yusuke1997/dblp-id-title huggingface dataset:
Magnetic Signatures of Hydroxyl- and Water-Terminated Neutral and Tetra-Anionic Mn12-Acetate
A charge equilibration formalism for treating charge transfer effects in MD simulations: Application to water clusters
MzDOCK : A free ready-to-use GUI-based pipeline for molecular docking simulations
A Variational Biothogonal Valence Bond Descriptions of 1, 3-Dipoles
Insights into molecular cluster materials with adamantane-like core structures by considering dimer interactions
Can MM/GBSA calculations be sped up by system truncation?
Competition between hydrogen and halogen bonding in halogenated 1-methyluracil: Water systems
Hydrogen-bonding interactions in the active site of a low molecular weight protein-tyrosine phosphatase
The shape of gaseous n -butylbenzene: Assessment of computational methods and comparison with experiments
Single-pass incremental force updates for adaptively restrained molecular dynamics
Density functionals with full nonlocal exchange, nonlocal rung-3.5 correlation, and D3 dispersion: Combined accuracy for general main-group thermochemistry, kinetics, and noncovalent interactions
Efficient treatment of solvation shells in 3D molecular theory of solvation
d-AO spherical aromaticity in Ce 6 O 8
DiTe2: Calculating the diffusion tensor for flexible molecules
BaTiO 3 -based nanolayers and nanotubes: First-principles calculations
First principle and ReaxFF molecular dynamics investigations of formaldehyde dissociation on Fe(100) surface
Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting
The hydration properties of carboxybetaine zwitterion brushes
Coupled folding and binding with 2D Window-Exchange Umbrella Sampling
(Ala) 4 -X-(Ala) 4 as a model system for the optimization of the χ 1 and χ 2 amino acid side-chain dihedral empirical force field parameters
Replica state exchange metadynamics for improving the convergence of free energy estimates
QM/MM calculations with DFT for taking into account protein effects on the EPR and optical spectra of metalloproteins. Plastocyanin as a case study
Predicting structural models for silicon clusters
Machine Learning-Corrected Simplified Time-Dependent DFT for Systems With Inverted Single-t-o-Triplet Gaps of Interest for Photocatalytic Water Splitting
Sparse group selection and analysis of function-related residue for protein-state recognition
An Electron Density Source-Function Study of DNA Base Pairs in Their Neutral and Ionized Ground States
DLPNO-CCSD(T) scaled methods for the accurate treatment of large supramolecular complexes
Substituent effect on electron affinity, gas-phase basicity, and structure of monosubstituted propynyl radicals and their anions: A theoretical study
Schwarz P-surface via isolated sp 2 carbon heptagons: Design and properties
Low-mode conformational search elucidated: Application to C39H80 and flexible docking of 9-deazaguanine inhibitors into PNP
Theoretical studies of spin state-specific [2 + 2] and [5 + 2] photocycloaddition reactions of n -(1-penten-5-yl)maleimide
A comparative molecular field analysis (CoMFA) study using semiempirical, density functional, ab initio methods and pharmacophore derivation using DISCOtech on sigma 1 ligands
Compressing molecular dynamics trajectories: Breaking the one-bit-per-sample barrier
Density functional study of S N 2 substitution reactions for CH 3 Cl + CX 1 X 2•- (X 1 X 2 = HH, HF, HCl, HBr, HI, FF, ClCl, BrBr, and II)
Program fullerene - a software package for constructing and analyzing structures of regular fullerenes
Alternative approaches to potential of mean force calculations: Free energy perturbation versus thermodynamic integration. Case study of some representative nonpolar interactions
DataPipeline: Automated importing and fitting of large amounts of biophysical data
Bond electron pair: Its relevance and analysis from the quantum chemistry point of view
On-the-fly reconstruction of free-energy profiles using logarithmic mean-force dynamics
Supersecondary structure prediction using Chou's pseudo amino acid composition
Accurate prediction of the blood-brain partitioning of a large set of solutes using ab initio calculations and genetic neural network modeling
Evaluating nonpolarizable nucleic acid force fields: A systematic comparison of the nucleobases hydration free energies and chloroform-to-water partition coefficients
Solvent models for protein-ligand binding: Comparison of implicit solvent poisson and surface generalized born models with explicit solvent simulations
Machine Learning Prediction of Physicochemical Properties in Lithium-Ion Battery Electrolytes With Active Learning Applied to Graph Neural Networks
Performance of range-separated hybrid exchange-correlation functionals for the calculation of magnetic exchange coupling constants of organic diradicals
CarbBuilder: Software for building molecular models of complex oligo- and polysaccharide structures
Prediction of peptide conformation: The adaptive simulated annealing approach
Molecular mechanism of binding between a therapeutic RNA aptamer and its protein target VEGF: A molecular dynamics study
Generalization of the Schrödinger Theory of Electrons
Systematic microsolvation approach with a cluster-continuum scheme and conformational sampling
Bonding situations in tricoordinated beryllium phenyl complexes
O‒O bond homolysis in hydrogen peroxide
An ant algorithm for the conformational analysis of flexible molecules
Surveying implicit solvent models for estimating small molecule absolute hydration free energies
A Fast Multipole Boundary Element Method for Molecular Electrostatics: An Optimal Approach for Large Systems
A genetic algorithm encoded with the structural information of amino acids and dipeptides for efficient conformational searches of oligopeptides
pKa, MM, and QM studies of mechanisms of -lactamases and penicillin-binding proteins: Acylation step
Electron tunneling in proteins program
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation
Theoretical prediction of vertical transition energies of diaminosilylenes and aminosubstituted disilenes
A toolchain for the automatic generation of computer codes for correlated wavefunction calculations
Time-dependent density functional calculations on the electronic spectra of the neutral nickel complex [Ni(L ISQ ) 2 ] (L ISQ = 3, 5-di- tert -butyl- o -diiminobenzosemiquinonate(1 - )) and its monoanion and dication
Electron localizability indicators ELI and ELIA: The case of highly correlated wavefunctions for the argon atom
GenIce: Hydrogen-Disordered Ice Generator
Protein secondary structure motifs: A kinematic construction
Ion-exchanged binuclear Ca 2 O X clusters, X = 1-4, as active sites of selective oxidation over MOR and FAU zeolites
Structure and dynamics of methanol in water: A quantum mechanical charge field molecular dynamics study
Application of the topological analysis of the electronic localization function to archetypical [Pb(II)L n ] p complexes: The bonding of Pb 2+ revisited
Three variations of genetic algorithm for searching biomolecular conformation space: Comparison of GAP 1.0, 2.0, and 3.0
Assessment of standard force field models against high-quality ab initio potential curves for prototypes of pi-pi, CH/pi, and SH/pi interactions
Ab initio direct dynamics studies on the reactions of chlorine atom with CH 3- n F n CH 2 OH ( n = 1-3)
Study of the Photoinduced Charge Injection in the Reaction Intermediate of the Dehydrogenation of Formic Acid on Palladium
RMC_POT: A computer code for reverse monte carlo modeling the structure of disordered systems containing molecules of arbitrary complexity
MolRWKV: Conditional Molecular Generation Model Using Local Enhancement and Graph Enhancement
Verification of DFT-predicted hydrogen storage capacity of VC 3 H 3 complex using molecular dynamics simulations
A consensus line search algorithm for molecular potential energy functions
VIBPACK: A package to treat multidimensional electron-vibrational molecular problems with application to magnetic and optical properties
Code interoperability and standard data formats in quantum chemistry and quantum dynamics: The Q5/D5Cost data model
Conformational searching methods for small molecules. I. Study of the sybyl search method
Size-consistency and orbital-invariance issues revealed by VQE-UCCSD calculations with the FMO scheme
Localization and Quantitative Evaluation of Potent Local Binding Sites on the Accessible Lennard-Jones Surface
Evaluation of Moment Statistics for Molecular Modeling
DFT/MRCI assessment of the excited-state interplay in a coumarin-schiff Mg2+ fluorescent sensor
Numerical characterization of the conformation of cyclic peptides and its application
Statistical analysis of computational docking of large compound data bases to distinct protein binding sites
Excited-State Reactivity of [Mn(im)(CO)3(phen)]+: A Structural Exploration
Hydrogen bonding in diols and binary diol-water systems investigated using DFT methods. II. Calculated infrared OH-stretch frequencies, force constants, and NMR chemical shifts correlate with hydrogen bond geometry and electron density topology. A reevaluation of geometrical criteria for hydrogen bonding
Developing adaptive QM/MM computer simulations for electrochemistry
A quantum chemical calculation on Fe(CO)5 revealing the operation of the Dewar-Chatt-Duncanson model
Computational Feasibility of an Exhaustive Search of Side-Chain Conformations in Protein-Protein Docking
