yusuke1997/dblp-id-title huggingface dataset:
Further insights in the ability of classical nonadditive potentials to model actinide ion-water interactions
Optimal position of solute for simulations
Force fields including charge transfer and local polarization effects: Application to proteins containing multi/heavy metal ions
Reaction of OH radical with mono-, di-, and trichloroacetaldehyde: an ab initio study
Influence of ionization on the conformational preferences of peptide models. Ramachandran surfaces of N -formyl-glycine amide and N -formyl-alanine amide radical cations
Prediction of approximate transition states by Bell-Evans-Polanyi principle: I
Putting error bars on the Ab Initio theoretical estimates of the magnetic coupling constants: The parent compounds of superconducting cuprates as a case study
Analysis of lipid surface area in protein-membrane systems combining voronoi tessellation and monte carlo integration methods
High order integration schemes on the unit sphere
The performance of ANI-ML potentials for ligand-n(H 2 O) interaction energies and estimation of hydration free energies from end-point MD simulations
Factor analysis of error in oxidation potential calculation: A machine learning study
Parallelization of multireference perturbation calculations with GAMESS
Revisiting the relationship between the bond length alternation and the first hyperpolarizability with range-separated hybrid functionals
QTAIM and stress tensor interpretation of the (H 2 O) 5 potential energy surface
VRI: 3D QSAR at variable resolution
Computational chemistry study of 3D-structure-function relationships for enzymes based on Markov models for protein electrostatic, HINT, and van der Waals potentials
Amorphous polymerization of nitrogen in compressed cupric azide
Charge parameterization of the metal centers in cytochrome c oxidase
ForConX: A forcefield conversion tool based on XML
Influence of a polarizable surrounding on the electronically excited states of aggregated perylene materials
Can we understand the different coordinations and structures of closed-shell metal cation-water clusters?
Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking
Parameterization of charge model 3 for AM1, PM3, BLYP, and B3LYP
Sprouting side chain conformations in X-PLOR simulations of peptides
Evolutionary method for the assembly of rigid protein fragments
Effect of solvation on the ionization of guanine nucleotide: A hybrid QM/EFP study
Resolutions of the Coulomb operator: VIII. Parallel implementation using the modern programming language X10
Similarity/dissimilarity studies of protein sequences based on a new 2D graphical representation
Three pillars for achieving quantum mechanical molecular dynamics simulations of huge systems: Divide-and-conquer, density-functional tight-binding, and massively parallel computation
An automatic three-dimensional finite element mesh generation system for the Poisson-Boltzmann equation
Concerning the reaction between singlet nitrenium ions and water: A computational investigation on competitive reaction paths
Implementation of machine learning protocols to predict the hydrolysis reaction properties of organophosphorus substrates using descriptors of electron density topology
Dual-level direct dynamics studies on the reaction Cl + CHBr2Cl
Two-level hierarchical parallelization of second-order Møller-plesset perturbation calculations in divide-and-conquer method
SIMONA 1.0: An efficient and versatile framework for stochastic simulations of molecular and nanoscale systems
QM/MM study of the taxadiene synthase mechanism
Mechanisms of CH 4 activation over oxygen-preadsorbed transition metals by ReaxFF and AIMD simulations
Unitary group adapted state specific multireference perturbation theory: Formulation and pilot applications
Reply to "Molecular mechanics models for the image charge"
Magnetic ordering and metal-atom site preference in tetragonal CrMnAs: Electronic correlation effects
Structural, spectroscopic aspects, and electronic properties of (TiO 2 ) n clusters: A study based on the use of natural algorithms in association with quantum chemical methods
Aspects of hybrid QM/MM calculations: The treatment of the QM/MM interface region and geometry optimization with an application to chorismate mutase
Finite group theory for large systems. 3. Symmetry-generation of reduced matrix elements for icosahedral C 20 and C 60 molecules
What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules
Ab initio study of cyclic siloxanes (H2SiO)n: n = 3, 4, 5
On the direct calculation of the free energy of quantization for molecular systems in the condensed phase
Quantum mechanical studies on model alpha-pleated sheets
Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations
Valence state parameters of all transition metal atoms in metalloproteins - development of ABEEMσπ fluctuating charge force field
The molecular modeling toolkit: A new approach to molecular simulations
Induction correction model for rotation of two or three dihedral angles
Computational study on the reactions of H 2 O 2 on TiO 2 anatase (101) and rutile (110) surfaces
A density functional study of propylene glycol conversion to propanal and propanone of various acid-catalyzed reaction models: A water-addition effect
