yusuke1997/dblp-id-title huggingface dataset:
Integrated design environment: A multi-use platform for design idea capture, evaluation, and tracking in medicinal chemistry
Variation of Atomic Charges during Proton Transfer in Hydrogen Bonds
Assessment and acceleration of binding energy calculations for protein-ligand complexes by the fragment molecular orbital method
Boron-doped diamond: Investigation of the stability of surface-doping versus bulk-doping using cyclic cluster model calculations
Gas-phase thermochemistry of noncovalent ligand-alkali metal ion clusters: An impact of low frequencies
Shift-and-invert parallel spectral transformation eigensolver: Massively parallel performance for density-functional based tight-binding
Towards optimal boundary integral formulations of the Poisson-Boltzmann equation for molecular electrostatics
The performance of different density functional methods in the calculation of molecular structures and vibrational spectra of platinum(II) antitumor drugs: cisplatin and carboplatin
Energetics of mechanism of OH-propene reaction at low pressures in inert atmosphere
An influence of electronic structure theory method, thermodynamic and implicit solvation corrections on the organic carbonates conformational and binding energies
Definition of Systematic, Approximately Separable, and Modular Internal Coordinates (SASMIC) for macromolecular simulation
A Truncated Newton Minimizer Adapted for CHARMM and Biomolecular Applications
Interaction identification of Zif268 and TATA ZF proteins with GC-/AT-rich DNA sequence: A theoretical study
Protein folding pathways extracted by OFLOOD: Outlier FLOODing method
Computational screening of transition metal/p-block hybrid electrocatalysts for CO2 reduction
Variation of free-energy landscape of the p53 C-terminal domain induced by acetylation: Enhanced conformational sampling
A Topological method for global optimization of clusters: Application to (TiO 2 ) n ( n = 1-6)
Theoretical analysis of the kinetic isotope effect on carboxylation in RubisCO
On the atomistic origin of the polymorphism and the dielectric physical properties of beryllium oxide
Finding the transition state without initial guess: The growing string method for Newton trajectory to isomerization and enantiomerization reaction of alanine dipeptide and poly(15)alanine
The trans effect in square-planar platinum(II) complexes - A density functional study
Conformations and binding pockets of HRas and its guanine nucleotide exchange factors complexes in the guanosine triphosphate exchange process
EPISOL: A software package with expanded functions to perform 3D-RISM calculations for the solvation of chemical and biological molecules
Decoupling approximations for quantum vibrational predissociation dynamics: The tests on the low-level golden rule approaches for some rare gas - Cl2, ICl complexes
Relative contributions of desolvation, inter- and intramolecular interactions to binding affinity in protein kinase systems
Atomic Charges Derived from a Fast and Accurate Method for Electrostatic Potentials Based on Modified AM1 Calculations
Electric field assisted oxygen removal from the basal plane of the graphitic material
Protein3D: Enabling analysis and extraction of metal-containing sites from the Protein Data Bank with molSimplify
Fast topological analysis of 2D and 3D grids of data: Application to the atoms in molecule (AIM) and the electron localization function (ELF)
Structure and spectroscopic aspects of water-halide ion clusters: A study based on a conjunction of stochastic and quantum chemical methods
A stationary-wave model of enzyme catalysis
Can TD-DFT calculations accurately describe the excited states behavior of stacked nucleobases? The cytosine dimer as a test case
An open-source framework for analyzing N -electron dynamics. I. Multideterminantal wave functions
Application of a simple diagonal force field to the simulation of cyclopentane conformational dynamics
Ground- and excited-state properties of DNA base molecules from plane-wave calculations using ultrasoft pseudopotentials
The hydroperoxy radical as a hydrogen bond acceptor. HOO-HCl complexes - Ab initio study
VoteDock: Consensus docking method for prediction of protein-ligand interactions
Isomerization and fragmentation pathways of 1, 2-azaborine
Reexamination of the π-bond strengths within H 2 C=XH n systems: A theoretical study
New AMBER force field parameters of heme iron for cytochrome P450s determined by quantum chemical calculations of simplified models
Overlapping electron density and the global delocalization of π -aromatic fragments as the reason of conductivity of the biphenylene network
Automated molecular mechanics parameterization with simultaneous utilization of experimental and quantum mechanical data
DFT calculations on molecular structures, HOMO-LUMO study, reactivity descriptors and spectral analyses of newly synthesized diorganotin(IV) 2-chloridophenylacetohydroxamate complexes
Complex configuration interaction calculations of the cross section for the dissociative electron attachment process e - + F 2 → F
Genetic algorithm for the determination of binodal curves in ternary systems polymer-liquid(1)-liquid(2) and polymer(1)-polymer(2)-solvent
C--H bond activation of methane in aqueous solution: A hybrid quantum mechanical/effective fragment potential study
Indexing molecules with chemical graph identifiers
Stereoelectronic properties of spiroquinazolinones in differential PDE7 inhibitory activity
Cover Image, Volume 41, Issue 12
Theoretical study on nonlinear optical properties of the Li + [calix[4]pyrrole]Li - dimer, trimer and its polymer with diffuse excess electrons
The calculation of static polarizabilities of 1-3D periodic compounds. the implementation in the crystal code
Molecular dynamics simulation of a rhinovirus capsid under rotational symmetry boundary conditions
Composition-selective full inclusion host-guest interaction of azobenzene-containing photoresponsive nanoring with fullerene C60
Rapidly converging lattice sums for nonelectrostatic interactions
A Highly Correlated, Multireference Study of the Lowest Lying Singlet and Triplet States of the Four Thiophene Diradicals
Binding of D- and L-captopril inhibitors to metallo--lactamase studied by polarizable molecular mechanics and quantum mechanics
An improved method for nonbonded list generation: Rapid determination of near-neighbor pairs
Structural, electronic, magnetic and thermoelectric properties of Tl 2 NbX 6 (X = Cl, Br) variant perovskites calculated via density functional theory
Systematic QM/MM investigation of factors that affect the cytochrome P450-catalyzed hydrogen abstraction of camphor
Prediction of self-diffusion coefficients of chemically diverse pure liquids by all-atom molecular dynamics simulations
Consistent scheme for computing standard hydrogen electrode and redox potentials
Perturbative formulation of dispersion contributions to interaction energy of van der Waals systems of closed-shell-open-shell type
Structures and stability of I 2 and ICl complexes with pyridine: Ab initio and DFT study
Saturn Systems
Localization of molecular orbitals on fragments
MOLCAS 7: The Next Generation
A molecular mechanics force field for lignin
ESCASA: Analytical estimation of atomic coordinates from coarse-grained geometry for nuclear-magnetic-resonance-assisted protein structure modeling. I. Backbone and Hβ protons
Fully optimized implementation of the cluster-in-molecule local correlation approach for electron correlation calculations of large systems
Artificial reaction coordinate "tunneling" in free-energy calculations: The catalytic reaction of RNase H
Electronic structures of NbGen-/0/+ (n = 1-3) clusters from multiconfigurational CASPT2 and density matrix renormalization group-CASPT2 calculations
Does the choice of the crystal structure influence the results of the periodic DFT calculations? A case of glycine alpha polymorph GIPAW NMR parameters computations
Flexible Ligand Docking without Parameter Adjustment across Four Ligand-Receptor Complexes
Fast evaluation of scaled opposite spin second-order Møller-Plesset correlation energies using auxiliary basis expansions and exploiting sparsity
Diffusive dynamics of DNA unzipping in a nanopore
Mechanistic studies on the formation of glycosidase-substrate and glycosidase-inhibitor covalent intermediates
Voids and necks in liquid ammonia and their roles in diffusion of ions of varying size
B, N-Codoped graphene as catalyst for the oxygen reduction reaction: Insights from periodic and cluster DFT calculations
DNA-backbone radio resistivity induced by spin blockade effect
Automated reaction mechanisms and kinetics with the nudged elastic band method-based AMK_Mountain and its description of the preliminary alkaline hydrolysis of nitrocellulose monomer
Search for transition states with external forces
Mechanistic insights into oxidosqualene cyclizations through homology modeling
Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates
Comment on the paper "indexing molecules with chemical graph Identifiers" by Elisabeth Gregori-Puigjané, Rut Garriga-Sust, and Jordi Mestres
The Ad-MD method to calculate NMR shift including effects due to conformational dynamics: The 31P NMR shift in DNA
Theoretical study of the atrazine pesticide interaction with pyrophyllite and Ca 2+ -montmorillonite clay surfaces
QM and QM/MM umbrella sampling MD study of the formation of Hg(II)-thymine bond: Model for evaluation of the reaction energy profiles in solutions with constant pH
Linear, planar, and tubular molecular structures constructed by double planar tetracoordinate carbon D 2 h C 2 (BeH) 4 species via hydrogen-bridged -BeH 2 Be- bonds
Geometry dependence of excitonic couplings and the consequences for configuration-space sampling
Relativistic all-electron density functional calculations
Basis-Modified hydrogen atoms as embedding atoms in ab initio chemisorption cluster model calculations on Si surfaces
Energy density analysis of cluster size dependence of surface-molecule interactions (II): Formate adsorption onto a Cu(111) surface
Predicting peptide binding sites on protein surfaces by clustering chemical interactions
The bergman cyclizations of the enediyne and its N-substituted analogs using multiconfigurational second-order perturbation theory
How cation nature controls the bandgap and bulk Rashba splitting of halide perovskites
Limitations of Global Hybrids in Predicting the Geometries and Torsional Energy Barriers of Dimeric Systems and the Role of Hartree Fock and DFT Exchange
Hydride-Triel Bonds
A DFT study of the mechanism of Ni superoxide dismutase (NiSOD): Role of the active site cysteine-6 residue in the oxidative half-reaction
Parameterization of Ca +2 -protein interactions for molecular dynamics simulations
On the many-body nature of intramolecular forces in FFLUX and its implications
Another look at energetically quasi-degenerate structures of the gold cluster Au27q with q = 1, 0, -1
A Density Functional Theory Study on Nonlinear Optical Properties of Double Cage Excess Electron Compounds: Theoretically Design M[Cu(Ag)@(NH3)n](M = Be, Mg and Ca; n = 1-3)
Energetics of Zn 2+ Binding to a Series of Biologically Relecant Ligands: A Molecular Mechanics Investigation Grounded on Ab Initio Self-Consistent Field Supermolecular Computations
Helix motion in protein C12A-p8MTCP1: Comparison of molecular dynamics simulations and multifield NMR relaxation data
Electron transfer in bis(hydrazines), a critical test for application of the Marcus model
A high-accuracy theoretical study of the CH n P Systems n = 1-3
Molecular symmetry and ab initio calculations: IV. Symmetry-matrix and symmetry-supermatrix in calculations of two-electron repulsion integrals
Local response dispersion method in periodic systems: Implementation and assessment
Ab initio study of bond stretching: Implications in force-field parametrization for molecular mechanics and dynamics
Comparison of computational methods applied to oxazole, thiazole, and other heterocyclic compounds
Intramolecular hydrogen bond energy and cooperative interactions in α-, β-, and γ-cyclodextrin conformers
Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins
Multidimensional virtual-system coupled canonical molecular dynamics to compute free-energy landscapes of peptide multimer assembly
Cyclobutadiene automerization and rotation of ethylene: Energetics of the barriers by using Spin-polarized wave functions
Structure-based ligand design by a build-up approach and genetic algorithm search in conformational space
Basis set dependence of solute-solvent interaction energy of benzene in water: A HF/DFT study
Evaluation of one-electron integrals for arbitrary operators V ( r ) over Cartesian Gaussians: Application to inverse-square distance and Yukawa operators
Quantitative decomposition of resonance-assisted hydrogen bond energy in β-diketones into resonance and hydrogen bonding (π- and σ-) components using molecular tailoring and function-based approaches
Multicut-HDMR with an application to an ionospheric model
Optimization of density fitting auxiliary Slater-type basis functions for time-dependent density functional theory
Molecular dynamics of liquid-electrode interface by integrating Coulomb interaction into universal neural network potential
2D-RNA-coupling numbers: A new computational chemistry approach to link secondary structure topology with biological function
Overcoming the limitations of cutoffs for defining atomic coordination in multicomponent systems
Sensing mechanism elucidation of a europium(III ) metal-organic framework selective to aniline: A theoretical insight by means of multiconfigurational calculations
Optimization of bimetallic Cu-Au and Ag-Au clusters by using a modified adaptive immune optimization algorithm
Erratum: Theoretical analysis of excited states and energy transfer mechanism in conjugated dendrimers
Probing the performance of DFT in the structural characterization of [FeFe] hydrogenase models
The competition and cooperativity of hydrogen/halogen bond and π-hole bond involving the heteronuclear ethylene analogues
A quantum chemical method for rapid optimization of protein structures
Fully quantum mechanical energy optimization for protein-ligand structure
Effect of Charge on Bond Strength in Hydrogenated Amorphous Silicon
Mechanistic insight on ( E )-methyl 3-(2-aminophenyl)acrylate cyclization reaction by multicatalysis of solvent and substrate
Influence of conventional hydrogen bonds in the intercalation of phenanthroline derivatives with DNA: The important role of the sugar and phosphate backbone
Superhalogen and Superacid
Development of hardware accelerator for molecular dynamics simulations: A computation board that calculates nonbonded interactions in cooperation with fast multipole method
Hierarchical atom type definitions and extensible all-atom force fields
On the importance of composite protein multiple ligand interactions in protein pockets
pyMolDyn: Identification, structure, and properties of cavities/vacancies in condensed matter and molecules
Origin of pressure-induced insulator-to-metal transition in the van der Waals compound FePS3 from first-principles calculations
Study of peptide conformation in terms of the ABEEM/MM method
A CASSCF/CASPT2 insight into excited-state intramolecular proton transfer of four imidazole derivatives
Dynamics of a protein and water molecules surrounding the protein: Hydrogen-bonding between vibrating water molecules and a fluctuating protein
Analytical TDHF second derivatives of dynamic electronic polarizability with respect to nuclear coordinates. Application to the dynamic ZPVA correction
Theoretical study of the role of solvent H 2 O in neopentyl and pinacol rearrangements
Parallel coupled perturbed CASSCF equations and analytic CASSCF second derivatives
The elastic net algorithm and protein structure prediction
Why do Congo Red, Evans Blue, and Trypan Blue differ in their complexation properties?
Fragmentation of natural orbital occupation numbers-based diagnostic of differential multireference character in complexes with hydrogen bonds
Application of structure-based focusing to the estrogen receptor
A toolkit to assist ONIOM calculations
The existence of secondary orbital interactions
Effects of an electric field on interaction of aromatic systems
Deformation of single-walled carbon nanotubes by interaction with graphene: A first-principles study
Fast lookup tables for interatomic interactions
Efficient lookup table using a linear function of inverse distance squared
Simple recipe for implementing computation of first-order relativistic corrections to electron correlation energies in framework of direct perturbation theory
A new set of bending T d symmetry coordinates for MX 4 molecules
Extending Chemoinformatics Techniques With JMolecular Energy: A Robust CDK-Based Force Field Library
Potential energy surfaces and dynamic properties via ab initio composite and density functional approaches
MARVEL analysis of high-resolution rovibrational spectra of 16 O 12 C 18 O
Force Field for Computation of Conformational Energies, Structures, and Vibrational Frequencies of Aromatic Polyesters
Effect of ligand volume correction on PMF scoring
Solvent effects on glycine. I. A supermolecule modeling of tautomerization via intramolecular proton transfer - Erratum
Nuclear magnetic resonance J coupling constant polarizabilities of hydrogen peroxide: A basis set and correlation study
SKATE: A docking program that decouples systematic sampling from scoring
A first principle study of the structural, vibrational and electronic properties of tetrathiafulvalene adsorbed on Ag(110) and Au(110) surfaces
GALAMOST: GPU-accelerated large-scale molecular simulation toolkit
Canonical Monte Carlo simulation of adsorption of O 2 and N 2 mixture on single walled carbon nanotube at different temperatures and pressures
Novel H-bonded base dimers as repeat units for information-bearing self-associative duplexes: A B3LYP/6-31G* search
Stability of (C 60 ) 2 and epoxide dimers, (C 60 ) 2 O N , and their anions
Mixed monte carlo/molecular dynamics simulations in explicit solvent
Four-component relativistic Kohn-Sham theory
Localization function study of excitation processes in a set of small isoelectronic molecules
PyFREC: Software for Förster electronic coupling evaluation in molecular fragments
Electronic structure of stoichiometric and reduced ZnO from periodic relativistic all electron hybrid density functional calculations using numeric atom-centered orbitals
Excitation and circular dichroism spectra of (-)-(3a S , 7a S )-2-chalcogena- trans -hydrindans(Ch = S, Se, Te): SAC and SAC-CI calculations
Characterization of molecular orbitals by counting nodal regions
Atomic and bond properties in functionalized esters and amides
Peptide models XXXI. Conformational properties of hydrophobic residues shaping the core of proteins. An ab initio study of N-formyl-L-valinamide and N-formyl-L-phenylalaninamide
Theoretical study on reaction mechanism of the CF radical with nitrogen dioxide
A parallel finite element simulator for ion transport through three-dimensional ion channel systems
An improved DIIS method using a versatile residual matrix to accelerate SCF starting from a crude guess
Theoretical study of the electronic spectra of oxidized and reduced states of lumiflavin and its derivative
Density functional study of guanine and uracil quartets and of guanine quartet/metal ion complexes
A systematic study of rare gas atoms encapsulated in small fullerenes using dispersion corrected density functional theory
Exploring the conformational space of Vpu from HIV-1: A versatile adaptable protein
Prediction of excited-state properties of oligoacene crystals using polarizable continuum model-tuned range-separated hybrid functional approach
A DFT study on the dimerization of C 62 , H 2 -C 62 , and F 2 -C 62
Hydrogen uptake capacity of C 2 H 4 Sc and its ions: A density functional study
A TDDFT investigation of bay substituted perylenediimides: Absorption and intersystem crossing
Cover Image, Volume 40, Issue 7
Comparison of aromatic NH***pi, OH***pi, and CH***pi interactions of alanine using MP2, CCSD, and DFT methods
An open-source framework for analyzing N -electron dynamics. II. Hybrid density functional theory/configuration interaction methodology
Algorithm for normal mode analysis with general internal coordinates
Computer simulation of trifluoromethane properties with ab initio force field
Chiral discrimination via nuclear magnetic shielding polarisabilities from NMR spectroscopy: Theoretical study of ( R a )-1, 3-dimethylallene, (2 R )-2-methyloxirane, and (2 R )- N -methyloxaziridine
Binding of piano-stool Ru(II) complexes to DNA; QM/MM study
Halogen bonding with the halogenabenzene bird structure, halobenzene, and halocyclopentadiene
Molecular dynamics coupled with a virtual system for effective conformational sampling
Energy transfer dynamics and kinetics of elementary processes (promoted) by gas-phase CO 2 -N 2 collisions: Selectivity control by the anisotropy of the interaction
Development of MD Engine: High-speed accelerator with parallel processor design for molecular dynamics simulations
Development of a multi-step screening procedure for redox active molecules in organic radical polymer anodes and as redox flow anolytes
Monte Carlo sampling algorithm for searching a scale-transformed energy space of polypeptides
Modern protein force fields behave comparably in molecular dynamics simulations
Reduced Variable Molecular Dynamics
Ab initio models for multiple-hydrogen exchange: Comparison of cyclic four- and six-center systems
Quantum crystallography: A perspective
An efficient hybrid explicit/implicit solvent method for biomolecular simulations†
MyMolDB: A micromolecular database solution with open source and free components
Role of structural water molecule in HIV protease-inhibitor complexes: A QM/MM study
Projected CAP/SAC-CI method with smooth Voronoi potential for calculating resonance states
Exploiting space-group symmetry in fragment-based molecular crystal calculations
Convergence and error estimation in free energy calculations using the weighted histogram analysis method
A Variational Biothogonal Valence Bond Method
DeepIon: Deep learning approach for classifying ion transporters and ion channels from membrane proteins
A homology/ ab initio hybrid algorithm for sampling near-native protein conformations
Exploring Mechanism and Kinetics of 1,4-Dioxane Oxidative Degradation by OH Radical: A Computational Quantum Chemistry Investigation
Approaches to Large-Scale Parallel Self-Consisten Field Calculations
A new QM/MM method oriented to the study of ionic liquids
Dynamics fingerprints of active conformers of epidermal growth factor receptor kinase
Ab initio study of the mechanism of singlet-dioxygen addition to hydroxyaromatic compounds: Negative evidence for the involvement of peroxa and endoperoxide intermediates
van der Waals corrected density functional calculations of the adsorption of benzene on the Cu (111) surface
autoCAS: A Program for Fully Automated Multiconfigurational Calculations
Exploration of high dimensional free energy landscapes by a combination of temperature-accelerated sliced sampling and parallel biasing
Analysis of XPS and XES of diamond and graphite by DFT calculations using model molecules
Density Functional Theory (DFT) and Time-Dependent DFT (TDDFT) Studies of Porphyrin Adsorption on Graphene: Insights on the Effect of Substituents and Central Metal on Adsorption Energies
Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform
A comparison of ground- and excited-state properties of [Ru(bz)2]2+ and bis(6-benzene)ruthenium(II) p-toluenesulfonate using the density functional theory
Interaction of sodium and potassium ions with sandwiched cytosine-, guanine-, thymine-, and uracil-base tetrads
Thermal isomerization rates in retinal analogues using Ab-Initio molecular dynamics
Pyrrolizidine alkaloids necine bases: II. Conformational analysis of free bases
Characterization of the role of Kunitz-type protease inhibitor domain in dimerization of amyloid precursor protein