Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method (Q40579705)

21 September 2017

Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method (English)

1 reference

21 September 2017

Hari S Muddana

1

1 reference

21 September 2017

Jian Yin

2

1 reference

21 September 2017

Neil V Sapra

3

1 reference

21 September 2017

Andrew T Fenley

4

1 reference

21 September 2017

Michael K Gilson

5

1 reference

21 September 2017

8 February 2014

1 reference

Journal of Computer - Aided Molecular Design

21 September 2017

1 reference

21 September 2017

28

1 reference

21 September 2017

4

1 reference

21 September 2017

463-474

1 reference

Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes

21 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

Blind prediction of HIV integrase binding from the SAMPL4 challenge

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

The electrostatic response of water to neutral polar solutes: implications for continuum solvent modeling

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

Entropy-enthalpy transduction caused by conformational shifts can obscure the forces driving protein-ligand binding

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

Calculation of Host-Guest Binding Affinities Using a Quantum-Mechanical Energy Model

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

Blind prediction of host-guest binding affinities: a new SAMPL3 challenge.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

Prediction of SAMPL3 host-guest binding affinities: evaluating the accuracy of generalized force-fields

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

Theory of free energy and entropy in noncovalent binding

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

Efficient drug lead discovery and optimization

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

Calculation of protein-ligand binding affinities.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

The cucurbit[n]uril family: prime components for self-sorting systems.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

How well can simulation predict protein folding kinetics and thermodynamics?

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

The many roles of computation in drug discovery

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

Free energy landscape of protein folding in water: Explicit vs. implicit solvent

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

A free energy analysis of nucleic acid base stacking in aqueous solution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

The interpretation of protein structures: Estimation of static accessibility

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

MOPAC: a semiempirical molecular orbital program

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

The SAMPL2 blind prediction challenge: introduction and overview.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

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

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

Identification of symmetries in molecules and complexes.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

Salt effects on the apparent stability of the cucurbit[7]uril-methyl viologen inclusion complex

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

Fast assignment of accurate partial atomic charges: an electronegativity equalization method that accounts for alternate resonance forms.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

Tork: Conformational analysis method for molecules and complexes

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053532

Comparison of Shape-Matching and Docking as Virtual Screening Tools

20 August 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9726-2

Semianalytical treatment of solvation for molecular mechanics and dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9726-2

COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9726-2

Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9726-2

A Transferable H-Bonding Correction for Semiempirical Quantum-Chemical Methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9726-2

A Blind Challenge for Computational Solvation Free Energies: Introduction and Overview

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24510191

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

SAMPL3: blinded prediction of host–guest binding affinities, hydration free energies, and trypsin inhibitors

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24510191

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The SAMPL3 blind prediction challenge: transfer energy overview

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24510191

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1007/S10822-014-9726-2

1 reference

journals/jcamd/MuddanaYSFG14

21 September 2017

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

21 September 2017

PubMed publication ID

24510191

1 reference