yusuke1997/dblp-id-title huggingface dataset:
Conformational state-specific free energy differences by one-step perturbation: Protein secondary structure preferences of the GROMOS 43A1 and 53A6 force fields
An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design
Comparison of generalized born and poisson models: Energetics and dynamics of HIV protease
Rb+/Cs+ selectivity of benzo and tribenzo derivatives of the 21C7 crown ether. A density functional study
The cyclic cluster model at hartree-fock level
The quest for best suited references for configuration interaction singles calculations of core excited states
Comment on "Aromatic-Backbone Interactions in Model alpha-Helical Peptides" [Palermo et al., J Comput Chem 2007, 28, 1208]
Introduction of periodic boundary conditions into UNRES force field
Estimation of the absolute internal-rotation entropy of molecules with two torsional degrees of freedom from stochastic simulations
ORBKIT: A modular python toolbox for cross-platform postprocessing of quantum chemical wavefunction data
On the mechanism of intramolecular nitrogen-atom hopping in the carbon chain of C 6 N radical: A Plausible 3c-4e crossover π̂ Long-Bond
CAN: A new program to streamline preparation of molecular coordinate files for molecular dynamics simulations
Development and testing of a general amber force field
Simple method for locating possible ligand binding sites on protein surfaces
Stochastic searches for lactone and cycloalkene conformers
Self-consistent field calculations using two-body density functionals for correlation energy component: II. Small molecules
SHARPEN - Systematic Hierarchical Algorithms for Rotamers and Proteins on an Extended Network
Influence of back donation effects on the structure of ZnO nanoclusters
Density functional study of neutral allopurinol tautomeric forms
Nuclear quantum effect and temperature dependency on the hydrogen-bonded structure of base pairs
Accurate prediction of enthalpies of formation for a large set of organic compounds
High-throughput screening of spin states for transition metal complexes with spin-polarized extended tight-binding methods
Electrode polarization effects on interfacial kinetics of ionic liquid at graphite surface: An extended lagrangian-based constant potential molecular dynamics simulation study
A precise boundary element method for macromolecular transport properties
Stability and bonding of carbon(0)-iron-N 2 complexes relevant to nitrogenase co-factor: EDA-NOCV analyses
Electronic structure and stability of Al n P n ( n = 2-4) clusters
Comparison of rigid and flexible simple point charge water models at supercritical conditions
Update on phosphate and charged post-translationally modified amino acid parameters in the GROMOS force field
Broken symmetry approach to calculation of exchange coupling constants for homobinuclear and heterobinuclear transition metal complexes
B -factor profile prediction for RNA flexibility using support vector machines
ORAC: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level
Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems
The role of water in the adsorption of oxygenated aromatics on Pt and Pd
A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations
Synergistic regulation of chloride anion recognition using a triple-functional sites receptor with two different cationic effectors
Excited states of GFP chromophore and active site studied by the SAC-CI method: Effect of protein-environment and mutations
How are the charge transfer descriptors affected by the quality of the underpinning electronic density?
