhaustive search and solvated interaction energy (SIE) for virtual screening and affinity prediction

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24474162

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Well-defined, organic nanoenvironments in water: the hydrophobic effect drives a capsular assembly

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24474162

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1007/S10822-014-9715-5

1 reference

journals/jcamd/HoguesSP14

20 June 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference