(Q47448946)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29096505%20AND%20SRC:MED&resulttype=core&format=json

8 April 2020

title

The BioFragment Database (BFDb): An open-data platform for computational chemistry analysis of noncovalent interactions (English)

1 reference

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8 April 2020

main subject

open data

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computational chemistry

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author

Lori A Burns

1

1 reference

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8 April 2020

Zheng Zheng

3

1 reference

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8 April 2020

John C Faver

2

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8 April 2020

Daniel G A Smith

5

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8 April 2020

David Sherrill

9

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8 April 2020

author name string

Michael S Marshall

4

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8 April 2020

Kenno Vanommeslaeghe

6

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8 April 2020

Alexander D MacKerell

7

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8 April 2020

Kenneth M Merz

8

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8 April 2020

language of work or name

English

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publication date

1 October 2017

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Journal of Chemical Physics

8 April 2020

published in

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8 April 2020

volume

147

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8 April 2020

issue

16

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8 April 2020

page(s)

161727

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How fast-folding proteins fold

8 April 2020

cites work

1 reference

Induction of peptide bond dipoles drives cooperative helix formation in the (AAQAA)3 peptide

21 January 2018

1 reference

Taming the complexity of protein folding

21 January 2018

1 reference

Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing

21 January 2018

1 reference

Predicting protein structures with a multiplayer online game

21 January 2018

1 reference

Computationally-guided optimization of a docking hit to yield catechol diethers as potent anti-HIV agents

21 January 2018

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Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations.

21 January 2018

1 reference

How does a drug molecule find its target binding site?

21 January 2018

1 reference

Dispersion-Corrected Mean-Field Electronic Structure Methods

21 January 2018

1 reference

Ab initio quantum mechanical study of the binding energies of human estrogen receptor alpha with its ligands: an application of fragment molecular orbital method

21 January 2018

1 reference

Divide-and-Conquer Hartree-Fock Calculations on Proteins

21 January 2018

1 reference

Molecular tailoring approach for geometry optimization of large molecules: energy evaluation and parallelization strategies

21 January 2018

1 reference

Natural triple excitations in local coupled cluster calculations with pair natural orbitals

21 January 2018

1 reference

Overview of the SAMPL5 host-guest challenge: Are we doing better?

21 January 2018

1 reference

CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma

21 January 2018

1 reference

Critical assessment of methods of protein structure prediction: Progress and new directions in round XI.

21 January 2018

1 reference

New encouraging developments in contact prediction: Assessment of the CASP11 results

21 January 2018

1 reference

Formal Estimation of Errors in Computed Absolute Interaction Energies of Protein-ligand Complexes

21 January 2018

1 reference

Origin of attraction and directionality of the pi/pi interaction: model chemistry calculations of benzene dimer interaction

21 January 2018

1 reference

An assessment of theoretical methods for nonbonded interactions: comparison to complete basis set limit coupled-cluster potential energy curves for the benzene dimer, the methane dimer, benzene-methane, and benzene-H2S.

21 January 2018

1 reference

S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures.

21 January 2018

1 reference

Benchmark Calculations of Interaction Energies in Noncovalent Complexes and Their Applications

21 January 2018

1 reference

Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples

21 January 2018

1 reference

A fifth-order perturbation comparison of electron correlation theories

21 January 2018

1 reference

Comparative Study of Selected Wave Function and Density Functional Methods for Noncovalent Interaction Energy Calculations Using the Extended S22 Data Set.

21 January 2018

1 reference

Assessment of Empirical Models versus High-Accuracy Ab Initio Methods for Nucleobase Stacking: Evaluating the Importance of Charge Penetration.

21 January 2018

1 reference

Large-Scale Quantitative Assessment of Binding Preferences in Protein-Nucleic Acid Complexes.

21 January 2018

1 reference

Representative Amino Acid Side-Chain Interactions in Protein-DNA Complexes: A Comparison of Highly Accurate Correlated Ab Initio Quantum Mechanical Calculations and Efficient Approaches for Applications to Large Systems

21 January 2018

1 reference

Efficient and Accurate Double-Hybrid-Meta-GGA Density Functionals-Evaluation with the Extended GMTKN30 Database for General Main Group Thermochemistry, Kinetics, and Noncovalent Interactions.

21 January 2018

1 reference

ωB97M-V: A combinatorially optimized, range-separated hybrid, meta-GGA density functional with VV10 nonlocal correlation

21 January 2018

1 reference

Revised Damping Parameters for the D3 Dispersion Correction to Density Functional Theory

21 January 2018

1 reference

Comparison of multiple Amber force fields and development of improved protein backbone parameters

21 January 2018

1 reference

Semianalytical treatment of solvation for molecular mechanics and dynamics

21 January 2018

1 reference

The energy computation paradox and ab initio protein folding

21 January 2018

1 reference

Appointing silver and bronze standards for noncovalent interactions: a comparison of spin-component-scaled (SCS), explicitly correlated (F12), and specialized wavefunction approaches.

21 January 2018

1 reference

Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen

21 January 2018

1 reference

Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy.

21 January 2018

1 reference

The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors

21 January 2018

1 reference

Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability

21 January 2018

1 reference

Basis-set convergence in correlated calculations on Ne, N2, and H2O

21 January 2018

1 reference

Generalized Gradient Approximation Made Simple

21 January 2018

1 reference

Density-functional exchange-energy approximation with correct asymptotic behavior

21 January 2018

1 reference

Density-functional approximation for the correlation energy of the inhomogeneous electron gas

21 January 2018

1 reference

Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density

21 January 2018

1 reference

Semiempirical GGA-type density functional constructed with a long-range dispersion correction.

21 January 2018

1 reference

Density-functional thermochemistry. III. The role of exact exchange

21 January 2018

1 reference

Design of Density Functionals by Combining the Method of Constraint Satisfaction with Parametrization for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions

21 January 2018

1 reference

Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections

21 January 2018

1 reference

Semiempirical hybrid density functional with perturbative second-order correlation

21 January 2018

1 reference

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

21 January 2018

1 reference

ωB97X-V: a 10-parameter, range-separated hybrid, generalized gradient approximation density functional with nonlocal correlation, designed by a survival-of-the-fittest strategy

21 January 2018

1 reference

A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu

21 January 2018

1 reference

Effect of the damping function in dispersion corrected density functional theory.

21 January 2018

1 reference

Consistent structures and interactions by density functional theory with small atomic orbital basis sets.

21 January 2018

1 reference

Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing.

21 January 2018

1 reference

Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges.

21 January 2018

1 reference

CHARMM: the biomolecular simulation program

21 January 2018

1 reference

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

21 January 2018

1 reference

Extension of the CHARMM General Force Field to sulfonyl-containing compounds and its utility in biomolecular simulations.

21 January 2018

1 reference

Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model

21 January 2018

1 reference

Estimates of the ab initio limit for pi-pi interactions: the benzene dimer

21 January 2018

1 reference

IPython: A System for Interactive Scientific Computing

21 January 2018

1 reference

Comparing Counterpoise-Corrected, Uncorrected, and Averaged Binding Energies for Benchmarking Noncovalent Interactions.

21 January 2018

1 reference

Introduction: Noncovalent Interactions

21 January 2018

1 reference

Extensions of the S66 Data Set: More Accurate Interaction Energies and Angular-Displaced Nonequilibrium Geometries

21 January 2018

1 reference

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

21 January 2018

1 reference

Benchmarking Density Functional Methods against the S66 and S66x8 Datasets for Non-Covalent Interactions

21 January 2018

1 reference

Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs

21 January 2018

1 reference

Basis set convergence of the coupled-cluster correction, δMP2CCSD(T): Best practices for benchmarking non-covalent interactions and the attendant revision of the S22, NBC10, HBC6, and HSG databases

21 January 2018

1 reference

12 December 2020

Levels of symmetry adapted perturbation theory (SAPT). I. Efficiency and performance for interaction energies

1 reference

12 December 2020

Simplified CCSD(T)-F12 methods: Theory and benchmarks

1 reference

12 December 2020

Assessment of the Performance of DFT and DFT-D Methods for Describing Distance Dependence of Hydrogen-Bonded Interactions

1 reference

12 December 2020

Assessment of a long-range corrected hybrid functional.

1 reference

12 December 2020

Improved supermolecular second order Møller-Plesset intermolecular interaction energies using time-dependent density functional response theory

1 reference

12 December 2020

Accurate Intermolecular Interaction Energies from a Combination of MP2 and TDDFT Response Theory

1 reference

12 December 2020

Dispersion-Weighted Explicitly Correlated Coupled-Cluster Theory [DW-CCSD(T**)-F12]

1 reference

12 December 2020

Density-functional approaches to noncovalent interactions: A comparison of dispersion corrections (DFT-D), exchange-hole dipole moment (XDM) theory, and specialized functionals

1 reference

12 December 2020

Identifiers

DOI

10.1063/1.5001028

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29096505%20AND%20SRC:MED&resulttype=core&format=json

8 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29096505%20AND%20SRC:MED&resulttype=core&format=json

8 April 2020

PubMed publication ID

29096505

1 reference