Crystal indexing method using a simulated annealing algorithm with particular applications in nanocrystal research
Modified MM2 scheme for computation of O‒C‒N-containing systems
Quantification of substituent and ligand size by the use of solid angles
Self-consistent field for fragmented quantum mechanical model of large molecular systems
Pattern recognition strategies for molecular surfaces. II. Surface complementarity
A model electronic Hamiltonian to describe low-lying d-d and metal-to-ligand charge-transfer excited states of [Fe(bpy)3]2+
X-Ray Crystal Structure of Embelin and Its DFT Scavenging of Superoxide Radical
Alcohols, ethers, carbohydrates, and related compounds. IV. carbohydrates
Investigation of two-dimensional hf-based MXenes as the anode materials for li/na-ion batteries: A DFT study
Accuracy and tractability of a kriging model of intramolecular polarizable multipolar electrostatics and its application to histidine
Modeling ligand electrochemical parameters by repulsion-corrected eigenvalues
Density functional study of electronic, bonding, and vibrational properties of Ca (NH 2 BH 3 ) 2
Pharmacophore alignment search tool: Influence of canonical atom labeling on similarity searching
Complete basis set limit of Ab initio binding energies and geometrical parameters for various typical types of complexes
Smoothed Spherical Truncation based on Fuzzy Membership Functions: Application to the Molecular Encoding
Fitted electronic density functions from H to Rn for use in quantum similarity measures: cis-diamminedichloroplatinum(II) complex as an application example
Complete basis set model chemistry applied to molecules of increasing molecular complexity: Thermochemical properties of organic sulfur derivatives
Low cost prediction of relative stabilities of hydrogen bonded complexes from atomic multipole moments for overly short intermolecular distances
Quality criteria of genetic algorithms for construction of phylogenetic trees
Reply to the comment on "A stationary-wave model of enzyme catalysis"
Enabling grand-canonical Monte Carlo: Extending the flexibility of GROMACS through the GromPy python interface module
Geometrical control of the interatomic coulombic decay process in quantum dots for infrared photodetectors
An efficient fluctuating charge model for transition metal complexes
Iterative method for finding the low-energy conformations based on the concept of molecular volumes
Absolute free energies of biomolecules from unperturbed ensembles
Low-energy structures of benzene clusters with a novel accurate potential surface
The impact of surface area, volume, curvature, and Lennard-Jones potential to solvation modeling
Gaussian induced dipole polarization model
Repurposing fusion inhibitor peptide against SARS-CoV-2
Transition metal-boron complexes BnM: From bowls (n = 8-14) to tires (n = 14)
The OH . + CH 3 SH reaction: Support for an addition-elimination mechanism from ab initio calculations
Data set and fitting dependencies when estimating protein mutant stability: Toward simple, balanced, and interpretable models
Periselectivity and ambimodal transition states in cycloadditions of tetrachloro- o -benzoquinone with 6,6-dimethylfulvene
Restriction on molecular fluxionality by substitution: A case study for the 1,10-dicyanobullvalene
Valence : A Massively Parallel Implementation of the Variational Subspace Valence Bond Method
Predicting PH vibrations of gas phase molecules and surface-adsorbed species using bond length-frequency correlations
Multi-multigrid solution of modified Poisson-Boltzmann equation for arbitrarily shaped molecules
A gradient-directed Monte Carlo approach for protein design
Reply to the comment of S. Rayne 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"
Refined metadynamics through canonical sampling using time-invariant bias potential: A study of polyalcohol dehydration in hot acidic solutions
Iterative Methods for the Calculation of a Few of the Lowest Eigenvalues and Corresponding Eigenvectors of the AX = Lamda BX Equation with Real Symmetric Matrices of Large Dimension
Theoretical Study of the Subsequent Decomposition Mechanisms of 1,1-Diamino-2,2-dinitroethene (FOX-7)
Designing novel antitrypanosomal agents from a mixed graph-theoretical substructural approach
Theoretical and kinetic study of the H + C 2 H 5 CN reaction
Force field development for cofactors in the photosystem II
XPS of oxygen atoms on Ag(111) and Ag(110) surfaces: Accurate study with SAC/SAC-CI combined with dipped adcluster model
Computing motif correlations in proteins
Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects
DFT study of the full catalytic cycle for the propene hydroformylation catalyzed by a heterobimetallic HPt(SnCl 3 )(PH 3 ) 2 model catalyst
Fast vibrational analysis of molecular systems
Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions. II. An energy decomposition analysis
An Fe-Ni-Cr embedded atom method potential for austenitic and ferritic systems
A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations
Ab initio characterization of the aluminum dimer in its X 3 Π u and A 3 ∑ g - electronic states
A Symmetry adapted tessellation of the GEPOL surface: applications to molecular properties in solution
Toward product control in ring-opening oligomerization of 9 H -9-borafluorenes
Graph-theoretical identification of dissociation pathways on free energy landscapes of biomolecular interaction
First Principles Global Optimization Method From Parallel Tempering Molecular Dynamics
Evaluation of the performance of post-Hartree-Fock methods in terms of intermolecular distance in noncovalent complexes
United atom force field for phospholipid membranes: Constant pressure molecular dynamics simulation of dipalmitoylphosphatidicholine/water system
MetREx: A protein design approach for the exploration of sequence-reactivity relationships in metalloenzymes
A 500-ps molecular dynamics simulation trajectory of cardiotoxin II from Taiwan cobra venom in solution: Correlation with NMR and X-ray crystallography data
Taking the Monte-Carlo gamble: How not to buckle under the pressure!
The effect of solvent on determining highest occupied molecular orbital energies of semiconducting organic molecules: Insight from a combined computational approach
Atomic multipoles: Electrostatic potential fit, local reference axis systems, and conformational dependence
Improved treatment of cyclic -amino acids and successful prediction of -peptide secondary structure using a modified force field: AMBER*C
Comparison of predicted native structures of Met-enkephalin based on various accessible-surface-area solvent models
An Empirical Force Field II. Crystalline Alkanes
Advanced Sampling for Molecular Simulation is Coming of Age
Polymer conformations in internal (polyspherical) coordinates
Nitrogen-doped C 60 as a robust catalyst for CO oxidation
Gabedit - A graphical user interface for computational chemistry softwares
A general efficient implementation of the BSSE-free SCF and MP2 methods based on the chemical Hamiltonian approach
Quantum Chemical and Trajectory Surface Hopping Molecular Dynamics Study of Iodine-Based BODIPY Photosensitizer
Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature
Electron-pair density decomposition for core-valence separable systems
Coupled-cluster reaction barriers of HO2+H2O+O3: An application of the coupled-cluster//Kohn-Sham density functional theory model chemistry
Semiempirical treatment of electrostatic potentials and partial charges in combined quantum mechanical and molecular mechanical approaches
Ab Inition Study of Some CH 3 OCXYCH 2 Radicals: The Influence of Anomeric Effects on Their Strucutre and Their Stability
Physical origins of the stability of aromatic amino acid core ring-polycyclic hydrocarbon complexes: A post-Hartree-fock and density functional study
Blind docking method combining search of low-resolution binding sites with ligand pose refinement by molecular dynamics-based global optimization
Electronic and nuclear flux analysis on nonadiabatic electron transfer reaction: A view from single-configuration adiabatic born-huang representation
Strain induced bond localization in strained aromatic compounds with extended systems
Effect of surrounding point charges on the density functional calculations of Ni x O x clusters ( x = 4-12)
PCASSO: A fast and efficient Cα-based method for accurately assigning protein secondary structure elements
Two-dimensional replica-exchange method for predicting protein-ligand binding structures
Identification of amyloidogenic peptide sequences using a coarse-grained physicochemical model
3-D molecular stars with covalent axial bonding
Integrating open-source software applications to build molecular dynamics systems
Some Mathematical Reasoning on the Artificial Force Induced Reaction Method
Basis sets for transition metals: Optimized outer p functions
Stereoselection in the diels-alderase ribozyme: A molecular dynamics study
Electrostatic multipole representation of a polypeptide chain: An algorithm for simulation of polypeptide properties
More bang for your buck: Improved use of GPU nodes for GROMACS 2018
SPINE X: Improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles
Reliable and efficient reaction path and transition state finding for surface reactions with the growing string method
Advances in vibrational configuration interaction theory - part 1: Efficient calculation of vibrational angular momentum terms