Open shell versus closed shell bonding interaction in cyclopropane derivatives: EDA-NOCV analyses
Introduction of a bounded penalty function in contact-assisted simulations of protein structures to omit false restraints
Hardness potential derivatives and their relation to fukui indices
Independent gradient model based on Hirshfeld partition: A new method for visual study of interactions in chemical systems
Energy partitioning scheme based on self-consistent method for subsystems: Populational space approach
Density functional theory calculation of cyclic carboxylic phosphorus mixed anhydrides as possible intermediates in biochemical reactions: Implications for the Pro-Tide approach
Transferable atom equivalent multicentered multipole expansion method
Geometric algorithms for the conformational analysis of long protein loops
Gas-phase detection of the HBCC (X1) molecule: a combined crossed beam and computational study of the B(2P)+C2H2(1g+) reaction
A stepwise retro-imino-ene as a key step in the mechanism of allene formation via the Crabbé acetylene homologation
The treatment of solvation by a generalized Born model and a self-consistent charge-density functional theory-based tight-binding method
PyFrag - Streamlining your reaction path analysis
2D depiction of nonbonding interactions for protein complexes
The electronic structure of thorium monoxide: Ligand field assignment of states in the range 0-5 eV
SEQCROW: A ChimeraX bundle to facilitate quantum chemical applications to complex molecular systems
Molecular mechanics parameters for the FapydG DNA lesion
Melting behaviors of icosahedral metal clusters studied by Monte Carlo simulations
Variation of spectral, structural, and vibrational properties within the intrinsically fluorescent proteins family: A density functional study
Non-Boltzmann sampling and Bennett's acceptance ratio method: How to profit from bending the rules
Cartesian constraints in QM/MM optimizations
Spin-flip approach within time-dependent density functional tight-binding method: Theory and applications
ICM - A New Method for Protein Modeling and Design: Applications to Docking and Strucutre Prediction from the Distorted Native Conformation
Molecular mechanics calculations on carbonyl compounds. III. Cycloketones
Instanton calculations of tunneling splittings in chiral molecules
Maximal orbital analysis of molecular wavefunctions
DFT study of the asymmetric nitroaldol (Henry) reaction catalyzed by a dinuclear Zn complex
Description of non-covalent interactions in SCC-DFTB methods
Modifying the OPLS-AA force field to improve hydration free energies for several amino acid side chains using new atomic charges and an off-plane charge model for aromatic residues
Computational study of ground-state chiral induction in small peptides: Comparison of the relative stability of selected amino acid dimers and oligomers in homochiral and heterochiral combinations
An analysis of valence electronic structure from a viewpoint of resonance theory: Tautomerization of formamide and diazadiboretidine
Using redundant internal coordinates to optimize equilibrium geometries and transition states
Why different water models predict different structures under 2D confinement
Divagations about the periodic table: Boolean hypercube and quantum similarity connections
Hydrogen bond-aromaticity cooperativity in self-assembling 4-pyridone chains
An ab initio quantum mechanical charge field molecular dynamics simulation of a dilute aqueous HCl solution
Simulations of thermodynamics and kinetics on rough energy landscapes with milestoning
Ab-initio molecular dynamics and hybrid explicit-implicit solvation model for aqueous and nonaqueous solvents: GFP chromophore in water and methanol solution as case study
Absorption and fluorescence emission spectroscopic characters of naphtho-homologated yy-DNA bases and effect of methanol solution and base pairing
Time-dependent density functional theory study on direction-dependent electron and hole transfer processes in molecular systems
Dynamic relaying properties of a β-turn peptide in long-range electron transfer
Erraturm - A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions
Improved free energy profile for reduction of NO in cytochrome c dependent nitric oxide reductase (cNOR)
Resolving a puzzling anomaly in the spin-coupled generalized valence bond description of benzene
A balanced procedure for the treatment of cluster-ligand interactions on gold phosphine systems in catalysis
A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons
Cover Image, Volume 41, Issue 14
QSAR models based on isomorphic and nonisomorphic data fusion for predicting the blood brain barrier permeability
Improving the reliability of machine learned potentials for modeling inhomogeneous liquids
PHI: A powerful new program for the analysis of anisotropic monomeric and exchange-coupled polynuclear d- and f-block complexes
Comparison of the boys and Pipek-Mezey localizations in the local correlation approach and automatic virtual basis selection
A DFT study on the insertion of CO 2 into styrene oxide catalyzed by 1-butyl-3-methyl-Imidazolium bromide ionic liquid
Characterizing amyloid-beta protein misfolding from molecular dynamics simulations with explicit water
Homology modeling and molecular dynamics simulation studies of human type 1 3beta-hydroxysteroid dehydrogenase: Toward the understanding of cofactor specificity
Foreword to the special issue for Elfi Kraka
Asymmetry in methyl group of ethane during internal rotation: Ab initio study
A new approach to counterpoise correction to BSSE
Attaining exponential convergence for the flux error with second- and fourth-order accurate finite-difference equations. I. Presentation of the basic concept and application to a pure diffusion system
The stability of oxygen-centered radicals and its response to hydrogen bonding interactions
OH hydrogen abstraction reactions from alanine and glycine: A quantum mechanical approach
Parallel DFT gradients using the Fourier Transform Coulomb method
Molecular dynamics simulations of fluid methane properties using ab initio intermolecular interaction potentials
Determination of spin-orbit coupling contributions in the framework of density functional theory
Combined Molecular Mechanical and Quantum Mechanical Potential Study of a Nucleophilic Addition Reaction in Solution
Nonlinear optical properties of the rhombic B4-cluster
Mapping of proteinase active sites by projection of surface-derived correlation vectors
Computational chemistry approach to protein kinase recognition using 3D stochastic van der Waals spectral moments
Elucidation of the methyl transfer mechanism catalyzed by chalcone O -methyltransferase: A density functional study
Solvation free energy arithmetic for small organic molecules
A hierarchical algorithm for molecular similarity (H-FORMS)
A scheme for rapid evaluation of the intermolecular three-body polarization effect in water clusters
Effect of the Solute Cavity on the Solvation Energy and its Derivatives within the Framework of the Gaussian Charge Scheme
Evaluation of density functional theory in the bond rupture of octane
Structure-breaking effects of solvated Rb(I) in dilute aqueous solution - An ab initio QM/MM MD approach
Analytical nuclear excited-state gradients for the Tamm-Dancoff approximation using uncoupled frozen-density embedding
H 2 adsorption on Ag-nanocluster/single-walled carbon nanotube composites: A molecular dynamics study on the effects of nanocluster size, diameter, and chirality of nanotube
Polarization effects on peptide conformations at water-membrane interface by molecular dynamics simulation
Enantioselective binding of -pinene and of some cyclohexanetriol derivatives by cyclodextrin hosts: A molecular modeling study
Natural bond critical point analysis: Quantitative relationships between natural bond orbital-based and QTAIM-based topological descriptors of chemical bonding
Prediction of the reduction potential of tris(2, 2′-bipyridinyl)iron(III/II) derivatives
Expanding molecular modeling and design tools to non-natural sidechains
Nuclear quantum effects induce metallization of dense solid molecular hydrogen
Identification of biomolecular conformations from incomplete torsion angle observations by hidden markov models
Molecular dynamics simulations of the detoxification of paraoxon catalyzed by phosphotriesterase
Application of MOLMAP approach for QSAR modeling of various biological activities using substituent electronic descriptors
Ab initio molecular orbital calculations for 3, 6-dihydro-1, 2-dithiin and 3, 6-dihydro-1, 2-dioxin
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
Pressure-assisted decomposition of tricresyl phosphate on amorphous FeO using hybrid quantum-classical simulations
Force-field parameters for the simulation of tetrahedral intermediates of serine hydrolases
Stability issues of covalently and noncovalently bonded peptide subunits
Use of multivariate methods in the analysis of calculated reaction pathways
A DFT study on the relative affinity for oxygen of the and subunits of hemoglobin
A TD-DFT study on the hydrogen bonding of three esculetin complexes in electronically excited states: Strengthening and weakening
Comment on "a minimal implementation of the AMBER-GAUSSIAN interface for Ab Initio QM/MM-MD simulation"
Potential of mean force of water-proton bath and molecular dynamic simulation of proteins at constant pH
Analytical gradients for subsystem density functional theory within the slater-function-based amsterdam density functional program
Graphene-induced planarization of cyclooctatetraene derivatives
Chemical potential and reaction electronic flux in symmetry controlled reactions
Quantum mechanical study of transition metal hydrides: Comparison of determined molecular properties with experimental data
Do surfaces of positive electrostatic potential on different halogen derivatives in molecules attract? like attracting like!
Photophysical properties of fluorescent imaging biological probes of nucleic acids: SAC-CI and TD-DFT Study
Automatic algorithms for completeness-optimization of Gaussian basis sets
Investigations of the hydrogen bond in the crystals of tropolone and thiotropolone via car-parrinello and path integral molecular dynamics
Computational study of the reactivity of cytosine derivatives
Substitutional carbon defects in silicon: A quantum mechanical characterization through the infrared and Raman spectra
Differential geometric analysis of alterations in MH α-helices
Best bang for your buck: GPU nodes for GROMACS biomolecular simulations
Conformational and energetic effects of truncating nonbonded interactions in an aqueous protein dynamics simulation
Methods for the Simulation of the Slowing of Low-Energy Electrons in Water
Comparing normal modes across different models and scales: Hessian reduction versus coarse-graining
Quantum bits with polyacetylene
Hydrogen- and Halogen-Bonds between Ions of like Charges: Are They Anti-Electrostatic in Nature?
A new method to locate saddle points for reactions in solution by using the free-energy gradient method and the mean field approximation
Density functional theory study of 1, 2-dioxetanone decomposition in condensed phase
Carbamic acid and its dimer: A computational study
autoDIAS: a python tool for an automated distortion/interaction activation strain analysis
Comparing the influence of explicit and implicit solvation models on site-specific thermodynamic stability of proteins
Clarifying and illustrating the electronic energy transfer pathways in trimeric and hexameric aggregation state of cyanobacteria allophycocyanin within the framework of Förster theory
Density functional theory for molecular and periodic systems using density fitting and continuous fast multipole method: Stress tensor
A [Fe(CB 6 )] platform for binding of small molecules: Insights from DFT calculations
A new massively parallel version of CRYSTAL for large systems on high performance computing architectures
Density functional investigation of reaction of borohydride cation BH2+ with propylene
Nonrigid water octamer: Computations with the 8-cube
Excitation energies of benzene from Kohn-Sham theory
Computational exploration of the copper(I)-catalyzed conversion of hydrazones to dihalogenated vinyldiazene derivatives
Simple computing of the viscosity of water-dioxane mixtures, according to a fluctuating SPC/E-I h interstitial model
Studies on 4, 7-di-substitution effects of one ligand in [Ru(Phen)3]2 with DFT method
Dispersive interactions in water bilayers at metallic surfaces: A comparison of the PBE and RPBE functional including semiempirical dispersion corrections
Extension of MST/SCRF method to organic solvents: Ab initio and semiempirical parametrization for neutral solutes in CCl4
Molecular dynamics study of solubilization of cyclohexane, benzene, and phenol into mixed micelles composed of sodium dodecyl sulfate and octaethylene glycol monododecyl ether
CHARMM-GUI DEER facilitator for spin-pair distance distribution calculations and preparation of restrained-ensemble molecular dynamics simulations
WebMTA: A web-interface for ab initio geometry optimization of large molecules using molecular tailoring approach
Application of reference-modified density functional theory: Temperature and pressure dependences of solvation free energy
Toward the complete range separation of non-hybrid exchange-correlation functional
Reactivities of silane coupling agents in the silica/rubber composites: Theoretical insights into the relationships between energy barriers and electronic characteristics
A minimal implementation of the AMBER-GAUSSIAN interface for ab initio QM/MM-MD simulation
Quantum-connectivity descriptors in modeling solubility of environmentally important organic compounds
Dipole and quadrupole polarizabilities of the water molecule as a function of geometry
Modeling the hERG potassium channel in a phospholipid bilayer: Molecular dynamics and drug docking studies
Giant magnetic moment of the core-shell Co 13 @Mn 20 clusters: First-principles calculations
An Optimized AM1/MST Method for the MST-SCRF Representation of Solvated Systems
Performance assessment of density-functional methods for study of charge-transfer complexes
A semiempirical computational study of electron transfer reactivity of one- vs. two-ring model systems for anthracycline pharmacophores. I. A rationale for mode of action
Geometric constraints within tripeptides and the existence of tripeptide reconstructions
Variational transition-state theory study of the rate constant of the DMS·OH scavenging reaction by O 2
All-electron relativistic computations on the low-lying electronic states, bond length, and vibrational frequency of CeF diatomic molecule with spin-orbit coupling effects
Force field parameters for rotation around chi torsion axis in nucleic acids
Transferable pseudoclassical electrons for aufbau of atomic ions
An analytical method for computing atomic contact areas in biomolecules
Ligand release mechanisms and channels in histone deacetylases
Structure, stability and bonding of the leapfrog B240, ±1, ±2
An interaction potential to study the thermal structure evolution of a thermoelectric material: β-Cu 2 Se
Informatics-Based Energy Fitting Scheme for Correlation Energy at Complete Basis Set Limit
Switching the nature of catalytic centers in Pd/NHC systems by solvent effect driven non-classical R-NHC Coupling
Infrared Spectroscopy of Ethanethiol Monomers and Dimers at MP2 Level: Characterizing the Dimer Formation and Hydrogen Bond
An interoperable implementation of collective-variable based enhanced sampling methods in extended phase space within the OpenMM package
High-performance transformation of protein structure representation from internal to Cartesian coordinates
Prediction of acid pKa values in the solvent acetone based on COSMO-RS
Absolute free energies of binding of peptide analogs to the HIV-1 protease from molecular dynamics simulations
Could the "Janus-like" properties of the halobenzene CX bond (X˭Cl, Br) be leveraged to enhance molecular recognition?
