CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed

Cites (734)

Items 601–732 of 732

1. Momentum Distribution as a Fingerprint of Quantum Delocalization in Enzymatic Reactions: Open-Chain Path-Integral Simulations of Model Systems and the Hydride Transfer in Dihydrofolate Reductase.
   H. Engel, Dvir Doron, A. Kohen, D. Major · 2012 · Journal of Chemical Theory and Computation
2. An ensemble dynamics approach to decipher solid-state NMR observables of membrane proteins.
   W. Im, Sunhwan Jo, Taehoon Kim · 2012 · Biochimica et Biophysica Acta
3. Role of Hydration Force in the Self-Assembly of Collagens and Amyloid Steric Zipper Filaments
   K. M. Ravikumar, W. Hwang · 2011 · Journal of the American Chemical Society
4. An Integrated Path Integral and Free-Energy Perturbation-Umbrella Sampling Method for Computing Kinetic Isotope Effects of Chemical Reactions in Solution and in Enzymes.
   D. T. Major, Jia-Li Gao · 2007 · Journal of Chemical Theory and Computation
5. Structure and electrostatic property of cytoplasmic domain of ZntB transporter
   Kemin Tan, Alicia Sather, Janice Robertson, Shiu F. Moy, Benoı̂t Roux, A. Joachimiak · 2009 · Protein Science
6. Global Optimization of the Lennard-Jones Parameters for the Drude Polarizable Force Field
   Chetan Rupakheti, Alexander D. MacKerell, B. Roux · 2021 · Journal of Chemical Theory and Computation
7. A Strategy for Proline and Glycine Mutations to Proteins with Alchemical Free Energy Calculations
   Ryan L. Hayes, C. Brooks · 2021 · Journal of Computational Chemistry
8. Molecular Dynamics Simulations Based on Polarizable Models Show that Ion Permeation Interconverts between Different Mechanisms as a Function of Membrane Thickness.
   Pei-Ran Chen, I. Vorobyov, B. Roux, T. Allen · 2021 · Journal of Physical Chemistry B
9. CHARMM‐GUI DEER facilitator for spin‐pair distance distribution calculations and preparation of restrained‐ensemble molecular dynamics simulations
   Yifei Qi, Ju-Min Lee, Xi Cheng, R. Shen, Shahidul M. Islam, B. Roux, W. Im · 2019 · Journal of Computational Chemistry
10. A double exponential potential for van der Waals interaction
    Xiong-Wu Wu, B. Brooks · 2019 · AIP Advances
11. Reservoir pH replica exchange.
    A. Damjanovic, Benjamin T. Miller, Asim Okur, B. Brooks · 2018 · Journal of Chemical Physics
12. Accurate calculation of conformational free energy differences in explicit water: the confinement-solvation free energy approach.
    J. Esque, M. Cecchini · 2015 · Journal of Physical Chemistry B
13. Factors that Determine the Variation of Equilibrium and Kinetic Properties of QM/MM enzyme simulations: QM region, Conformation and Boundary Condition
    Darren Demapan, J. Kussmann, C. Ochsenfeld, Q. Cui · 2022 · Journal of Chemical Theory and Computation
14. Deep Neural Network Model to Predict the Electrostatic Parameters in the Polarizable Classical Drude Oscillator Force Field
    Anmol Kumar, Poonam Pandey, P. Chatterjee, Alexander D. MacKerell · 2022 · Journal of Chemical Theory and Computation
15. Proper Balance of Solvent-Solute and Solute-Solute Interactions in the Treatment of the Diffusion of Glucose using the Drude Polarizable Force Field
    Mingjun Yang, Asaminew H. Aytenfisu, Alexander D. MacKerell · 2018 · Carbohydrate Research
16. Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics—Monte Carlo Simulations Guided by a Coarse-Grained Model
    Yunjie Chen, B. Roux · 2015 · Journal of Chemical Theory and Computation
17. Simulations of Remote Mutants of Dihydrofolate Reductase Reveal the Nature of a Network of Residues Coupled to Hydride Transfer
    Daniel Roston, A. Kohen, Dvir Doron, D. Major · 2014 · Journal of Computational Chemistry