Detailed analysis of grid-based molecular docking: A case study of CDOCKER - A CHARMm-based MD docking algorithm
Spinor product computations for protein conformations
A chemometric analysis of ab initio vibrational frequencies and infrared intensities of methyl fluoride
Real-time feedback from iterative electronic structure calculations
Cover Image, Volume 41, Issue 5
Structural, electronic, bonding, magnetic, and optical properties of bimetallic [Ru n Au m ] 0/+ ( n + m <= 3) clusters
The way of stabilizing non-IPR fullerenes and structural elucidation of C 54 Cl 8
Efficient use of nonequilibrium measurement to estimate free energy differences for molecular systems
NBO 7.0: New vistas in localized and delocalized chemical bonding theory
Accuracy of distributed multipoles and polarizabilities: Comparison between the LoProp and MpProp models
Pre-training strategy for antiviral drug screening with low-data graph neural network: A case study in HIV-1 K103N reverse transcriptase
Reaction rate of propene pyrolysis
Fast and accurate molecular dynamics simulation of a protein using a special-purpose computer
Accurate conformation-dependent molecular electrostatic potentials for high-throughput in silico drug discovery
Simulations of proteins with inhomogeneous degrees of freedom: The effect of thermostats
A protocol to evaluate one electron redox potential for iron complexes
The destabilization of hydrogen bonds in an external E-field for improved switch performance
Erratum: "Martini Coarse-Grained Model for Polyethylenimine" [J. Comput. Chem. 2019 40, 607-618, DOI : 10.1002/jcc.25747]
Pharmacophore alignment search tool: Influence of scoring systems on text-based similarity searching
Polarizable molecular mechanics studies of Cu(I)/Zn(II) superoxide dismutase: Bimetallic binding site and structured waters
Applying strong external electric field to thiophene-based oligomers: A promising approach to upgrade semiconducting performance
Investigating the interplay between charge transfer and CO 2 insertion in the adsorption of a NiFe catalyst for CO 2 electroreduction on a graphite support through DFT computational approaches
Maximal occupation by bases of π-hole bands surrounding linear molecules
A reliable and efficient first principles-based method for predicting p K a values. 4. organic bases
The Structures of LiNC, NaNC, and KNC: Potential Energy Surface for the Orbiting Motion of the Metal Cation around the CN Group
Ultrafast shape recognition to search compound databases for similar molecular shapes
vmdICE: A plug-in for rapid evaluation of molecular dynamics simulations using VMD
Relativistic all-electron Dirac-Fock-Breit calculations on xenon fluorides (XeF n , n = 1, 2, 4, 6)
Simulating ion channel activation mechanisms using swarms of trajectories
Rotational superposition and least squares: The SVD and quaternions approaches yield identical results. Reply to the preceding comment by G. Kneller
Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamics
Combining ab initio techniques with analytical potential functions for structure predictions of large systems: Method and application to crystalline silica polymorphs
CellSys: An open-source tool for building initial structures for bio-membranes and drug-delivery systems
AutoGridFR: Improvements on AutoDock Affinity Maps and Associated Software Tools
A Computaional Study of Azine, Azoethene, and Diimine Linkages
Energy decomposition analysis of cation-π, metal ion-lone pair, hydrogen bonded, charge-assisted hydrogen bonded, and π-π interactions
Mechanistic investigation inspired "on water" reaction for hydrobromic acid-catalyzed Friedel-Crafts-type reaction of β -naphthol and formaldehyde
Hydrolysis of chemically distinct sites of human serum albumin by polyoxometalate: A hybrid QM/MM (ONIOM) study
Flexible docking simulations: Scaled collective variable Monte Carlo minimization approach using Bezier splines, and comparison with a standard Monte Carlo algorithm
Electronic stress tensor analysis of molecules in gas phase of CVD process for gesbte alloy
Hydrogen bonding in the hydroxysulfinyl radical-formic acid-water system: A theoretical study
DefPol: New procedure to build molecular surfaces and its use in continuum solvation methods
Incorporating deep learning with convolutional neural networks and position specific scoring matrices for identifying electron transport proteins
Using atomic clustering based on structural and electronic descriptors that consider surrounding environment to evaluate local properties of DFT functionals
Why it is sometimes difficult to determine the accurate position of a hydrogen atom by the semiexperimental method: Structure of molecules containing the OH or the CH 3 group