Flexibility-rigidity index for protein-nucleic acid flexibility and fluctuation analysis
iVI: An iterative vector interaction method for large eigenvalue problems
Charge transfer excitations in TDDFT: A ghost-hunter index
Conformational changes of ubiquitin under high pressure conditions: A pressure simulated tempering molecular dynamics study
Potential energy surfaces and nonadiabatic transitions in the asymptotic regions of ICN photodissociation to study the interference effects in the F1 and F2 spin-rotation levels of the CN products
Variational treatment of the vibrational Hamiltonian for NH3 and H2NO
Topological analysis of the electron delocalization range
Analytical first derivatives of molecular surfaces with respect to nuclear coordinates
Quantum chemical geometry optimizations in proteins using crystallographic raw data
Structural and dynamical analysis of the hydration of the Alzheimer's beta-amyloid peptide
Exploring the molecular basis of UG-rich RNA recognition by the human splicing factor TDP-43 using molecular dynamics simulation and free energy calculation
CH Bond Activation Mechanism by a High-Valent Dinuclear Copper Complex: Unraveling the Effect of a Base by a Theoretical Study
Interactions between free radicals and a graphene fragment: Physical versus chemical bonding, charge transfer, and deformation
Exact analytical loop closure in proteins using polynomial equations
Describing ground and excited state potential energy surfaces for molecular photoswitches using coupled cluster models
Effect of a complex formation on the calculated low-pressure rate constant of a bimolecular gas-phase reaction governed by tunneling
Performance of 3D-space-based atoms-in-molecules methods for electronic delocalization aromaticity indices
Reactive orbital energy theory serving a theoretical foundation for the electronic theory of organic chemistry
Using grey dynamic modeling and pseudo amino acid composition to predict protein structural classes
Bond-based 3D-chiral linear indices: Theory and QSAR applications to central chirality codification
CENCALC: A computational tool for conformational entropy calculations from molecular simulations
Precise and efficient Ewald summation for periodic fast multipole method
Ab Initio Molecular Orbital Study of 1-Fluorosilatrane
Derivatives of molecular surface area and volume: Simple and exact analytical formulas
LINCS: A linear constraint solver for molecular simulations
Local hartree-fock orbitals using a three-level optimization strategy for the energy
Interaction and protection mechanism between li@C 60 and nucleic acid bases (NABs): Performance of PM6-DH2 on noncovalent interaction of NABs-Li@C60
Steric repulsions, rotation barriers, and stereoelectronic effects: A real space perspective
Stable Conformations of CH 3 CH 2 OCH 2 CH 2 OH: A Comparison of Theoretical Methods
Theoretical study on photooxidation mechanism of ruthenium complex [Ru(II)-(bpy) 2 (TMBiimH 2 )] 2+ with molecular oxygen
Testing the limits of model membrane simulations - bilayer composition and pressure scaling
Small molecules (CO 2 , i PrNCO, and i PrNCN i Pr) activation by the metallomimetics (μ-Hydrido) diborane anion: A DFT investigation on mechanism and chemoselectivity controlling
Exploring the influence of metal cations on individual hydrogen bonds in Watson-Crick guanine-cytosine DNA base pair: An interacting quantum atoms analysis
NMR chemical shifts in MNDO approximation: Parameters and results for H, C, N, and O
Redox-induced configuration conversion for thioacetamide dimer can function as a molecular switch
Transferability of parameters of strictly local geminals' wave function and possibility of sequential derivation of molecular mechanics
Conformational Sensitivity Analysis of FKBP-FK506/ Rapamycin Complexes
On the flexibility of -peptides
A computational investigation of the selectivity and mechanism of the Lewis acid catalyzed oxa-Diels-Alder cycloaddition of substituted diene with benzaldehyde
Benchmarking biomolecular force field-based Zn 2+ for mono- and bimetallic ligand binding sites
Intervals and the Deduction of Drug Binding Site Models
An ab initio study of nuclear volume effects for isotope fractionations using two-component relativistic methods
Treatment of reactions in solutions with isodensity surfaces
Natural resonance theory: I. General formalism