(Q34249481)

31 July 2017

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

1 reference

31 July 2017

Hari S Muddana

1

1 reference

PubMed ID

22274835

31 July 2017

Michael K Gilson

series ordinal

2

1 reference

31 July 2017

25 January 2012

1 reference

Journal of Computer - Aided Molecular Design

31 July 2017

1 reference

31 July 2017

26

1 reference

31 July 2017

5

1 reference

31 July 2017

517-525

1 reference

https://scigraph.springernature.com/pub.10.1007/s10822-012-9544-3

31 July 2017

0 references

cites work

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383906

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383906

Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383906

The energy computation paradox and ab initio protein folding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383906

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383906

Limits of Free Energy Computation for Protein-Ligand Interactions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383906

Theory of free energy and entropy in noncovalent binding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383906

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383906

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383906

Hydrogen bonding and pi-stacking: how reliable are force fields? A critical evaluation of force field descriptions of nonbonded interactions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383906

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383906

Calculation of protein-ligand binding affinities.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383906

Enhancing the accuracy, the efficiency and the scope of free energy simulations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383906

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383906

Development and testing of a general amber force field

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383906

The many roles of computation in drug discovery

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383906

Binding Affinities of Host–Guest, Protein–Ligand, and Protein–Transition‐State Complexes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383906

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383906

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383906

MOPAC: a semiempirical molecular orbital program

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383906

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

6 July 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9544-3

Tork: Conformational analysis method for molecules and complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9544-3

Identification of symmetries in molecules and complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9544-3

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9544-3

An all atom force field for simulations of proteins and nucleic acids

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9544-3

Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-012-9544-3

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%2FS10822-012-9544-3

Multiple-site titration and molecular modeling: two rapid methods for computing energies and forces for ionizable groups in proteins

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22274835

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1007/S10822-012-9544-3

1 reference

journals/jcamd/MuddanaG12

31 July 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

31 July 2017

1 reference

PubMed ID

22274835