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

scientific article published in October 2017

The BioFragment Database (BFDb): An open-data platform for computational chemistry analysis of noncovalent interactions. is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.1063/1.5001028
P932PMC publication ID5656042
P698PubMed publication ID29096505

P50authorLori A BurnsQ39750123
Zheng ZhengQ40277470
David SherrillQ56442166
John C FaverQ58369051
Daniel G A SmithQ88713697
P2093author name stringKenneth M Merz
Alexander D MacKerell
Michael S Marshall
Kenno Vanommeslaeghe
P2860cites workDevelopment of the Colle-Salvetti correlation-energy formula into a functional of the electron densityQ21708802
Density-functional exchange-energy approximation with correct asymptotic behaviorQ21709057
Predicting protein structures with a multiplayer online gameQ24255001
IPython: A System for Interactive Scientific ComputingQ24492861
Taming the complexity of protein foldingQ24617692
CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fieldsQ24632987
CHARMM: the biomolecular simulation programQ24658108
Density-functional thermochemistry. III. The role of exact exchangeQ25938987
Generalized Gradient Approximation Made SimpleQ25938998
Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogenQ26778446
Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular modelQ26778456
Density-functional approximation for the correlation energy of the inhomogeneous electron gasQ27440259
Comparison of multiple Amber force fields and development of improved protein backbone parametersQ27861040
Estimates of the ab initio limit for pi-pi interactions: the benzene dimerQ28220121
Long-range corrected hybrid density functionals with damped atom-atom dispersion correctionsQ28300017
The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errorsQ29039690
CSAR 2014: A Benchmark Exercise Using Unpublished Data from PharmaQ30387722
Critical assessment of methods of protein structure prediction: Progress and new directions in round XI.Q30388020
The energy computation paradox and ab initio protein foldingQ30402305
Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations.Q30501558
Comparative Study of Selected Wave Function and Density Functional Methods for Noncovalent Interaction Energy Calculations Using the Extended S22 Data Set.Q31028839
Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computingQ33962262
Induction of peptide bond dipoles drives cooperative helix formation in the (AAQAA)3 peptideQ34080081
How fast-folding proteins foldQ34228223
Extension of the CHARMM General Force Field to sulfonyl-containing compounds and its utility in biomolecular simulations.Q34347574
Semiempirical hybrid density functional with perturbative second-order correlationQ34488458
Formal Estimation of Errors in Computed Absolute Interaction Energies of Protein-ligand ComplexesQ35031108
Computationally-guided optimization of a docking hit to yield catechol diethers as potent anti-HIV agentsQ35673318
Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and InteroperabilityQ36367823
Benchmark Calculations of Interaction Energies in Noncovalent Complexes and Their ApplicationsQ38760675
Dispersion-Corrected Mean-Field Electronic Structure MethodsQ38808179
Overview of the SAMPL5 host-guest challenge: Are we doing better?Q38818618
How does a drug molecule find its target binding site?Q39280041
ωB97M-V: A combinatorially optimized, range-separated hybrid, meta-GGA density functional with VV10 nonlocal correlationQ39700190
S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures.Q39718353
Revised Damping Parameters for the D3 Dispersion Correction to Density Functional TheoryQ39749720
Divide-and-Conquer Hartree-Fock Calculations on ProteinsQ40000531
New encouraging developments in contact prediction: Assessment of the CASP11 resultsQ40256442
Comparing Counterpoise-Corrected, Uncorrected, and Averaged Binding Energies for Benchmarking Noncovalent Interactions.Q40309043
Assessment of Empirical Models versus High-Accuracy Ab Initio Methods for Nucleobase Stacking: Evaluating the Importance of Charge Penetration.Q40313844
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 SystemsQ40313859
Consistent structures and interactions by density functional theory with small atomic orbital basis sets.Q40645856
Appointing silver and bronze standards for noncovalent interactions: a comparison of spin-component-scaled (SCS), explicitly correlated (F12), and specialized wavefunction approaches.Q42176484
Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges.Q42184293
Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing.Q42199119
A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-PuQ43084146
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.Q43290242
Origin of attraction and directionality of the pi/pi interaction: model chemistry calculations of benzene dimer interactionQ43842672
Ab initio quantum mechanical study of the binding energies of human estrogen receptor alpha with its ligands: an application of fragment molecular orbital methodQ45134713
ωB97X-V: a 10-parameter, range-separated hybrid, generalized gradient approximation density functional with nonlocal correlation, designed by a survival-of-the-fittest strategyQ46357133
Molecular tailoring approach for geometry optimization of large molecules: energy evaluation and parallelization strategiesQ47589406
Natural triple excitations in local coupled cluster calculations with pair natural orbitals.Q48922529
Large-Scale Quantitative Assessment of Binding Preferences in Protein-Nucleic Acid Complexes.Q50709228
Effect of the damping function in dispersion corrected density functional theory.Q51596718
Efficient and Accurate Double-Hybrid-Meta-GGA Density Functionals-Evaluation with the Extended GMTKN30 Database for General Main Group Thermochemistry, Kinetics, and Noncovalent Interactions.Q51606499
Semiempirical GGA-type density functional constructed with a long-range dispersion correction.Q51629241
Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy.Q51961792
A fifth-order perturbation comparison of electron correlation theoriesQ55981123
Basis-set convergence in correlated calculations on Ne, N2, and H2OQ56813616
Semianalytical treatment of solvation for molecular mechanics and dynamicsQ56866446
Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and ExamplesQ56878955
Advances in molecular quantum chemistry contained in the Q-Chem 4 program packageQ57250392
Design of Density Functionals by Combining the Method of Constraint Satisfaction with Parametrization for Thermochemistry, Thermochemical Kinetics, and Noncovalent InteractionsQ57402160
Introduction: Noncovalent InteractionsQ58176337
Extensions of the S66 Data Set: More Accurate Interaction Energies and Angular-Displaced Nonequilibrium GeometriesQ58176506
A Transferable H-Bonding Correction for Semiempirical Quantum-Chemical MethodsQ58176565
Benchmarking Density Functional Methods against the S66 and S66x8 Datasets for Non-Covalent InteractionsQ58201168
Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairsQ58445407
Density-functional approaches to noncovalent interactions: A comparison of dispersion corrections (DFT-D), exchange-hole dipole moment (XDM) theory, and specialized functionalsQ59448054
Simplified CCSD(T)-F12 methods: Theory and benchmarksQ60190567
Levels of symmetry adapted perturbation theory (SAPT). I. Efficiency and performance for interaction energiesQ62018620
Assessment of the Performance of DFT and DFT-D Methods for Describing Distance Dependence of Hydrogen-Bonded InteractionsQ62018628
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 databasesQ62018633
Accurate Intermolecular Interaction Energies from a Combination of MP2 and TDDFT Response TheoryQ62098191
Assessment of a long-range corrected hybrid functional.Q64989139
Improved supermolecular second order Møller-Plesset intermolecular interaction energies using time-dependent density functional response theoryQ81084697
Dispersion-Weighted Explicitly Correlated Coupled-Cluster Theory [DW-CCSD(T**)-F12]Q86776695
P433issue16
P407language of work or nameEnglishQ1860
P921main subjectopen dataQ309901
computational chemistryQ369472
P304page(s)161727
P577publication date2017-10-01
P1433published inJournal of Chemical PhysicsQ900472
P1476titleThe BioFragment Database (BFDb): An open-data platform for computational chemistry analysis of noncovalent interactions
P478volume147

Reverse relations

cites work (P2860)
Q89703160Electron density learning of non-covalent systems
Q89540527How accurate are approximate quantum chemical methods at modelling solute-solvent interactions in solvated clusters?
Q61445559PEPCONF, a diverse data set of peptide conformational energies
Q47667911Preface: Special Topic: From Quantum Mechanics to Force Fields
Q94945792Psi4 1.4: Open-source software for high-throughput quantum chemistry

Search more.