yusuke1997/dblp-id-title huggingface dataset:
Modeling of diarylalkyl-imidazole and diarylalkyl-triazole derivatives as potent aromatase inhibitors for treatment of hormone-dependent cancer
BSSE-correction scheme for consistent gaussian basis sets of double- and triple-zeta valence with polarization quality for solid-state calculations
Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models
Book Review: "Electron Localization-Delocalization Matrices" by Chérif F. Matta, Paul W. Ayers, and Ronald Cook
Molecular dynamics simulations of the dinuclear zinc--lactamase from Bacteroides fragilis complexed with imipenem
Optimization of the Lennard-Jones parameters for a combined ab initio quantum mechanical and molecular mechanical potential using the 3-21G basis set
Fluoride anion sensing mechanism of a BODIPY-linked hydrogen-bonding probe
Atomistic detailed free-energy landscape of intrinsically disordered protein studied by multi-scale divide-and-conquer molecular dynamics simulation
Polarized basis sets of Slater-type orbitals: H to Ne atoms
Ground-state structures of polymers
A Monte Carlo approach to study the effect of ions on the nucleation of sulfuric acid-water clusters
Cover Image, Volume 39, Issue 21
Accurate relativistic adapted Gaussian basis sets for Cesium through Radon without variational prolapse and to be used with both uniform sphere and Gaussian nucleus models
Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential
Evaluation of replica exchange with repulsive scaling approach for docking glycosaminoglycans
A fully analytical integration of properties over the 3D volume of the β sphere in topological atoms
The SAAP force field. A simple approach to a new all-atom protein force field by using single amino acid potential (SAAP) functions in various solvents
Discovering targeted inhibitors for Escherichia coli efflux pump fusion proteins using computational and structure-guided approaches
Is there a unique melting temperature for two-state proteins?
Multiple field three dimensional quantitative structure-activity relationship (MF-3D-QSAR)
Reaction mechanism of palladium-catalyzed silastannation of allenes by density functional theory
Including ligand-induced protein flexibility into protein tunnel prediction
Insights into the cooperativity between multiple interactions of dimethyl sulfoxide with carbon dioxide and water
DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding
Additive empirical force field for hexopyranose monosaccharides
Electrostatic potentials and fields from density expansions of deformed atoms in molecules
Spectral density calculation by using the Chebyshev expansion
Empirical force field and ab initio calculations on allyl cations
Reactions involving some gas molecules through sequestration on Al12Be cluster: An electron density based study
Variational transition state theory rate constants and H/D kinetic isotope effects for CH3 + CH3OCOH reactions
LIBEFP: A new parallel implementation of the effective fragment potential method as a portable software library
Multidimensional scaling of combinatorial libraries without explicit enumeration
Computational NMR spectroscopy of 205 Tl
Theoretical calculations: Can Gibbs free energy for intermolecular complexes be predicted efficiently and accurately?
Theoretical studies on a possible synthesis reaction pathway on N8 (CS) clusters
Theoretical study of intramolecular hydrogen bonding and molecular geometry of 2-trifluoromethylphenol
Substrates (Acyl-CoA and Diacylglycerol) Entry and Products (CoA and Triacylglycerol) Egress Pathways in DGAT1
Strength of hydrogen bonds in helices
Enantioselective organocatalytic diels-Alder reactions: A density functional theory and kinetic isotope effects study
Pharmacophore alignment search tool: Influence of the third dimension on text-based similarity searching
Advancing molecular graphs with descriptors for the prediction of chemical reaction yields
Internal coordinate modeling of DNA: Force field comparisons
Hydration effects on the vibrational properties of carboxylates: From continuum models to QM/MM simulations
Intensity-carrying modes important for vibrational polarizabilities and hyperpolarizabilities of molecules: Derivation from the algebraic properties of formulas and applications
Through-Space/Through-Bond Energy Decomposition Analysis Clarifies the Mechanism of Transition Mutation in DNA Containing O6-Methylguanine Lesion
Distributed and multicore QuBiLS-MIDAS software v2.0: Computing chiral, fuzzy, weighted and truncated geometrical molecular descriptors based on tensor algebra
Method and algorithm of obtaining the molecular intrinsic characteristic contours (MICCs) of organic molecules
Cr 2 Ge n - ( n = 15-20) clusters with two Cr atoms exhibited antiferromagnetic coupling
Thermodynamic calculations for molecules with asymmetric internal rotors. II. Application to the 1, 2-dihaloethanes
Interpreting the behavior of the NICSzz by resolving in orbitals, sign, and positions
Structural fluctuation and concerted motions in F 1 -ATPase: A molecular dynamics study
Comparison of basis set effects and the performance of ab initio and DFT methods for probing equilibrium fluctuations
How do spin-scaled double hybrids designed for excitation energies perform for noncovalent excited-state interactions? An investigation on aromatic excimer models
Temperature-shuffled parallel cascade selection molecular dynamics accelerates the structural transitions of proteins
Spin State Energetics of VGe n-/0 (n = 5-7) Clusters and New Assignments of the Anion Photoelectron Spectra
A quasi-flexible automatic docking processing for studying stereoselective recognition mechanisms. Part I. Protocol validation
Fluctuating charge normal modes: An algorithm for implementing molecular dynamics simulations with polarizable potentials
Extension of CAVS coarse-grained model to phospholipid membranes: The importance of electrostatics
Electronic structure study of the initiation routes of the dimethyl sulfide oxidation by OH
DNA base stacking: The stacked uracil/uracil and thymine/thymine minima
Argentophillic interactions in argentum chalcogenides: First principles calculations and topological analysis of electron density
Generalized Foldy-Wouthuysen transformation for relativistic two-component methods: Systematic analysis of two-component Hamiltonians
Density functional Gaussian-type orbital approach in theoretical study of S2F2 isomerization
Challenging the electrostatic σ-hole picture of halogen bonding using minimal models and the interacting quantum atoms approach
The Effects of Solvent Screening in Quantum Mechanical Calculations in Protein Systems
Counterpoise correction is not useful for short and Van der Waals distances but may be useful at long range
Bond detectors for molecular dynamics simulations, Part I: Hydrogen bonds
Protegrin-1 orientation and physicochemical properties in membrane bilayers studied by potential of mean force calculations
Modulating the oxygen affinity of porphyrins with metals, ligands, and functional groups: A DFT study
A flexible nudged elastic band program for optimization of minimum energy pathways using ab initio electronic structure methods
Block-adaptive quantum mechanics: An adaptive divide-and-conquer approach to interactive quantum chemistry
Acceleration of self-consistent-field convergence by combining conventional diagonalization and a diagonalization-free procedure
PM3 geometry optimization and CNDO/S-CI computation of UV/Vis spectra of large organic structures: Program description and application to poly(triacetylene) hexamer and taxotere
Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation
Water molecules inside protein structure affect binding of monosaccharides with HIV-1 antibody 2G12
Analysis of the transferability of atomic multipoles for amino acids in modeling macromolecular charge distribution from fragments
GPCR-CA: A cellular automaton image approach for predicting G-protein-coupled receptor functional classes
Conformational analysis of model compounds of vitamin D by theoretical calculations
Density functional theory study on electron and hole transport properties of organic pentacene derivatives with electron-withdrawing substituent
The explicit role of electron exchange in the hydrogen bonded molecular complexes
DFT-D4 counterparts of leading meta-generalized-gradient approximation and hybrid density functionals for energetics and geometries
Hydrated germanium (II): Irregular structural and dynamical properties revealed by a quantum mechanical charge field molecular dynamics study
AQUARIUS2: Knowledge-based modeling of solvent sites around proteins
Endo- and exohedral complexes of superphane with cations
A theoretical investigation on doping superalkali for triggering considerable nonlinear optical properties of Si 12 C 12 nanostructure
Are the solvent effects critical in the modeling of polyoxoanions?
The Dirac equation in quantum chemistry: Strategies to overcome the current computational problems
Molecular acidity: An accurate description with information-theoretic approach in density functional reactivity theory
The verification of delta SCF and Slater's transition state theory for the calculation of core ionization energy
Cyclization of an α , β -Unsaturated hydrazone catalyzed by a BINOL-phosphoric acid: Pericyclic or not?