Exploring the relevance of thiophene rings as bridge unit in acceptor-bridge-donor dyes on self-aggregation and performance in DSSCs
The Relaxation of Molecular Crystal Structures Using a Distributed Multipole Electrostatic Model
Conformational analysis of cocaine, the potent analog 2β-carbomethoxy-3β-(4-fluorophenyl)tropane (CFT), and other dopamine reuptake blockers
An efficient, differentiable hydration potential for peptides and proteins
Conformational and electronic study of dopamine interacting with the D2 dopamine receptor
A hierarchical algorithm for fast debye summation with applications to small angle scattering
Quantum Mechanical Computations on Very Large Molecular Systems: The Local Self-Consistent Field Method
Long-range interaction for dimers of atmospheric interest: dispersion, induction and electrostatic contributions for O 2 -O 2 , N 2 -N 2 and O 2 -N 2
DOCK 6: Impact of new features and current docking performance
Theoretical study of intermolecular potential energy surface for HCl dimer: Example of nonspherical atom-atom exchange repulsion interaction
Model calculations for small closed-ring CdS clusters and chemisorption processes by a quantum chemical cluster approach
A comparative study of semiempirical, ab initio , and DFT methods in evaluating metal-ligand bond strength, proton affinity, and interactions between first and second shell ligands in Zn-biomimetic complexes
Computational investigation of the radical-mediated mechanism of formation of difluoro methyl oxindoles: Elucidation of the reaction selectivity and yields
Ab initio and density functional study of the conformational space of 1 C 4 ALFA -L-fucose
The Effects of Conformational Sampling and QM Region Size in QM/MM Simulations: An Adaptive QM/MM Study With Model Systems
Equivalent potential of water molecules for electronic structure of glutamic acid
Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA
Monte Carlo-MST: New strategy for representation of solvent configurational space in solution
Dr.Emb Appyter: A web platform for drug discovery using embedding vectors
Electronic structure and reactivity of guanylthiourea: A quantum chemical study
StreaMD: Advanced analysis of molecular dynamics using R
Ab initio conformational studies on diols and binary diol-water systems using DFT methods. Intramolecular hydrogen bonding and 1: 1 complex formation with water
Adsorption of organic substances on broken clay surfaces: A quantum chemical study
Local approach to coupled cluster evaluation of polarizabilities for long conjugated molecules
QM/MM vibrational mode tracking
Role of atomicity in the oxygen reduction reaction activity of platinum sub nanometer clusters: A global optimization study
Parallelization of CPPTRAJ enables large scale analysis of molecular dynamics trajectory data
Integral algorithm and density matrix integration scheme for ab initio band structure calculations on polymeric systems
DFT assessment of the spectroscopic constants and absorption spectra of neutral and charged diatomic species of group 11 and 14 elements
All-atom polarizable force field for DNA based on the classical drude oscillator model
A comparison of energetic criteria to probe the stabilizing interaction resulting from a bond path between congested atoms
Low-memory iterative density fitting
Anisotropic numerical potentials for coarse-grained modeling from high-speed multidimensional lookup table and interpolation algorithms
Spin parameter optimization for spin-polarized extended tight-binding methods
Producing DFT/MM enzyme reaction trajectories from SCC-DFTB/MM driving forces to probe the underlying electronics of a glycosyltransferase reaction
Effects of external electromagnetic fields on the conformational sampling of a short alanine peptide
Ab initio study of the reaction of CHO+ with H2O and NH3
Conceptual DFT properties-based 3D QSAR: Analysis of inhibitors of the nicotine metabolizing CYP2A6 enzyme
GAMPMS: Genetic algorithm managed peptide mutant screening
Computational insight into excited states of the ring-opening radicals from the pyrolysis of furan biofuels
Improved partition-expansion of two-center distributions involving slater functions
Increasing the time step with mass scaling in Born-Oppenheimer ab initio QM/MM molecular dynamics simulations
Semiempirical PM5 molecular orbital study on chlorophylls and bacteriochlorophylls: Comparison of semiempirical, ab initio, and density functional results
Isomers and isomerization reactions of four nitro derivatives of methane
Display of the Flow of Energy in Molecules
MB-Isoster: A software for bioisosterism simulation
Aspartate: An interesting model for analyzing dipole-ion and ion pair interactions through its oppositely charged amine and acid groups
Force field dependence of phospholipid headgroup and acyl chain properties: Comparative molecular dynamics simulations of DMPC bilayers
Heterogeneous dielectric generalized Born model with a van der Waals term provides improved association energetics of membrane-embedded transmembrane helices
A systematic DFT study of structure and electronic properties of titanium dioxide
CPMD/GULP QM/MM interface for modeling periodic solids: Implementation and its application in the study of Y-zeolite supported Rh n clusters
Cyclooctatetraene dianion - an artifact?
The Extended Law of Corresponding States and the Intermolecular Potentials for Je-He and Ne-Ne
Performance of Range Separated Density Functional in Solvent Continuum: Tuning Long-range Hartree-Fock Exchange for Improved Orbital Energies
Electronic structures of 3d-metal mononitrides
Conformational searching using a population-based incremental learning algorithm
Search for nondegenerate real vertex invariants and derived topological indexes
A finite B-spline basis set for accurate diatomic molecule calculations
Recent advances in planar tetracoordinate carbon chemistry
Theoretical studies of structures and stabilities of a new odd-numbered fullerene dimer: C141
Unraveling individual host-guest interactions in molecular recognition from first principles quantum mechanics: Insights into the nature of nicotinic acetylcholine receptor agonist binding
Excited state relaxation mechanisms of paracetamol and acetanilide
A molecular evolution algorithm for ligand design in DOCK
Pnictogen bond-driven control of the molecular interaction between organophosphorus and acetylcholinesterase enzyme
Effective way of modeling chemical catalysis: Empirical valence bond picture of role of solvent and catalyst in alkylation reactions
Prediction of pKas of Late Transition-Metal Hydrides via a QM/QM Approach
Advancing beyond charge analysis using the electronic localization function: Chemically intuitive distribution of electrostatic moments
Efficient implementation of periodic boundary conditions in Monte Carlo simulation
Rotamer decomposition and protein dynamics: Efficiently analyzing dihedral populations from molecular dynamics
Theoretical model of internal rotation in monosubstituted derivatives of furfural
Theoretical studies for structures and energetics of RgnN2O (RgHe, Ne, Ar) clusters
Enthalpies of formation from B3LYP calculations
Role of bridging water molecules in GSK3β-inhibitor complexes: Insights from QM/MM, MD, and molecular docking studies
Calculation of sequence-dependent free energies of hydration of dipeptides formed by alanine and glycine
Insertion of C 50 into single-walled carbon nanotubes: Selectivity in interwall spacing and C 50 isomers
Comparison of Various Means of Evaluating Molecular Electrostatic Potentials for Noncovalent Interactions
Overcoming dissipation in the calculation of standard binding free energies by ligand extraction
Comment on "A posteriori localization of many-body excited states through simultaneous diagonalization"
Imidazole and nitroimidazole derivatives as NADH-fumarate reductase inhibitors: Density functional theory studies, homology modeling, and molecular docking
Molecular dynamics simulation of O3 photolysis by ultraviolet light in solid argon
Theoretical calculations on C30H12 bowl-shaped hydrocarbons: NMR shielding constants, stability, and aromaticity
Design of [2]rotaxane through image threshold segmentation of electrostatic potential image
A morphometric approach for the accurate solvation thermodynamics of proteins and ligands
Identifying and reducing error in cluster-expansion approximations of protein energies
Low- and high-spin iron (II) complexes studied by effective crystal field method combined with molecular mechanics
Large-scale, long-term nonadiabatic electron molecular dynamics for describing material properties and phenomena in extreme environments
Effect of substitution on the bonding in He dimer confined within dodecahedrane: A computational study
Merck molecular force field. III. Molecular geometries and vibrational frequencies for MMFF94
Making and breaking of small water clusters: A combined quantum chemical and molecular dynamics approach
An efficient algorithm for multistate protein design based on FASTER
Message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines
PROCOS: Computational analysis of protein-protein complexes
Prediction of interactiveness between small molecules and enzymes by combining gene ontology and compound similarity
Use of STOs in Hartree-Fock calculations: Error analysis and variance-minimized pseudospectral method
Electrostatic potentials and covalent radii
Simulations of remote mutants of dihydrofolate reductase reveal the nature of a network of residues coupled to hydride transfer
The mechanism of ring-opening polymerization of L-lactide by ICl3 catalysts: Halogen bond catalysis or participating in reactions?
Enhanced docking with the mining minima optimizer: Acceleration and side-chain flexibility
Theoretical study on the gas-phase reaction mechanism between palladium monoxide and methane
Molecular mechanics calculations of conjugated amides and an ab initio investigation of acrylamide and its -amino derivative: Conformational analysis and rotational barriers
Method for computing protein binding affinity
Theoretical study on the mechanism of the 1CHCl + NO2 reactions
Benchmark of density functional theory methods for the study of organic polysulfides
A multi-descriptor analysis of substituent effects on the structure and aromaticity of benzene derivatives: π-Conjugation versus charge effects
GalaxyDock2-HEME: Protein-ligand docking for heme proteins
Simulating Biomolecules: Festschrift to commemorate the 60th birthday of Charles L. Brooks III
Efficient evaluation of sampling quality of molecular dynamics simulations by clustering of dihedral torsion angles and Sammon mapping
Effect of sampling on BACE-1 ligands binding free energy predictions via MM-PBSA calculations
Sampling potential energy surface of glycyl glycine peptide: Comparison of Metropolis Monte Carlo and stochastic dynamics
Massively parallelization strategy for material simulation using high-dimensional neural network potential
Newly developed basis sets for density functional calculations
Efficient modeling of liquid phase photoemission spectra and reorganization energies: Difficult case of multiply charged anions
Global optimization of parameters in the reactive force field ReaxFF for SiOH
Atomic Partitioning of the MPn (n = 2, 3, 4) Dynamic Electron Correlation Energy by the Interacting Quantum Atoms Method: A Fast and Accurate Electrostatic Potential Integral Approach
Self-organizing superimposition algorithm for conformational sampling
Comparative study of various normal mode analysis techniques based on partial Hessians
Structural, electronic, and optical properties of 9-heterofluorenes: A quantum chemical study
Theoretical study of the prion protein based on the fragment molecular orbital method
Harmonic modes as variables to approximately account for receptor flexibility in ligand-receptor docking simulations: Application to DNA minor groove ligand complex
Physical nature of silane⋯carbene dimers revealed by state-of-the-art ab initio calculations
An alternative to the "Star Path" enhancement of the ADMA linear scaling method for protein modeling
Drug repositioning to target NSP15 protein on SARS-CoV-2 as possible COVID-19 treatment
Improving the accuracy of the spatial discretization in finite-difference electrochemical kinetic simulations, by means of the extended Numerov method
Hydrogen bonding of carbonyl, ether, and ester oxygen atoms with alkanol hydroxyl groups
Assessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin-DNA duplex complexes in aqueous solution
Re-examination of structure optimization of off-lattice protein AB models by conformational space annealing
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
Conformational Memories and a Simulated Annealing Program That Learns: Application to LTB 4
Estimations of energy of noncovalent bonding from integrals over interatomic zero-flux surfaces: Correlation trends and beyond
The Role of the Carboxylate Ion in Models of Acyl-Chymotrypsin
Free energy simulation of helical transitions
Implementation of a graphical user interface for the virtual multifrequency spectrometer: The VMS-Draw tool
Generalized morse analytic function for the "true" diatomic potential of the RKR type
To be or not to be butterfly: New mechanistic insights in the Aza-Michael asymmetric addition of lithium ( R )- N -benzyl- N -(α-methylbenzyl)amide
Stochastic search for isomers on a quantum mechanical surface
Attractive electron-electron interactions within robust local fitting approximations
Rapid evaluation of the binding energies in hydrogen-bonded amide-thymine and amide-uracil dimers in gas phase
Cover Image, Volume 41, Issue 1
Use of caps in the auxiliary basis set formulation of the fragment molecular orbital method
A challenging system: Free energy prediction for factor Xa
Thermodynamics of chemical reactions with COSMO-RS: The extreme case of charge separation or recombination
Efficient combination of Wang-Landau and transition matrix Monte Carlo methods for protein simulations
Simulations of the Solution Structure of HIV-1 Protease in the Presence and Absence of Bound Zinc
Negative influence of pKa on activation energy barrier: A case study for double proton transfer reaction in inorganic acid dimers
Linear response theory in dihedral angle space for protein structural change upon ligand binding
Strike a balance: Optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides
Electronic structure, X-ray absorption, and optical spectroscopy of LaCoO 3 in the ground-state and excited-states
MIBPB: A software package for electrostatic analysis
Atomic Orbital Basis Sets for Molecular Interactions
A new hierarchical parallelization scheme: Generalized distributed data interface (GDDI), and an application to the fragment molecular orbital method (FMO)
Automated handling of complex chemical structures in Z -matrix coordinates - The chemcoord library
Accuracy and convergence of free energy differences calculated from nonequilibrium switching processes
Characterization of the structure and reactivity of monocopper-oxygen complexes supported by -diketiminate and anilido-imine ligands
Modulation of Intramolecular Proton Transfer by Electronic Excitation and Environment: 2-Pyridone as a Case Study
The role of databases in support of computational chemistry calculations
Theoretical Insights Into Structures and U-C Bonding in the Uranium Benzyl Derivatives
MkVsites: A tool for creating GROMACS virtual sites parameters to increase performance in all-atom molecular dynamics simulations
Conformations, energies, and intramolecular hydrogen bonds in dicarboxylic acids: Implications for the design of synthetic dicarboxylic acid receptors
Improving the scaling and performance of multiple time stepping-based molecular dynamics with hybrid density functionals
Hybrid molecular dynamics-quantum mechanics simulations of solute spectral properties in the condensed phase: Evaluation of simulation parameters
Linear-scaling soft-core scheme for alchemical free energy calculations
Accelerating atomistic simulations of proteins using multiscale enhanced sampling with independent tempering
FALDI-based decomposition of an atomic interaction line leads to 3D representation of the multicenter nature of interactions
A machine learning potential construction based on radial distribution function sampling
Improvements of network approach for analysis of the folding free-energy surface of peptides and proteins
Revisiting the geometry of nd10 (n+1)s0 [M(H2O)]p+ complexes using four-component relativistic DFT calculations and scalar relativistic correlated CSOV energy decompositions (Mp+ = Cu+, Zn2+, Ag+, Cd2+, Au+, Hg2+)
Determining Optimal Coarse-Grained Representation for Biomolecules Using Internal Cluster Validation Indexes
Comparison of embedded cluster models to study zeolite catalysis: Proton transfer reactions in acidic chabazite
Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. I. The method
Theoretical investigation of anthracene-9, 10-endoperoxide vertical singlet and triplet excitation spectra
[Cu 6 (NGuaS) 6 ] 2+ and its oxidized and reduced derivatives: Confining electrons on a torus
Excited states of ortho-nitrobenzaldehyde as a challenging case for single- and multi-reference electronic structure theory
Three-dimensional representation of the pure electric-dipole and the mixed first hyperpolarizabilities: The modified unit sphere representation
Constrained optimization in cartesian coordinates
Fully polarizable QM/MM calculations: An application to the nonbonded iodine-oxygen interaction in dimethyl-2-iodobenzoylphosphonate
A semi-implicit solvent model for the simulation of peptides and proteins
On the use of big-bang method to generate low-energy structures of atomic clusters modeled with pair potentials of different ranges
Interacting quantum fragments-rooted preorganized-interacting fragments attributed relative molecular stability of the Be II complexes of nitrilotriacetic acid and nitrilotri-3-propionic acid
Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA
Exploring the Possibility of a Planar Tetracoordinate Boron in BXY 3 (X = B, Al, Ga; Y = C, Si, Ge) Clusters: A Theoretical Study
Conformational analysis by intersection: CONAN
CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data