Reference health
Tinker 8: Software Tools for Molecular Design
169/169 checkable references clean · checked 2026-09-07
Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a retraction, withdrawal, or removal notice.
15 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.
The 169 checked references that resolve
resolves10.1039/C7SC04531J
Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields
resolves10.1002/jcc.24853
Tinker‐OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs
resolves10.1021/ja00467a001
Conformational analysis. 130. MM2. A hydrocarbon force field utilizing V1 and V2 torsional terms
resolves10.1002/jcc.540080710
An efficient newton‐like method for molecular mechanics energy minimization of large molecules
resolves10.1002/bip.10219
Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing
resolves10.1016/j.bpj.2015.06.062
Dead-End Elimination with a Polarizable Force Field Repacks PCNA Structures
resolves10.1016/j.bpj.2015.08.015
MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories
resolves10.1023/B:JCAM.0000035186.90683.f2
VEGA – An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming
resolves10.1002/jcc.21224
P
<scp>ACKMOL</scp>
: A package for building initial configurations for molecular dynamics simulations
resolves10.1021/ct300857j
OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation
resolves10.1371/journal.pcbi.1005659
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
resolves10.1038/nmeth.4067
CHARMM36m: an improved force field for folded and intrinsically disordered proteins
resolves10.1021/acs.jctc.5b00255
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
resolves10.1021/acs.jctc.5b00356
Improved Peptide and Protein Torsional Energetics
with the OPLS-AA Force Field
resolves10.1002/bip.10254
Potential energy functions: From consistent force fields to spectroscopically determined polarizable force fields
resolves10.1002/jcc.540080713
On the out‐of‐plane deformation of aromatic rings, and its representation by molecular mechanics
resolves10.1021/ja00046a032
The representation of van der Waals (vdW) interactions in molecular mechanics force fields: potential form, combination rules, and vdW parameters
resolves10.1002/(SICI)1096-987X(19980715)19:9<1001::AID-JCC2>3.0.CO;2-U
Directional hydrogen bonding in the MM3 force field: II
resolves10.1021/jp0735987
Accurate and Efficient Corrections for Missing Dispersion Interactions in Molecular Simulations
resolves10.1021/jp027815+
Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation
resolves10.1021/ct200304d
Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules
resolves10.1002/jcc.10126
Effective Born radii in the generalized Born approximation: The importance of being perfect
resolves10.1002/jcc.1137
Effective atom volumes for implicit solvent models: comparison between Voronoi volumes and minimum fluctuation volumes
resolves10.1063/1.1595641
Deficiency of the Coulomb-field approximation in the generalized Born model: An improved formula for Born radii evaluation
resolves10.1002/pro.5560010204
Atomic solvation parameters applied to molecular dynamics of proteins in solution
resolves10.1016/j.str.2007.05.004
Hydrophobic Potential of Mean Force as a Solvation Function for Protein Structure Prediction
resolves10.1016/0022-2836(82)90505-8
Calculation of the electric potential in the active site cleft due to α-helix dipoles
resolves10.1002/prot.340010109
Focusing of electric fields in the active site of Cu‐Zn superoxide dismutase: Effects of ionic strength and amino‐acid modification
resolves10.1146/annurev.bb.19.060190.001505
Electrostatic Interactions in Macromolecules: Theory and Applications
resolves10.1073/pnas.181342398
Electrostatics of nanosystems: Application to microtubules and the ribosome
resolves10.1002/jcc.23190
A valence bond model for aqueous Cu(II) and Zn(II) ions in the AMOEBA polarizable force field
resolves10.1021/ct400778h
An Angular Overlap Model for Cu(II) Ion in the AMOEBA Polarizable Force Field
resolves10.1016/S0006-3495(01)75675-5
The Functional Form of Angular Forces around Transition Metal Ions in Biomolecules
resolves10.1021/ja00124a002
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
resolves10.1007/978-94-017-1120-3_2
The development/application of a ‘minimalist’ organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimental data
resolves10.1080/07391102.1999.10508297
A Modified Version of the Cornell
<i>et al.</i>
Force Field with Improved Sugar Pucker Phases and Helical Repeat
resolves10.1002/1096-987X(200009)21:12<1049::AID-JCC3>3.0.CO;2-F
How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
resolves10.1002/prot.21123
Comparison of multiple Amber force fields and development of improved protein backbone parameters
resolves10.1021/jp973084f
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
resolves10.1002/(SICI)1096-987X(20000130)21:2<86::AID-JCC2>3.0.CO;2-G
All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data
resolves10.1002/jcc.20065
Extending the treatment of backbone energetics in protein force fields: Limitations of gas‐phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
resolves10.1021/ja9621760
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
resolves10.1021/jp003919d
Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides
resolves10.1021/ja00315a051
A new force field for molecular mechanical simulation of nucleic acids and proteins
resolves10.1021/ja00168a022
Aromatic-aromatic interactions: free energy profiles for the benzene dimer in water, chloroform, and liquid benzene
resolves10.1002/jcc.540160807
A comprehensive study of the rotational energy profiles of organic systems by <i>ab initio</i> MO theory, forming a basis for peptide torsional parameters
resolves10.1021/ja00214a001
The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin
resolves10.1021/ja00205a003
Molecular mechanics. The MM3 force field for hydrocarbons. 3. The van der Waals' potentials and crystal data for aliphatic and aromatic hydrocarbons
resolves10.1002/(SICI)1096-987X(199604)17:5/6<587::AID-JCC4>3.0.CO;2-Q
Merck molecular force field. IV. conformational energies and geometries for MMFF94
resolves10.1002/jcc.10127
Consistent treatment of inter‐ and intramolecular polarization in molecular mechanics calculations
resolves10.1021/ct100091j
Polarizable Molecular Dynamics Simulation of Zn(II) in Water Using the AMOEBA Force Field
resolves10.1021/ja037005r
Ion Solvation Thermodynamics from Simulation with a Polarizable Force Field
resolves10.1063/1.462555
Development of nonadditive intermolecular potentials using molecular dynamics: Solvation of Li+ and F− ions in polarizable water
resolves10.1016/0009-2614(94)01118-4
Interionic potentials of mean force for SrCl2 in polarizable water
resolves10.1063/1.473820
Molecular dynamics study of water clusters, liquid, and liquid–vapor interface of water with many-body potentials
resolves10.1063/1.478884
Intermolecular interactions of liquid dichloromethane and equilibrium properties of liquid–vapor and liquid–liquid interfaces: A molecular dynamics study
resolves10.1021/jp064661f
Molecular Simulation Analysis and X-ray Absorption Measurement of Ca<sup>2+</sup>, K<sup>+</sup> and Cl<sup>-</sup> Ions in Solution
resolves10.1021/jp076608c
Molecular Dynamics Study of Ion Transfer and Distribution at the Interface of Water and 1,2-Dichlorethane
resolves10.1021/jp901950g
Solvation of Dimethyl Succinate in a Sodium Hydroxide Aqueous Solution. A Computational Study
resolves10.1063/1.3697840
Note: Interionic potentials of mean force for Ca2+-Cl− in polarizable water
resolves10.1016/0009-2614(77)80574-5
The synchronous-transit method for determining reaction pathways and locating molecular transition states
resolves10.1021/ct200654u
Incorporating Linear Synchronous Transit Interpolation into the Growing String Method: Algorithm and Applications
resolves10.1063/1.458491
Reaction path study of conformational transitions in flexible systems: Applications to peptides
resolves10.1016/0021-9991(92)90271-Y
An evaluation of the sniffer global optimization algorithm using standard test functions
resolves10.1002/(SICI)1096-987X(19991130)20:15<1671::AID-JCC7>3.0.CO;2-Y
Low-mode conformational search elucidated: Application to C39H80 and flexible docking of 9-deazaguanine inhibitors into PNP
resolves10.1073/pnas.84.19.6611
Monte Carlo-minimization approach to the multiple-minima problem in protein folding.
resolves10.1021/jp970984n
Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms
resolves10.1021/j100197a057
Application of the diffusion equation method for global optimization to oligopeptides
resolves10.1021/jp982255t
Analysis and Application of Potential Energy Smoothing and Search Methods for Global Optimization
resolves10.1038/4922
resolves10.1016/0021-9991(76)90059-0
Some multistep methods for use in molecular dynamics calculations
resolves10.1090/S0025-5718-2012-02594-4
Langevin dynamics with constraints and computation of free energy differences
resolves10.1063/1.1458542
Efficient multiple-time-step integrators with distance-based force splitting for particle-mesh-Ewald molecular dynamics simulations
resolves10.1016/0021-9991(83)90014-1
Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations
resolves10.1002/jcc.540151111
A rapidly convergent simulation method: Mixed Monte Carlo/stochastic dynamics
resolves10.1080/08927028808080959
On the Approximation of Solvent Effects on the Conformation and Dynamics of Cyclosporin A by Stochastic Dynamics Simulation Techniques
resolves10.1080/00268976.2013.844369
Stochastic, resonance-free multiple time-step algorithm for molecular dynamics with very large time steps
resolves10.1063/1.1534582
Algorithms and novel applications based on the isokinetic ensemble. I. Biophysical and path integral molecular dynamics
resolves10.1021/ct050161z
All-Atom Calculation of the Normal Modes of Bacteriorhodopsin Using a Sliding Block Iterative Diagonalization Method
resolves10.1063/1.1740409
High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases
resolves10.1016/0021-9991(76)90078-4
Efficient estimation of free energy differences from Monte Carlo data
resolves10.1016/j.cpc.2012.05.006
Massively parallel chemical potential calculation on graphics processing units
resolves10.1021/jp103050u
New Estimators for Calculating Solvation Entropy and Enthalpy and Comparative Assessments of Their Accuracy and Precision
resolves10.1039/C6CP02509A
Calculating binding free energies of host–guest systems using the AMOEBA polarizable force field
resolves10.1007/s00214-012-1138-6
Automation of AMOEBA polarizable force field parameterization for small molecules
resolves10.1063/1.1630791
Towards an accurate representation of electrostatics in classical force fields: Efficient implementation of multipolar interactions in biomolecular simulations
resolves10.1063/1.4964866
An empirical extrapolation scheme for efficient treatment of induced dipoles
resolves10.1063/1.4933375
An efficient and stable hybrid extended Lagrangian/self-consistent field scheme for solving classical mutual induction
resolves10.1021/acs.jpclett.7b00450
Accurate Classical Polarization Solution with No Self-Consistent Field Iterations
resolves10.1063/1.4985911
The truncated conjugate gradient (TCG), a non-iterative/fixed-cost strategy for computing polarization in molecular dynamics: Fast evaluation of analytical forces
resolves10.1073/pnas.0810631106
Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems
resolves10.1063/1.3153841
Simultaneous escaping of explicit and hidden free energy barriers: Application of the orthogonal space random walk strategy in generalized ensemble based conformational sampling
resolves10.1021/ct500202q
Hydration
Free Energy from Orthogonal Space Random
Walk and Polarizable Force Field
resolves10.1021/ct300035u
The Structure, Thermodynamics, and Solubility of Organic Crystals from Simulation with a Polarizable Force Field
resolves10.1021/ct200726v
Practically Efficient and Robust Free Energy Calculations: Double-Integration Orthogonal Space Tempering
resolves10.1007/BF02192799
Sampling and efficiency of metric matrix distance geometry: A novel partial metrization algorithm
resolves10.1002/bip.360310905
Effects of limited input distance constraints upon the distance geometry algorithm
resolves10.1006/jmbi.1996.0663
The NMR Solution Structure of Intestinal Fatty Acid-binding Protein Complexed with Palmitate: Application of a Novel Distance Geometry Algorithm
resolves10.1002/pro.5560070916
Distance geometry generates native‐like folds for small helical proteins using the consensus distances of predicted protein structures
resolves10.1002/(SICI)1096-987X(199906)20:8<786::AID-JCC5>3.0.CO;2-B
Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems
resolves10.2174/138161206777585256
Development, Validation, and Applications of Anisotropic Polarizable Molecular Mechanics to Study Ligand and Drug-Receptor Interactions
resolves10.1063/1.2363374
Generalization of the Gaussian electrostatic model: Extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods
resolves10.1002/jcc.24257
Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short‐range penetration correction up to quadrupoles
resolves10.1021/acs.jctc.5b00267
General Model for Treating Short-Range Electrostatic
Penetration in a Molecular Mechanics Force Field
resolves10.1021/ct401096t
Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: I. Toward Massively Parallel Direct Space Computations
resolves10.1021/acs.jctc.5b00171
Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II. Toward Massively Parallel Computations Using Smooth Particle Mesh Ewald
The 15 references without a DOI — listed, not checked
no DOI — not checkedPonder, J. W. Tinker Molecular Modeling. https://dasher.wustl.edu/tinker/ (accessed July 23, 2018).
no DOI — not checkedPiquemal, J.P. Piquemal Research & Software. http://piquemalresearch.com/research-and-softwares/ (accessed July 23, 2018).
no DOI — not checkedRen, P. Tinker GPU Main Page. http://biomol.bme.utexas.edu/tinkergpu/ (accessed July 23, 2018).
no DOI — not checkedPonder, J. W. Tinker: Software Tools for Molecular Design. https://github.com/TinkerTools/tinker (accessed July 23, 2018).
no DOI — not checkedRen, P. Tinker-OpenMM Toolkit for Molecular Simulation Using High Performance GPU Code. https://github.com/pren/tinker-openmm/ (accessed July 23, 2018).
no DOI — not checkedChemOffice
no DOI — not checkedref13/cit13
no DOI — not checkedSwails, J.; Hernandez, C.; Mobley, D.; Nguyen, H.; Wang, L.P.; Janowski, P. ParmEd: Parameter/Topology Editor and Molecular Simulator. https://github.com/ParmEd/ParmEd (accessed July 23, 2018).
no DOI — not checkedWebMO Enterprise
no DOI — not checkedComputer Simulation of Liquids
no DOI — not checkedNumerical Optimization
no DOI — not checkedAlgorithms for Molecular Dynamics at Constant Temperature and Pressure
no DOI — not checkedCCP5 Newsletter
no DOI — not checkedUnderstanding Molecular Simulation: From Algorithms to Applications
no DOI — not checkedDistance Geometry and Molecular Conformation
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