Use of ab initio methods for the interpretation of the experimental IR reflectance spectra of crystalline compounds
Charge carrier mobilities in organic semiconductor crystals based on the spectral overlap
Mechanism and Stereoselectivity of the Elementometalation Process of Activated Alkyne RCCR(RCO2Me) by Cp2TaH3
Dynamics and mechanism of structural diffusion in linear hydrogen bond
Inherent structure versus geometric metric for state space discretization
The structure of 1-chlorosilatrane: An ab initio molecular orbital and a density functional theory study
G-Protein-Coupled Receptor-Membrane Interactions Depend on the Receptor Activation State
System truncation accelerates binding affinity calculations with the fragment molecular orbital method: A benchmark study
Soft-core potentials in thermodynamic integration: Comparing one- and two-step transformations
From simulation data to conformational ensembles: Structure and dynamics-based methods
Chemical bonding in view of electron charge density and kinetic energy density descriptors
GPU-accelerated molecular mechanics computations
Visualizing energy landscapes with metric disconnectivity graphs
On combining Thole's induced point dipole model with fixed charge distributions in molecular mechanics force fields
Building molecular charge distributions from fragments: Application to HIV-1 protease inhibitors
A simple and consistent quantum-chemical fragmentation scheme for proteins that includes two-body contributions
Accurate molecular electrostatic potentials based on modified PRDDO/M wave functions: II. Electrostatic potentials inside the molecular van der Waals envelope
Pattern recognition strategies for molecular surfaces: III. Binding site prediction with a neural network
WavePacket: A Matlab package for numerical quantum dynamics. III. Quantum-classical simulations and surface hopping trajectories
Rapid and accurate assessment of GPCR-ligand interactions Using the fragment molecular orbital-based density-functional tight-binding method
Pattern recognition strategies for molecular surfaces. I. Pattern generation using fuzzy set theory
On the strength of hydrogen bonding within water clusters on the coordination limit
Nonempirical analysis of nature of catalytic effects in ribonuclease A active site
Theoretical studies on nonlinear optical properties of formaldehyde oligomers by ab initio and density functional theory methods
Distance geometry and protein loop modeling
Stereodynamics of bond rotation in tertiary 1-naphthoic acid amides: A computational study
The Pfizer Crystal Structure Database: An essential tool for structure-based design at Pfizer
Comparison of free-energy methods using a tripeptide-water model system
Equilibrium inversion barrier of NH3 from extrapolated coupled-cluster pair energies
Theoretical study on the reaction mechanism of the methyl radical with nitrogen oxides
Analytical excited state forces for the time-dependent density-functional tight-binding method
Influence of calculation level and effect of methylation on axial/equatorial equilibria in piperidines
First-principle investigation of magnetic coupling mechanism in hypothesized A-site-ordered perovskite YMn 3 Sc 4 O 12
Optimization of complex slater-type functions with analytic derivative methods for describing photoionization differential cross sections
Revisiting the concept of the (a)synchronicity of diels-alder reactions based on the dynamics of quasiclassical trajectories
Calculation of atomic integration data
Closed loop folding units from structural alignments: Experimental foldons revisited
Cohesive properties of CeN and LaN from first principles
Extension and validation of the GROMOS 53A6 glyc parameter set for glycoproteins
On orthogonality constrained multiple core-hole states and optimized effective potential method
ACCDB: A collection of chemistry databases for broad computational purposes
A revised quantum chemistry-based potential for poly(ethylene oxide) and its oligomers in aqueous solution
Evaluating thermodynamic integration performance of the new amber molecular dynamics package and assess potential halogen bonds of enoyl-ACP reductase (FabI) benzimidazole inhibitors
Solvent-driven symmetry of self-assembled nanocrystal superlattices - A computational study
Improved intermolecular force field for molecules containing H, C, N, and O atoms, with application to nucleoside and peptide crystals
Glycan reader: Automated sugar identification and simulation preparation for carbohydrates and glycoproteins
QuickFF: A program for a quick and easy derivation of force fields for metal-organic frameworks from ab initio input
Hydrogen bonding, solvation, and hydrolysis of cisplatin: A theoretical study
Urea: An ab initio and force field study of the gas and solid phases
On the molecular electron structure of three phosphinine-containing macrocycles
Molecular dynamics for very large systems on massively parallel computers: The MPSim program
Computational study of energetic nitrogen-rich derivatives of 1, 1′- and 5, 5′-bridged ditetrazoles
Comparative study of the photocatalytic activity of g-C 3 N 4 /MN 4 (M = Mn, Fe, Co) for water splitting reaction: A theoretical study
Importance of selecting proper basis set in quantum mechanical studies of potential energy surfaces of carbohydrates
Structure of isolated and solvated peroxyl radicals
Spin densities in two-component relativistic density functional calculations: Noncollinear versus collinear approach
Structure and bonding of proximity-enforced main-group dimers stabilized by a rigid naphthyridine diimine ligand
Effect of an underdamped vibration with both diagonal and off-diagonal exciton-phonon interactions on excitation energy transfer
Gaussian-type function set without prolapse for the Dirac-Fock-Roothaan equation
Reliable protein structure refinement using a physical energy function
Molecular dynamics simulation of liquid water and ice nanoclusters using a new effective HFD-like model
Estimation of p K a for organic oxyacids using calculated atomic charges
Ab initio study of the formation of C3H3+ from the reaction of CH3+ with acetylene
Density functional theory study on mechanisms of epoxy-phenol curing reaction
Comparative first principles-based molecular dynamics study of catalytic mechanism and reaction energetics of water oxidation reaction on 2D-surface
Qmd-plot: A graphical utility for rapid preliminary analysis of time series of fluctuating data, developed in the context of molecular dynamics simulations
pyEFP: Automatic decomposition of the complex molecular systems into rigid polarizable fragments
Application of a semi-empirical dispersion correction for modeling water clusters
High performance collision cross section calculation - HPCCS
New invariant of DNA sequence based on 3DD-curves and its application on phylogeny
Perturbative treatment of anharmonic vibrational effects on bond distances: An extended langevin dynamics method
Numerical instabilities in the computation of pseudopotential matrix elements
Chemical repair of damaged leucine and tryptophane by thiophenols at close to diffusion-controlled rates: Mechanisms and kinetics
Visualization and integration of quantum topological atoms by spatial discretization into finite elements
Directional hydrogen bonding in the MM3 force field: II
The role of water in the proton transfer reaction mechanism in tryptophan
Methodological aspects of QM/MM calculations: A case study on matrix metalloproteinase-2
Thermally induced phase transition in helical comblike poly(-peptide)s: An atomistic simulation
Computational study of ground-state properties of μ 2 -bridged group 14 porphyrinic sandwich complexes
Modeling loop backbone flexibility in receptor-ligand docking simulations
pmx: Automated protein structure and topology generation for alchemical perturbations
Continuous medium theory for nonequilibrium solvation: III. Solvation shift by monopole approximation and multipole expansion in spherical cavity
Accurate Kohn-Sham ionization potentials from scaled-opposite-spin second-order optimized effective potential methods
A universal Gaussian basis set for atoms cerium through lawrencium generated with the generator coordinate Hartree-Fock method
Implementation of empirical dispersion corrections to density functional theory for periodic systems
Conformational selection of protein kinase A revealed by flexible-ligand flexible-protein docking
Benzene is not very rigid
A comparative study of some red- and blue-shifted linear H-bonded complexes of N 2
Assessing protein-ligand docking for the binding of organometallic compounds to proteins
Photoionization cross sections with optimized orbital exponents within the complex basis function method
Global exploration of isomers and isomerization channels on the quantum chemical potential energy surface of H 3 CNO 3
Theoretical study on the luminescent and reaction mechanism of dansyl-based fluorescence probe for detecting hydrogen sulfide
Peptide docking using dynamic programming
Finite-State and Reduced-Parameter Representations of Protein Backbone Conformations
Fitting atomic correlation parameters for RECEP (rapid estimation of correlation energy from partial charges) method to estimate molecular correlation energies within chemical accuracy
Realization of the structural fluctuation of biomolecules in solution: Generalized Langevin mode analysis
Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC
DOX: A new computational protocol for accurate prediction of the protein-ligand binding structures
Minimization of empirical energy functions in proteins including hydrophobic surface area effects
Ab initio calculations of the ground and excited states of the ZrN molecule including spin-orbit effects
Photoionization cross sections of H 2 + and H 2 with complex Gaussian-type basis functions optimized for the frequency-dependent polarizabilities
General Parameterization of a Reaction Field Theory Combined with the Boundary Element Method
Calculation of rovibrational energy levels of diatomic molecules by Dunham method with potential obtained from ab initio calculations
Application of conformational space annealing to the protein structure modeling using cryo-EM maps
Force field-dependent solution properties of glycine oligomers
Fluctuation analysis and accuracy of a large-scale in silico screen
Using projection operators with maximum overlap methods to simplify challenging self-consistent field optimization
MAGPACK1 A package to calculate the energy levels, bulk magnetic properties, and inelastic neutron scattering spectra of high nuclearity spin clusters
d-electron count, ion-pairing and diagonal twist angles in metallo-bis(dithiolene) complexes
DFT-GIAO calculations of 19F NMR chemical shifts for perfluoro compounds
Comment on "QSAR model reproducibility and applicability: A case study of rate constants of hydroxyl radical reaction models applied to polybrominated diphenyl ethers and (Benzo-)triazoles"
A theoretical investigation of benzothiadiazole derivatives for high efficiency OLEDs
Exact and efficient calculation of lagrange multipliers in biological polymers with constrained bond lengths and bond angles: Proteins and nucleic acids as example cases
MSINDO study of acid promoted dissolution of planar MgO and NiO surfaces
Parametrization of aliphatic CHn united atoms of GROMOS96 force field
Machine-learning assisted scheduling optimization and its application in quantum chemical calculations
Improving the accuracy of predicting disulfide connectivity by feature selection
Radical reaction C3H+NO: A mechanistic study
Maxima of |Ψ|2: A connection between quantum mechanics and Lewis structures
Brownian dynamics simulations on CPU and GPU with BD_BOX
Numerical Solution of t he Nonlinear Poisson-Blotzmann Equation: Developing More Robust and Efficient Methods
Effects of spin-orbit coupling on magnetic properties of discrete and extended magnetic systems
Modeling exact exchange potential in spherically confined atoms
Interactive quantum chemistry: A divide-and-conquer ASED-MO method
What Happens Without Nickel? Cyclization Reactions of Ethylene with Ethanedithial and Related Molecules
Silaacetylene: A possible target for experimental studies
QSAR model reproducibility and applicability: A case study of rate constants of hydroxyl radical reaction models applied to polybrominated diphenyl ethers and (benzo-)triazoles
Interaction of NO molecules with Pd clusters: Ab initio density-functional study
Comparative DFT study of vibrational, electronic, and optical properties of energetic alkali metal salts based on nitrogen-rich 5-aminotetrazole
Low barrier kinetics: Dependence on observables and free energy surface
A partition function-based weighting scheme in force field parameter development using ab initio calculation results in global configurational space
Ab initio computational study of positron emission tomography ligands interacting with lipid molecule for the prediction of nonspecific binding
Improved grid-based algorithm for Bader charge allocation
Conjugated circuits currents in hexabenzocoronene and its derivatives formed by joining proximal carbons
Protein-protein docking by shape-complementarity and property matching
A comment to the nudged elastic band method
Elongation cutoff technique armed with quantum fast multipole method for linear scaling
Multiple-site ligand binding to flexible macromolecules: Separation of global and local conformational change and an iterative mobile clustering approach
Determination of the effective dielectric constant from the accurate solution of the Poisson equation
An extensible interface for QM/MM molecular dynamics simulations with AMBER
Searching for local order parameters to classify water structures at triple points
A new hybrid DFT approach to electronic excitation and first hyperpolarizabilities of transition metal complexes
Can DFT methods correctly and efficiently predict the coordination number of copper(I) complexes? A case study
Development of spin-orbit coupling for stochastic configuration interaction techniques
An optimum strategy for solution chemistry using semiempirical molecular orbital method. II. Primary importance of reproducing electrostatic interaction in the QM/MM framework
The hardness kernel as the basis for global and local reactivity indices
Study of localized molecular orbitals using group theory methods and its approach to the many-electron correlation problem. III. Orthogonal bonded functions
The role of different sampling methods in improving biological activity prediction using deep belief network
The effect of the sixth sulfur ligand in the catalytic mechanism of periplasmic nitrate reductase
Correspondence between GTO and STO molecular basis sets
CH/ interactions involving aromatic amino acids: Refinement of the CHARMM tryptophan force field