18. Protein arcs may form stable pores in lipid membranes.
    Lidia Prieto, Yi He, T. Lazaridis · 2014 · Biophysical Journal
19. Modeling peptide binding to anionic membrane pores
    Yi He, Lidia Prieto, T. Lazaridis · 2013 · Journal of Computational Chemistry
20. Structural and mechanistic basis for preferential deadenylation of U6 snRNA by Usb1
    Yuichiro Nomura, Daniel Roston, Eric Montemayor, Qiang Cui, Samuel E. Butcher · 2018 · Nucleic Acids Research
21. Dynamic Interactions of Fully Glycosylated SARS-CoV-2 Spike Protein with Various Antibodies
    Yiwei Cao, Yeol Kyo Choi, Martin Frank, Hyeonuk Woo, Sang‐Jun Park, Min Sun Yeom, Chaok Seok, Wonpil Im · 2021 · Journal of Chemical Theory and Computation
22. Detection of long-range concerted motions in protein by a distance covariance
    Roy, Amitava, Post, Carol Beth · 2012 · Journal of Chemical Theory and Computation
23. Harnessing Deep Learning for Optimization of Lennard-Jones Parameters for the Polarizable Classical Drude Oscillator Force Field
    P. Chatterjee, M. Sengul, Anmol Kumar, A. MacKerell · 2022 · Journal of Chemical Theory and Computation
24. Balanced Polarizable Drude Force Field Parameters for Molecular Anions: Phosphates, Sulfates, Sulfamates and Oxides
    A. Kognole, Asaminew H. Aytenfisu, Alexander D. Jr MacKerell · 2020 · Journal of Molecular Modeling
25. Classical Molecular Dynamics with Mobile Protons
    T. Lazaridis, G. Hummer · 2017 · Journal of Chemical Information and Modeling
26. Interactions of Amino Acid Side Chain Analogs within Membrane Environments
    V. Mirjalili, M. Feig · 2015 · Journal of Physical Chemistry B
27. Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-temperature string method.
    V. Ovchinnikov, M. Karplus · 2014 · Journal of Chemical Physics
28. A Coupled Polarization-Matrix Inversion and Iteration Approach for Accelerating the Dipole Convergence in a Polarizable Potential Function
    Wangshen Xie, J. Pu, Jia-Li Gao · 2009 · Journal of Physical Chemistry A
29. Bridging semiempirical and ab initio QM/MM potentials by Gaussian process regression and its sparse variants for free energy simulation
    Ryan Snyder, Bryant Kim, Xiaoliang Pan, Yihan Shao, Jingzhi Pu · 2023 · The Journal of Chemical Physics
30. Efficient Alchemical Intermediate States in Free Energy Calculations Using λ-Enveloping Distribution Sampling.
    G. König, Benjamin Ries, P. Hünenberger, Sereina Riniker · 2021 · Journal of Chemical Theory and Computation
31. Drude Polarizable Force Field for Aliphatic Ketones and Aldehydes, and their Associated Acyclic Carbohydrates
    Meagan C. Small, Asaminew H. Aytenfisu, Fang-Yu Lin, Xibing He, Alexander D. MacKerell · 2017 · Journal of Computer-Aided Molecular Design
32. Decomposition of energy and free energy changes by following the flow of work along reaction path.
    K. Haas, J. Chu · 2009 · Journal of Chemical Physics
33. Novel free energy calculations to explore mechanisms and energetics of membrane protein structure and function
    W. Im, Jinhyuk Lee, Taehoon Kim, Huan Rui · 2009 · Journal of Computational Chemistry
34. Multistate Reactive Molecular Dynamics Simulations of Proton Diffusion in Water Clusters and in the Bulk
    Zhen-Hao Xu, Markus Meuwly · 2019 · The Journal of Physical Chemistry B
35. Flexibility of Binding Site is Essential to the Ca2+ Selectivity in EF-hand Calcium-binding Proteins
    Rui Lai, Guohui Li, Q. Cui · 2024 · Journal of the American Chemical Society
36. Molecular Simulation for Atmospheric Reactions: Non-Equilibrium Dynamics, Roaming, and Glycolaldehyde Formation following Photoinduced Decomposition of syn-Acetaldehyde Oxide.
    Meenu Upadhyay, Kai Töpfer, Markus Meuwly · 2023 · Journal of Physical Chemistry Letters
37. Kinetic Analysis and Structural Interpretation of Competitive Ligand Binding for NO Dioxygenation in Truncated Hemoglobin N
    Akshaya Kumar Das, Markus Meuwly · 2018 · Angewandte Chemie International Edition
38. Second-shell residues contribute to catalysis by predominately pre-organizing the apo state in PafA
    Jiahua Deng, Q. Cui · 2023 · Journal of the American Chemical Society
39. Effect of the QM Size, Basis Set, and Polarization on QM/MM Interaction Energy Decomposition Analysis
    Álvaro Pérez-Barcia, G. Cárdenas, J. Nogueira, M. Mandado · 2023 · Journal of Chemical Information and Modeling
40. Addressing Intersite Coupling Unlocks Large Combinatorial Chemical Spaces for Alchemical Free Energy Methods
    Ryan L. Hayes, Jonah Z. Vilseck, Carl L. Brooks · 2022 · Journal of Chemical Theory and Computation
41. Determining Free-Energy Differences Through Variationally Derived Intermediates
    M. Reinhardt, H. Grubmüller · 2020 · Journal of Chemical Theory and Computation
42. Replica exchanging self-guided Langevin dynamics for efficient and accurate conformational sampling.
    Xiong-Wu Wu, M. Hodošček, B. Brooks · 2012 · Journal of Chemical Physics
43. Calculation of the standard binding free energy of sparsomycin to the ribosomal peptidyl‐transferase P‐site using molecular dynamics simulations with restraining potentials
    Xiaoxia Ge, B. Roux · 2010 · Journal of Molecular Recognition
44. Far‐infrared permanent and induced dipole absorption of diatomic molecules in rare‐gas fluids. II. Application to the CO–Ar system
    J. M. M. Roco, A. Medina, A. Hernández, S. Velasco · 1995
45. Computational Assessment of Protein–Protein Binding Specificity within a Family of Synaptic Surface Receptors
    Prithviraj Nandigrami, Florence Szczepaniak, Christopher T. Boughter, François Dehez, Christophe J. Chipot, Benoı̂t Roux · 2022 · The Journal of Physical Chemistry B
46. Putative Structures of Membrane-Embedded Amyloid β Oligomers
    Aliasghar Sepehri, Themis Lazaridis · 2022 · ACS Chemical Neuroscience
47. CHARMM-GUI Implicit Solvent Modeler for Various Generalized Born Models in Different Simulation Programs
    K. Wang, Ju-Min Lee, Han Zhang, Donghyuk Suh, W. Im · 2022 · Journal of Physical Chemistry B
48. Molecular Dynamics with Conformationally Dependent, Distributed Charges.
    Eric D. Boittier, M. Devereux, M. Meuwly · 2022 · Journal of Chemical Theory and Computation
49. Distinct modes of action of IAPP oligomers on membranes
    A. Sepehri, B. Nepal, T. Lazaridis · 2021 · bioRxiv
50. pKa Calculations with the Polarizable Drude Force Field and Poisson-Boltzmann Solvation Model
    A. Aleksandrov, B. Roux, Alexander D. MacKerell · 2020 · Journal of Chemical Theory and Computation
51. Structure Refinement of Membrane Proteins via Molecular Dynamics Simulations
    Bercem Dutagaci, Lim Heo, M. Feig · 2018 · Proteins: Structure, Function, and Bioinformatics
52. OH-Stretching Overtone Induced Dynamics in HSO3F from Reactive Molecular Dynamics Simulations.
    Sebastian Brickel, M. Meuwly · 2017 · Journal of Physical Chemistry A
53. Prediction of conformationally dependent atomic multipole moments in carbohydrates
    Salvatore Cardamone, P. Popelier · 2015 · Journal of Computational Chemistry
54. Solid-state NMR ensemble dynamics as a mediator between experiment and simulation.
    Taehoon Kim, Sunhwan Jo, W. Im · 2011 · Biophysical Journal
55. Acceptable protein and solvent behavior in primary hydration shell simulations of hen lysozyme.
    M. Hamaneh, M. Buck · 2007 · Biophysical Journal
56. Complementation between dimeric mutants as a probe of dimer-dimer interactions in tetrameric dihydrofolate reductase encoded by R67 plasmid of E. coli.
    J. Dam, T. Rose, M. Goldberg, A. Blondel · 2000 · Journal of Molecular Biology
57. Preserving the Integrity of Empirical Force Fields
    Asuka A. Orr, Suliman Sharif, Junmei Wang, Alexander D. MacKerell · 2022 · Journal of Chemical Information and Modeling
58. CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site
    Hugo Guterres, Sang‐Jun Park, Yiwei Cao, Wonpil Im · 2021 · Journal of Chemical Information and Modeling
59. Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field
    Andrew C. Thiel, M. Speranza, Sanika Jadhav, Lewis L. Stevens, D. Unruh, Peng-Yu Ren, J. Ponder, Jana Shen, Michael J. Schnieders · 2024 · Journal of Chemical Theory and Computation
60. Extension of the CHARMM Classical Drude Polarizable Force Field to N- and O-Linked Glycopeptides and Glycoproteins
    A. Kognole, Asaminew H. Aytenfisu, Alexander D. MacKerell · 2022 · Journal of Physical Chemistry B
61. Mechanism of negative membrane curvature generation by I-BAR domains
    B. Nepal, A. Sepehri, T. Lazaridis · 2021 · Structure
62. Statistical mechanics of polarizable force fields based on classical Drude oscillators with dynamical propagation by the dual-thermostat extended Lagrangian.
    Chetan Rupakheti, G. Lamoureux, Alexander D. MacKerell, B. Roux · 2020 · Journal of Chemical Physics
63. Acceleration of Semiempirical QM/MM Methods through Message Passage Interface (MPI), Hybrid MPI/Open Multiprocessing, and Self-Consistent Field Accelerator Implementations.
    P. Ojeda-May, Kwangho Nam · 2017 · Journal of Chemical Theory and Computation
64. Finite domain simulations with adaptive boundaries: accurate potentials and nonequilibrium movesets.
    Jason A. Wagoner, V. Pande · 2013 · Journal of Chemical Physics
65. Optimizing the Calculation of Free Energy Differences in Nonequilibrium Work SQM/MM Switching Simulations
    Andreas Schöller, Fiona L. Kearns, H. Lee Woodcock, Stefan Boresch · 2022 · The Journal of Physical Chemistry B
66. Protonation state of the selectivity filter of bacterial voltage‐gated sodium channels is modulated by ions
    A. Damjanovic, Ada Y Chen, R. Rosenberg, D. Roe, Xiong-Wu Wu, B. Brooks · 2020 · Proteins: Structure, Function, and Bioinformatics
67. Modeling induction phenomena in amino acid cation–$$\pi $$π interactions
    Chetan Rupakheti, B. Roux, F. Dehez, C. Chipot · 2018 · Theoretical Chemistry accounts
68. Combining the Polarizable Drude Force Field with a Continuum Electrostatic Poisson-Boltzmann Implicit Solvation Model
    A. Aleksandrov, Fang-Yu Lin, B. Roux, Alexander D. MacKerell · 2018 · Journal of Computational Chemistry
69. Far‐infrared permanent and induced dipole absorption of diatomic molecules in rare‐gas fluids. I. Spectral theory
    J. M. M. Roco, A. Hernández, S. Velasco · 1995
70. Structural Modeling of Cytokine-Receptor-JAK2 Signaling Complexes Using AlphaFold Multimer
    Irina D. Pogozheva, