yusuke1997/dblp-id-title huggingface dataset:
Theoretical study on the kinetics of OH radical reactions with CH 3 OOH and CH 3 CH 2 OOH
Recent performance improvements to the DFT and TDDFT in GAMESS
Conformational searching methods for small molecules. II. Genetic algorithm approach
Correlation consistent auxiliary basis sets in density fitting Hartree-Fock: The atoms sodium through argon revisited
Structural and energetic relations between turns
A program for automatically predicting supramolecular aggregates and its application to urea and porphin
Electrostatically embedded molecules-in-molecules approach and its application to molecular clusters
Using one-step perturbation to predict the effect of changing force-field parameters on the simulated folding equilibrium of a beta-peptide in solution
High performance global exploration of isomers and isomerization channels on quantum chemical potential energy surface of H5C2NO2
New developments in the symmetry-adapted algorithm of the Polarizable Continuum Model
A fourth-order accurate, Numerov-type, three-point finite-difference discretization of electrochemical reaction-diffusion equations on nonuniform (exponentially expanding) spatial grids in one-dimensional space geometry
Internal coordinate density of state from molecular dynamics simulation
The True Diatomic Potential as a Perturbed Morse Function
Comparative study of relativistic density functional methods applied to actinide species AcO22+ and AcF6 for Ac = U, Np
XEDA, a fast and multipurpose energy decomposition analysis program
Improved algorithm for accurate computation of molecular solid angles
Model transition states for methane diazonium ion methylation of guanine runs in oligomeric DNA
The Degree and Origin of the Cooperativity of the Chalcogen (Ch···N) and Dihydrogen (H···H) Bonds in Some Triad Systems
Radial behavior of gradient expansion approximation to atomic Fukui function and shell structure of atoms
Parameterization of Org27569: An allosteric modulator of the cannabinoid CB 1 G protein-coupled receptor
PEPCAT - A new tool for conformational analysis of peptides
Excitation energies expressed as orbital energies of Kohn-Sham density functional theory with long-range corrected functionals
Segmentation and additive approach: A reliable technique to study noncovalent interactions of large molecules at the surface of single-wall carbon nanotubes
How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
New implementation of high-level correlated methods using a general block tensor library for high-performance electronic structure calculations
A possible overestimation of the effect of acetylation on lysine residues in KQ mutant analysis
Global minimum geometries of acetylene clusters (HCCH) n with n <= 55 obtained by a heuristic method combined with geometrical perturbations
Theoretical study and rate constants calculation for the reactions X + CF 3 CH 2 OCF 3 (X = F, Cl, Br)
PyRad: A software shell for simulating radiolysis with Qball package
The effect of conjugated spacer on novel carbazole derivatives for dye-sensitized solar cells: Density functional theory/time-dependent density functional theory study
Accelerating molecular modeling applications with graphics processors
Feature vector clustering molecular pairs in computer simulations
PSSKB: A Web Application to Study Protein Structures
Chalcogen bonds: Hierarchical ab initio benchmark and density functional theory performance study
Erratum: Symmetrization of the AMBER and CHARMM force fields [J. Comp. Chem. 31, 1402]
CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field
Enhanced conformational exploration of protein loops using a global parameterization of the backbone geometry
Modeling hydrogen evolution from the Fe 4 S 4 and Fe 8 S 9 X (X = N, C) clusters. Can a Fe-S high-spin cluster serve as a surrogate for the FeMo cofactor?
Predicting peptide structures using NMR data and deterministic global optimization
A Bayesian statistical approach of improving knowledge-based scoring functions for protein-ligand interactions
Crystal contacts as nature's docking solutions
Simplified Multireference Coupled-Cluster Methods: Hybrid Approaches With Averaged Coupled Pair Theories
Effects of a Polarizable Force Field on Membrane Dynamics: Surface Viscosity, Lipid Diffusion, and Peptide Induced Pore Formation
Improving performance of polarizable continuum model for study of large molecules in solution
Optimal scaling factors for CM1 and CM3 atomic charges in RM1-based aqueous simulations
Molecular dynamics simulation of benzene in graphite and amorphous carbon slit pores
Fast and accurate grid representations for atom-based docking with partner flexibility
Estimation on the intramolecular 10-membered ring N-H***O-C hydrogen-bonding energies in glycine and alanine peptides
Site specificity of alpha-H abstraction reaction among secondary structure motif - An ab initio study
Conformational Sampling of Hydrocarbon and Lipid Chains in an Orienting Potential
Extreme biophysics: Enzymes under pressure
Efficient calculation of Franck-Condon factors and vibronic couplings in polyatomics
Global minimum structure searches via particle swarm optimization
Very efficient search for protein alignment - VESPA
Theoretical study on photophysical properties of a series of functional pyrimidine-based organic light-emitting diodes emitters presenting thermally activated delayed fluorescence
Activation of C-H bond in methane by Pd atom from the bonding evolution theory perspective
Modeling the effect of ion-induced shock waves and DNA breakage with the reactive CHARMM force field
Computational study of basis set and electron correlation effects on anapole magnetizabilities of chiral molecules
Molecular mechanics (MM4) vibrational frequency calculations for alkenes and conjugated hydrocarbons
CONCEPTS: New dynamic algorithm for de novo drug suggestion
A TD-DFT study on the cyanide-chemosensing mechanism of 8-formyl-7-hydroxycoumarin
Macrocyclic vs. dendrimeric effect. A DFT study
An ANI-2 enabled open-source protocol to estimate ligand strain after docking
GMCT : A Monte Carlo simulation package for macromolecular receptors
Buckybowls as adsorbents for CO 2 , CH 4 , and C 2 H 2 : Binding and structural insights from computational study
PROFASI: A Monte Carlo simulation package for protein folding and aggregation
LigDockCSA: Protein-ligand docking using conformational space annealing
Three-dimensional reference interaction site model self-consistent field analysis of solvent and substituent effects on the absorption spectra of Brooker's merocyanine
CGPDTA: An Explainable Transfer Learning-Based Predictor With Molecule Substructure Graph for Drug-Target Binding Affinity
Free Energy Derivatives: A New Method for Probing the Convergence Problem in Free Energy Calculations
Quantum vs. classical models of the nitro group for proton chemical shift calculations and conformational analysis
An interacting quantum atom study of model SN2 reactions (X-···CH3X, X = F, Cl, Br, and I)
New force field for calcium binding sites in annexin-membrane complexes
Massively parallel algorithm and implementation of RI-MP2 energy calculation for peta-scale many-core supercomputers
Metalophilic interaction in gold halide: Quantum chemical study of AuX (X = F‒at)
Structural stability and the low-lying singlet and triplet states of BN- n -acenes, n = 1-7
Bringing about matrix sparsity in linear-scaling electronic structure calculations
The effect of different cutoff schemes in molecular simulations of proteins
Models for the description of the H3O+ and OH- ions in water
Development of a new parameter optimization scheme for a reactive force field based on a machine learning approach
The Reactivity of Ambident Nucleophiles: Marcus Theory or Hard and Soft Acids and Bases Principle?
Pseudopotentials for coarse-grained cross-link-assisted modeling of protein structures
Molecular dynamics of a calix[4]arene-containing polymer in dichloromethane solution: Ability of the solvent molecules to fill the cavity of the macrocycle
Additive CHARMM force field for naturally occurring modified ribonucleotides
Linear-scaling Cholesky decomposition
Effects of long-range electrostatic forces on simulated protein folding kinetics
Computing the superexchange electronic factor of electron transfer theory using a grid-based numerical method
Molecular dynamics simulations of ion solvation by flexible-boundary QM/MM: On-the-fly partial charge transfer between QM and MM subsystems
A Comprehensive Study of the Rotational Energy Profiles of Orgenic Systems by Ab Initio MO Theory, Forming a Base for Pepetide Torsional Parameters
Thiophenols, Promising Scavengers of Peroxyl Radicals: Mechanisms and kinetics
A QM/MM study of the nature of the entatic state in plastocyanin
Lennard-Jones parameters for small diameter carbon nanotubes and water for molecular mechanics simulations from van der Waals density functional calculations
The effect of structure and phase transformation on the mechanical properties of Re 2 N and the stability of Mn 2 N
Growth pattern and electronic and magnetic properties of Cr-doped silver clusters
Electron localization function comparative study of ground state, triplet state, radical anion, and cation in model carbonyl and imine compounds
Performance of six functionals (LDA, PBE, PBESOL, B3LYP, PBE0, and WC1LYP) in the simulation of vibrational and dielectric properties of crystalline compounds. The case of forsterite Mg 2 SiO 4
The best density functional theory functional for the prediction of 1H and 13C chemical shifts of protonated alkylpyrroles
Polypeptide folding on a conformational-space network: Dependence of network topology on the structural discretization procedure
Theoretical study of proton coupled electron transfer reaction in the light state of the AppA BLUF photoreceptor
Simulation of DNA electrophoresis in systems of large number of solvent particles by coarse-grained hybrid molecular dynamics approach
Ab Initio Diabatic energies and dipole moments of the electronic states of RbLi molecule
The MPSim-Dock hierarchical docking algorithm: Application to the eight trypsin inhibitor cocrystals
Inequivalence of substitution pairs in hydroxynaphthaldehyde: A theoretical measurement by intramolecular hydrogen bond strength, aromaticity, and excited-state intramolecular proton transfer reaction
Addressing an instability in unrestricted density functional theory direct dynamics simulations
Comparative assessment of computational methods for the determination of solvation free energies in alcohol-based molecules
A new strategy to improve the predictive ability of the local lazy regression and its application to the QSAR study of melanin-concentrating hormone receptor 1 antagonists
Fast search algorithms for computational protein design
Effects of electron attachment on C 5' -O 5' and C 1' -N 1 bond cleavages of pyrimidine nucleotides: A theoretical study
PyMOL360: Multi-user gamepad control of molecular visualization software
Consistent gaussian basis sets of double- and triple-zeta valence with polarization quality of the fifth period for solid-state calculations
Fast, Fuzzy C-Means Clustering of Data Sets with Many Features
Docking by Monte Carlo minimization with a solvation correction: Application to an FKBP - substrate complex
A spherical harmonic transform spectral analysis of a localized surface plasmon on a gold nano shell
sDFIRE: Sequence-specific statistical energy function for protein structure prediction by decoy selections
Explicit solvent repulsive scaling replica exchange molecular dynamics (RS-REMD) in molecular modeling of protein-glycosaminoglycan complexes
Pseudopotentials for hybridized carbon atoms
Double-buffered, heterogeneous CPU + GPU integral digestion algorithm for single-excitation calculations involving a large number of excited states
Water/organic liquid interface properties with amine, carboxyl, thiol, and methyl terminal groups as seen from MD simulations
PM3-compatible zinc parameters optimized for metalloenzyme active sites
Theoretical study on HBO + and HOB + cations using multiconfiguration second-order perturbation theory
Assessment of ab initio MP2 and density functionals for characterizing the potential energy profiles of the SN2 reactions at N center
An extension of the grid empowered molecular simulator to quantum reactive scattering
Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis
Mean force based temperature accelerated sliced sampling: Efficient reconstruction of high dimensional free energy landscapes
ARGOS: An adaptive refinement goal-oriented solver for the linearized Poisson-Boltzmann equation
Internal Dynamics of a Global Protein under External Force Field
Long-Range multicenter integrals with slater functions: Gauss transform-based methods
Evaluation of bonding, electron affinity, and optical properties of M@C 28 (M = Zr, Hf, Th, and U): Role of d- and f-orbitals in endohedral fullerenes from relativistic DFT calculations
Analysis of the segmented contraction of basis functions using density matrix theory
Improving the calculation of magnetic coupling constants in MRPT methods
An efficient and extensible format, library, and API for binary trajectory data from molecular simulations
Generate: A program for 3-D structure generation and conformational analysis of peptides and peptidomimetics
eSHAFTS: Integrated and graphical drug design software based on 3D molecular similarity
Azobenzene-bridged diradical janus nucleobases with photo-converted magnetic properties between antiferromagnetic and ferromagnetic couplings
Software news and commentsVMD: a graphical tool for the modern chemists
Cover Image, Volume 39, Issue 12
Evaluating quantum entanglement generation in two-dimensional graphene systems through lithium ion interactions: A DFT-based study
GPU accelerated implementation of NCI calculations using promolecular density
Properties of halogen atoms for representing intermolecular electrostatic interactions related to halogen bonding and their substituent effects
A general expression for the statistical error in a diffusion coefficient obtained from a solid-state molecular-dynamics simulation
Novel graph distance matrix
Transition state docking: A probe for noncovalent catalysis in biological systems. Application to antibody-catalyzed ester hydrolysis
Theoretical calculation about the valence and rydberg excited states of hydrogen cyanide
Speeding up parallel GROMACS on high-latency networks
Effects of zero point vibration on the reaction dynamics of water dimer cations following ionization
Constraint dynamics algorithm for simulation of semiflexible macromolecules
SM-TF: A structural database of small molecule-transcription factor complexes
Protein structure prediction aided by geometrical and probabilistic constraints
Ab initio exploration of low-lying electronic states of linear and bent MNX + (M = Ca, Sr, Ba, Ra; X = O, S, Se, Te, Po) and their origins
Calibration of forcefields for molecular simulation: Sequential design of computer experiments for building cost-efficient kriging metamodels
When does a hydrogen bond become a van der Waals interaction? a topological answer
Solvent viscosity dependence of the folding rate of a small protein: Distributed computing study
Efficient bond function basis set for pi-pi interaction energies
Stabilization of Zn group dimers: A theoretical study
Prediction of acidity in acetonitrile solution with COSMO-RS
The unusual stability of H-bonded complexes in solvent caused by greater solvation energy of complex compared to those of isolated fragments
Macrotricyclic quaternary tetraammonium receptors: Halide anion recognition and interfacial activity at an aqueous interface. A molecular dynamics investigation
Force Field Studies of Cholesterol and Chelesteryl Acetate Crystals and Cholesterol-Cholesterol Intermolecular Interactions
The performance of computational techniques in locating the charge separated intermediates in organocatalytic transformations
Theoretical insights into the 1D-charge transport properties in a series of hexaazatrinaphthylene-based discotic molecules
On Restraints in End-Point Protein-Ligand Binding Free Energy Calculations
Exhaustive enumeration of molecular substructures
A multipolar approach to the interatomic covalent interaction energy
Enhanced sampling simulations of DNA step parameters
Comparison of a posteriori and a priori BSSE correction schemes for SCF intermolecular energies
Prediction of consensus binding mode geometries for related chemical series of positive allosteric modulators of adenosine and muscarinic acetylcholine receptors
Electron correlation in large molecular systems using the atomic orbital formalism. The case of intermolecular interactions in crystalline urea as an example
Impact of different potentials on the structures and energies of clusters
Theoretical studies on the formation mechanism and explosive performance of nitro-substituted 1, 3, 5-triazines
ToBaD: A MEthod for the Estimation of Torsion Barriers from Crystal Structure Data; Conformational Analysis of N, N-Dimethylaniline and Derivatives
Calculating particle pair potentials from fluid-state pair correlations: Iterative ornstein-zernike inversion
NE-RDFE: A protocol and toolkit for computing relative dissociation free energies with GROMACS between dissimilar molecules using bidirectional nonequilibrium dual topology schemes
Modeling solvent effects and convergence of 31 P-NMR shielding calculations with COBRAMM
A theoretical investigation of the lead-free double perovskites halides Rb 2 XCl 6 (X = Se, Ti) for optoelectronic and thermoelectric applications
A comprehensive theoretical study on the hydrolysis of carbonyl sulfide in the neutral water
Network visualization system for computational chemistry
Automatic generation of complementary auxiliary basis sets for explicitly correlated methods
A theoretical perspective of the ultrafast transient absorption dynamics of CsPbBr3
Analysis and prediction of hydrogen bonding in protein-DNA complexes using parallel processors
Isomers of C20: An energy profile II
Carbon boronyls: Species with higher viable possibility than boron carbonyls at the density functional theory
On the accuracy of density functional theory for iron - sulfur clusters
DFT conformational studies of alpha-maltotriose
Detection and characterization of nonspecific, sparsely populated binding modes in the early stages of complexation
Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations
Automatic analysis of computed catalytic cycles
Investigation of the molecular surface area and volume: Defined and calculated by the molecular face theory
Harmonic and anharmonic vibrational computations for biomolecular building blocks: Benchmarking DFT and basis sets by theoretical and experimental IR spectrum of glycine conformers
On the joint time-frequency characteristics of chemical oscillations
Coarse-grained force field for the nucleosome from self-consistent multiscaling
Effects of mussel-inspired co-deposition of 2-hydroxymethyl methacrylate and poly (2-methoxyethyl acrylate) on the hydrophilicity and binding tendency of common hemodialysis membranes: Molecular dynamics simulations and molecular docking studies
A simplified homology-model builder toward highly protein-like structures: An inspection of restraining potentials
Atomic-resolution dissection of the energetics and mechanism of isomerization of hydrated ATP-Mg 2+ through the SOMA string method
Growth format, electronic architecture, magnetic, and optical properties of aromatic cyclo -Cu 3 Au 3 homotops
Protein inherent structures by different minimization strategies
Theoretical study on the gas-phase reaction mechanism between nickel monoxide and methane for syngas production
LIMONADA: A database dedicated to the simulation of biological membranes
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
On the structure of the inverse kinematics map of a fragment of protein backbone
Electron localizability indicators from spinor wavefunctions
The tetracycline: Mg2+ complex: A molecular mechanics force field
Learning organo-transition metal catalyzed reactions by graph neural networks
Attraction between electrophilic caps: A counterintuitive case of noncovalent interactions
MIMIC: A molecular-field matching program. Exploiting applicability of molecular similarity approaches
Monte Carlo simulations of the hydration of substituted benzenes with OPLS potential functions
On the applicability of multireference second-order perturbation theory to study weak magnetic coupling in molecular complexes
Predicting protein folding rates using the concept of Chou's pseudo amino acid composition
Isomers of C20: An energy profile III
An improvement of Davidson's iteration method: Applications to MRCI and MRCEPA calculations
Bonding and singlet-triplet gap of silicon trimer: Effects of protonation and attachment of alkali metal cations
Interaction of Metamitron and Fenhexamid with Ca2+-Montmorillonite Clay Surfaces: A Density Functional Theory Molecular Dynamics Study
Catenanes: A molecular mechanics analysis of the (C 13 H 26 ) 2 Structure 13-13 D2
Insights into the dynamics of evaporation and proton migration in protonated water clusters from large-scale born-oppenheimer direct dynamics
Prediction on dielectric strength and boiling point of gaseous molecules for replacement of SF 6
Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for zinc complexes
Proton transfer in phenol-amine complexes: Phenol electronic effects on free energy profile in solution
O ( NlogN ) Continuous electrostatics method for fast calculation of solvation energies of biomolecules
t 2 g d orbital ordering patterns in KBF 3 (B = Sc, Ti, Fe, Co) perovskites
New insights in quantum chemical topology studies using numerical grid-based analyses
What is the minimum number of water molecules required to dissolve a potassium chloride molecule?
Prediction of infinite dilution activity coefficients of chlorinated organic compounds in aqueous solution from quantum-chemical descriptors
Theoretical studies on the molecular dependence of bond dissociation after core excitations II: CH3CO(CH2)nCN, n = 0-3
The MP2-F12 method in the TURBOMOLE program package
Pteros 2.0: Evolution of the fast parallel molecular analysis library for C++ and python
Molecular mechanics force field parameterization of the fluorescent probe rhodamine 6G using automated frequency matching
Time-dependent density functional theory study on the hydrogen bonding-induced twisted intramolecular charge-transfer excited states of 2-(4'- N , N -dimethylaminophenyl)imidazo[4, 5- b ]pyridine
How does hybrid bridging core modification enhance the nonlinear optical properties in donor-π-acceptor configuration? A case study of dinitrophenol derivatives
Constant advance replicas method for locating minimum energy paths and transition states
Free-energy differences between states with different conformational ensembles
Evaluation of the performance of four molecular docking programs on a diverse set of protein-ligand complexes
Photophysics of tz Adenine and tz Guanine fluorescent nucleobases embedded into DNA and RNA
Interaction of aromatic units of amino acids with guanidinium cation: The interplay of π···π, X‒H···π, and M + ···π contacts
Stepwise disproportionation in polyelectrolyte complexes
Reactions of a hydrogen atom with haloacetates in aqueous solutions: Computational evidence for proton-coupled electron transfer and competing mechanisms
Efficient implementation of the analytical second derivatives of hartree-fock and hybrid DFT energies within the framework of the conductor-like polarizable continuum model
Components for integral evaluation in quantum chemistry
Isomerism of CH 2 SO : Accurate structural, energetic, and spectroscopic characterization
Computation of the mean residence time of water in the hydration shells of biomolecules
Cover Image, Volume 40, Issue 12