yusuke1997/dblp-id-title huggingface dataset:
Monte Carlo simulation and thermodynamic integration applied to protein charge transfer
Automated input structure generation for single-ended reaction path optimizations
QMX: A versatile environment for hybrid calculations applied to the grafting of Al 2 Cl 3 Me 3 on a silica surface
HIV-1 protease cleavage site prediction based on amino acid property
Implementation and validation of the Lacks-Gordon exchange functional in conventional density functional and adiabatic connection methods
Computation of magnetic circular dichroism by sum-over-states summations
Adsorption-induced changes of intramolecular optical transitions: PTCDA/NaCl and PTCDA/KCl
Adaptive integration of molecular dynamics
Atomistic Insights Into Interaction of Doxorubicin With DNA: From Duplex to Nucleosome
Potential polymorphs of aspirin
Consequences for exchange energy density functional of exponentially decaying nature of atomic electron densities
A new size extensive multireference perturbation theory
QSPR analysis of HPLC column capacity factors for a set of high-energy materials using electronic van der waals surface property descriptors computed by transferable atom equivalent method
A theoretical investigation of the interaction between substituted carbonyl derivatives and water: Open or cyclic complexes?
[DBU-H] + and H 2 o as effective catalyst form for 2, 3-dihydropyrido[2, 3- d ]pyrimidin-4(1 H )-ones: A DFT Study
Diffusion-collision model algorithms for protein folding kinetics
Performance of group additivity methods for predicting the stability of uranyl complexes
Comparison of a quantum random number generator with pseudorandom number generators for their use in molecular Monte Carlo simulations
Free-energy calculations of residue mutations in a tripeptide using various methods to overcome inefficient sampling
"On-the-fly" Crystal : How to reliably and automatically characterize and construct potential energy surfaces
Theoretical characterization of intramolecular proton transfer in the ground and the lowest-lying triplet excited states of 1-amino-3-propenal: a methodological comparison
Simulaid: A simulation facilitator and analysis program
Derivation of class II force fields: V. Quantum force field for amides, peptides, and related compounds
An Improbed Description of the Molecular Charge Density in Force Fields with Atomic Multipole Moments
Models for the treatment of crystalline solids and surfaces
Investigation of binding mechanism and downregulation of elacestrant for wild and L536S mutant estrogen receptor-α through molecular dynamics simulation and binding free energy analysis
A Molecular Mechanical Model That Reproduces the Relative Energies for Chair and Twist-Boat Conformations of 1, 3-Dioxanes
The effect of polarization on multiple hydrogen-bond formation in models of self-assembling materials
Cover Image, Volume 41, Issue 24
An extensible and systematic force field, ESFF, for molecular modeling of organic, inorganic, and organometallic systems
Molecular modeling of polymer-clay nanocomposite precursors: Lysine in montmorillonite interlayers
Theoretical study on the reaction of SiH(CH 3 ) 3 with SiH 3 radical
The 1: 1 glycine zwitterion-water complex: An ab initio electronic structure study
Restricted dead-end elimination: Protein redesign with a bounded number of residue mutations
Vibrational echo spectroscopy of aqueous sodium bromide solutions from first principles simulations
Predicting the vibrational spectra of some simple fluorocarbons by direct scaling of primitive valence force constants
Membrane lipids are both the substrates and a mechanistically responsive environment of TMEM16 scramblase proteins
Benchmarking boron cluster calculations: Establishing reliable geometrical and energetic references for B n ( n = 1-4)
Full configuration interaction calculation of the low lying valence and Rydberg states of BeH
Development and implementation of (Q)SAR modeling within the CHARMMing web-user interface
Electrostatic component of binding energy: Interpreting predictions from poisson-boltzmann equation and modeling protocols
Computational study on noncovalent interactions between (n, n) single-walled carbon nanotubes and simple lignin model-compounds
Response to comment on "Superposition of waves or densities: Which is the nature of chemical resonance?"
Further test of the isolated pentagon rule: Thermodynamic and kinetic stabilities of C84 fullerene isomers
Optimization of parallel implementation of UNRES package for coarse-grained simulations to treat large proteins
Theoretical study on the mechanism of the CH2F + NO2 reaction
Calculating rate constants with updated Hessians using variational transition state theory with multidimensional tunneling
Theoretical understanding on the v 1 -SO 4 2- band perturbed by the formation of magnesium sulfate ion pairs
Chemical interpretation of molecular electron density distributions
MSINDO parameterization for third-row main group elements
Topology-based models and NMR structures in protein folding simulations
Cover Image, Volume 40, Issue 14
LOBSTER : Local orbital projections, atomic charges, and chemical-bonding analysis from projector-augmented-wave-based density-functional theory
A high-resolution electron momentum spectroscopy and density functional theory study into the complete valence electronic structure of allene
Effect of monovalent ion binding on molecular dynamics of the S100-family calcium-binding protein calbindin D9k
Performance of TDDFT Vertical Excitation Energies of Core-Substituted Naphthalene Diimides
Rate coefficients of the CF 3 CHFCF 3 + H → CF 3 CFCF 3 + H 2 reaction at different temperatures calculated by transition state theory with ab initio and DFT reaction paths
Comparative DFT study of N2 and no adsorption on vanadium clusters V n ( n = 2-13)
QM/MM study of aqueous solvation of the uranyl fluoride [UO2F42-] complex
MM3 parametrization of four- and five-coordinated rhenium complexes by a genetic algorithm - Which factors influence the optimization performance?
Extending fragment-based free energy calculations with library monte carlo simulation: Annealing in interaction space
Binding structures of tri- N -acetyl-β-glucosamine in hen egg white lysozyme using molecular dynamics with a polarizable force field
Computer generation of Hadamard matrices
Corrigendum: Inter- and intramolecular dispersion interactions
Chemical fragments in real space: Definitions, properties, and energetic decompositions
Theoretical investigation of an energetic fullerene derivative
Constrained numerical gradients and composite gradients: Practical tools for geometry optimization and potential energy surface navigation
Optimization of Gaussian surface calculations and extension to solvent-accessible surface areas
Comparison of 6-31G*-based MST/SCRF and FEP evaluations of the free energies of hydration for small neutral molecules
Modeling nonlinear optics of nanosystems with sum-over-states model
ClassicalGSG: Prediction of logP using classical molecular force fields and geometric scattering for graphs
PyADF - A scripting framework for multiscale quantum chemistry
Assessment of DFT Functionals for Predicting the Magnetic Exchange Coupling Constants of Nonalternant Hydrocarbon Diradicals: The Role of Hartree-Fock Exchange
A dissected ring current model for assessing magnetic aromaticity: A general approach for both organic and inorganic rings
Isomers of C20: An energy profile
Kinetic isotope effects calculated with the instanton method
Calculation of relative solvation free energy differences by thermodynamic perturbation method: Dependence of free energy results on simulation length
An automatized workflow from molecular dynamic simulation to quantum chemical methods to identify elementary reactions and compute reaction constants
Application of error-ranked singular value decomposition for the determination of potential-derived atomic-centered point charges
Understanding the molecular mechanism of γ-elimination of nitrous acid in the framework of the molecular electron density theory
MesoBioNano explorer - A universal program for multiscale computer simulations of complex molecular structure and dynamics
Poling: Promoting Conformational Variation
A scoring function for docking ligands to low-resolution protein structures
Trigger bond analysis of nitroaromatic energetic materials using wiberg bond indices
Comparison of localization and delocalization indices obtained with Hartree-Fock and conventional correlated methods: Effect of Coulomb correlation
Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes
"Full numerical" diatomic matrix elements: Simplified shooting method
Exchange coupling constants using density functional theory: Long-range corrected functionals
Importance of ligand conformational energies in carbohydrate docking: Sorting the wheat from the chaff
Diving into chemical bonding: An immersive analysis of the electron charge rearrangement through virtual reality
Theoretical and practical aspects of the convergence properties of the dynamically defined reaction path method
Nonfitting protein-ligand interaction scoring function based on first-principles theoretical chemistry methods: Development and application on kinase inhibitors
A high-performance parallel-generalized born implementation enabled by tabulated interaction rescaling
Double hybrid DFT calculations with Slater type orbitals
A density fitting scheme for the fast evaluation of molecular electrostatic potential
Structures, stabilities, electronic, and optical properties of C 64 fullerene isomers, anions (C 64 2- and C 64 4- ), metallofullerene Sc 2 @C 64 , and Sc 2 C 2 @C 64
A multiple time step scheme for multiresolved models of Macromolecules
Structural and electronic properties of boron-doped lithium clusters: Ab initio and DFT studies
A Samle Yet Accurate Boundary Element Method for Contituum Dielectric Calculations
MoCalc: A new graphical user interface for molecular calculations
Development of an ATP force field for coarse-grained simulation of ATPases and its application to the maltose transporter
Normal Mode Analysis of Oligomeric Proteins: Reduction of the Memory Requirement by Consideration of Rigid Geomertry and Molecular Symmetry
Implementation of probe rheology simulation technique in atomistically detailed molecular dynamics simulations
Single-step perturbations to calculate free energy differences from unphysical reference states: Limits on size, flexibility, and character
New formulation for derivatives of torsion angles and improper torsion angles in molecular mechanics: Elimination of singularities
Unraveling Reaction Path Bifurcation: Insights Into Electron Movement via Natural Reaction Orbitals
Empirical force fields for biological macromolecules: Overview and issues
DFT mechanistic study of the chemical fixation of CO 2 by aziridine derivatives
Evaluation of activation energy of thermally stimulated solid-state reactions under arbitrary variation of temperature
PepPro: A Nonredundant Structure Data Set for Benchmarking Peptide-Protein Computational Docking
Prediction of protein-protein complexes using replica exchange with repulsive scaling
Deriving the phylogenetic information from some physicochemical properties of protein sequences computed
Tork: Conformational analysis method for molecules and complexes
Structures and Solvation Energies Effects Versus Temperature. An MP2 Investigations in the Framework of Cluster Model
Recersed Stereochemical Preference in Binding of Ro31-8959 to HIV-1 Proteinase: A Free Energy Perturbation Analysis
Ab initio studies for the photodissociation mechanism of hydroxyacetone
Internucleotide J -couplings and chemical shifts of the N---H···N hydrogen-bonds in the radiation-damaged guanine-cytosine base pairs
Electronic structures and nonlinear optical properties of highly deformed halofullerenes C 3 v C 60 F 18 and D 3 d C 60 Cl 30
Accurate atomic Gaussian basis functions for second-row atoms: Small split-valence 3-21SP and 4-22SP basis sets
An Efficient Simulation Technique for Electrostatic Free Energies with Applications to Azurin
Structural, electronic, and optical properties of phosphole-containing pi-conjugated oligomers for light-emitting diodes
Predicting the catalytic activities of transition metal (Cr, Fe, Co, Ni) complexes towards ethylene polymerization by machine learning
Deterministic global optimization of molecular structures using interval analysis
Theoretical study of structure sensitivity on ceria-supported single platinum atoms and its influence on carbon monoxide adsorption
Site-directed analysis on protein hydrophobicity
PHAISTOS: A framework for Markov chain Monte Carlo simulation and inference of protein structure
Electronic reorganization triggered by electron transfer: The intervalence charge transfer of a Fe 3+ /Fe 2+ bimetallic complex
Small lithium-chloride clusters: Superalkalis, superhalogens, supersalts and nanocrystals
A new perspective of shape recognition to discover the phase transition of finite-size clusters
Improved Modeling of Cation-π and Anion-Ring Interactions Using the Drude Polarizable Empirical Force Field for Proteins
Photoelectron spectrum of NO2-: SAC-CI gradient study of vibrational-rotational structures
Exploring the similarities between potential smoothing and simulated annealing
Calculation of the free energy of solvation for neutral analogs of amino acid side chains
Vibrational molecular force field of model compounds with biologic interest. II. Harmonic dynamics of both anomers of glucose in the crystalline state
Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST
First-principles calculations on the energetics, electronic structures and magnetism of SrFeO 2
Thermodynamic Integration Calculations on the Relative Free Energies of Complex Ions in Aqueous Solution: Application to Ligands of Dihydrofolate Reductace
Assessing small molecule conformational sampling methods in molecular docking
Role of binding entropy in the refinement of protein-ligand docking predictions: Analysis based on the use of 11 scoring functions
porE: A code for deterministic and systematic analyses of porosities
Filling the Gap in LogP $$ LogP $$ and pK a $$ {pK}_a $$ Evaluation for Saturated Fluorine-Containing Derivatives With Machine Learning
Exact ligand cone angles
Role of alkylated residues in the tetrapeptide self-assembly - A molecular dynamics study
Benchmarking applicability of medium-resolution cryo-EM protein structures for structure-based drug design
Machine learning-assisted search for novel coagulants: When machine learning can be efficient even if data availability is low
Application of torsion angle molecular dynamics for efficient sampling of protein conformations
Ab initio copper-water interaction potential for the simulation of aqueous solutions
Model studies of the optical rotation, and theoretical determination of its sign for beta-pinene and trans -pinane
Absolute free energies estimated by combining precalculated molecular fragment libraries
Evaluating the conformational space of the active site of D2 dopamine receptor. Scope and limitations of the standard docking methods
Symplectic Integrators and the Conservation of Angular Momentum
New 2D graphical representation of DNA sequences
MILCH SHAKE: An efficient method for constraint dynamics applied to alkanes
Atomistic chemical computation of Olefin polymerization reaction catalyzed by (pyridylamido)hafnium(IV) complex: Application of Red Moon simulation
Scents and sense: In silico perspectives on olfactory receptors
Evaluation of the searching abilities of HBOP and HBSITE for binding pocket detection
Stability of carbon-centered radicals: Effect of functional groups on the energetics of addition of molecular oxygen
The role of the halogen bond in iodothyronine deiodinase: Dependence on chalcogen substitution in naphthyl-based mimetics
Efficient algorithm for "on-the-fly" error analysis of local or distributed serially correlated data
Theoretical Study of the Gas-Phase Addition of HF and HCI to Ethylene: Analysis of the Catalytic Action of Dimeric Halides
Cluster Analysis of Molecular Conformations
Automated and efficient quantum chemical determination and energetic ranking of molecular protonation sites
A variant on the CREST iMTD algorithm for noncovalent clusters of flexible molecules
Computational study of methane activation by mercury(II) complexes
Theoretical studies on the electronic and optical properties of two new alternating fluorene/carbazole copolymers
An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials
Merging multiconfigurational wavefunctions and correlation functionals to predict magnetic coupling constants
In silico concurrent multisite pH titration in proteins
A method to obtain a near-minimal-volume molecular simulation of a macromolecule, using periodic boundary conditions and rotational constraints
Stochastic dynamics simulation of alanine dipeptide: Including solvation interaction determined by boundary element method
Preprocessing of rotamers for protein design calculations
Dividing a complex reaction involving a hypervalent iodine reagent into three limiting mechanisms by ab initio molecular dynamics
Ab Initio Calculation of structures and properties of halogenated general anesthetics: halothane and sevoflurane
A compound QM/MM procedure: Comparative performance on a pyruvate formate-lyase model system
Study of mechanical, optical, and thermoelectric characteristics of Ba 2 XMoO 6 (X = Zn, Cd) double perovskite for energy harvesting
Optimization of Carbó molecular similarity index using gradient methods
A multipole-based water potential with implicit polarization for biomolecular simulations
Cationic Closo -carboranes 2. Do computed 11 B and 13 C NMR chemical shifts support their experimental availability?
Curvature-dependent adsorption of water inside and outside armchair carbon nanotubes
Direct INDO/SCI method for excited state calculations
First-principle modelling of forsterite surface properties: Accuracy of methods and basis sets
Carbondioxide rare-gas systems: Sensitivity of basis sets and double-hybrid density functionals
Number of sites-based solver for determining coverages from steady-state mean-field micro-kinetic models
A comprehensive DFT investigation of bulk and low-index surfaces of ZrO 2 polymorphs
A comparison of low and high activity precatalysts: Do the calculated energy barriers during the self-metathesis reaction of 1-Octene correlate with the precatalyst metathesis activity?
pyVib, a computer program for the analysis of infrared and Raman optical activity
Ab initio prediction of helical segments in polypeptides
Implementation of nuclear gradients of range-separated hybrid density functionals and benchmarking on rotational constants for organic molecules
Machine learning for accuracy in density functional approximations
Highlighting and trying to overcome a serious drawback with qspr studies; data collection in different experimental conditions (mixed-QSPR)
Design of a reaction field using a linear-combination-based isotropic periodic sum method
Paramfit: Automated optimization of force field parameters for molecular dynamics simulations
Point scattering: A new geometric invariant with applications from (Nano)clusters to biomolecules
ProteinUnet - An efficient alternative to SPIDER3-single for sequence-based prediction of protein secondary structures
Solvated ensemble averaging in the calculation of partial atomic charges
From orientation disordered to ordered - An ab initio simulation on ammonia borane phase transition within van der Waals corrections
Failure of Net Atomic Charge Models to Represent the van der Waals Envelope Electric Potential of n-Alkanes
Algorithm to minimize MPI communications in the parallelized fast multipole method combined with molecular dynamics calculations
Elongation method with intermediate mechanical and electrostatic embedding for geometry optimizations of polymers
Conformational dependence of charges in protein simulations
Fully atomistic molecular-mechanical model of liquid alkane oils: Computational validation
Comparison of two force fields by molecular dynamics simulations of glucose crystals: Effect of using ewald sums
Fep1d: A script for the analysis of reaction coordinates
A generalized expression for the similarity of spectra: application to powder diffraction pattern classification
Influence of environment on proton-transfer mechanisms in model triads from theoretical calculations
Accessing the applicability of polarized protein-specific charge in linear interaction energy analysis
Monte Carlo Simulations on Short Single-Stranded Oligonucleotides. I. Application to RNA Trimers
The possibility of the decomposition of 2'-deoxyribose moiety of thymidine induced by the low energy electron attachment
On the Stability of Cis- and Trans -2-Butene Isomers. An Insight Based on the FAMSEC, IQA, and ETS-NOCV Schemes
Randomized tree construction algorithm to explore energy landscapes
A new analytical method for computing solvent-accessible surface area of macromolecules and its gradients
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. II. Results, comparison with statistical potentials, and implementation in the UNRES force field
N -dimensional switch function for energy conservation in multiprocess reaction dynamics
Very efficient search for nucleotide alignments
Statistical investigation of surface bound ions and further development of BION server to include pH and salt dependence
Biased fragment distribution in MC simulation of protein folding
A coupled density functional-molecular mechanics Monte Carlo simulation method: The water molecule in liquid water
Using support vector machines for prediction of protein structural classes based on discrete wavelet transform
Vibrational spectra of nucleic acid bases and their Watson-Crick pair complexes
Powder pattern indexing using the weighted crosscorrelation and genetic algorithms
FDS: Flexible ligand and receptor docking with a continuum solvent model and soft-core energy function
Web-4D-QSAR: A web-based application to generate 4D-QSAR descriptors
Accurate relativistic adapted gaussian basis sets for francium through ununoctium without variational prolapse and to be used with both uniform sphere and gaussian nucleus models
Force field-dependant structural divergence revealed during long time simulations of Calbindin d9k
Enveloping triangulation method for detecting internal cavities in proteins and algorithm for computing their surface areas and volumes
Density functional theory study of high-pressure effect on crystalline 4, 4′, 6, 6′-tetra(azido)hydrazo-1, 3, 5-triazine
MoBioTools: A toolkit to setup quantum mechanics/molecular mechanics calculations
Docking Survey, ADME, Toxicological Insights, and Mechanistic Exploration of the Diels-Alder Reaction Between Hexachlorocyclopentadiene and Dichloroethylene
Coarse-grained molecular dynamics simulations of polymerization with forward and backward reactions
Correction of cavity-induced errors in polarization charges of continuum solvation models
Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO)
Alchemical Grid Dock (AlGDock): Binding Free Energy Calculations between Flexible Ligands and Rigid Receptors
Toward universal substituent constants: Model chemistry sensitivity of descriptors from the quantum theory of atoms in molecules
Benchmark study on deep neural network potentials for small organic molecules
Cluster-based molecular docking study for in silico identification of novel 6-fluoroquinolones as potential inhibitors against mycobacterium tuberculosis
Relationship between dye-iodine binding and cell voltage in dye-sensitized solar cells: A quantum-mechanical look
Quantum monte carlo for large chemical systems: Implementing efficient strategies for petascale platforms and beyond
On the applicability of the HSAB principle through the use of improved computational schemes for chemical hardness evaluation
The Nobel history of computational chemistry. A personal perspective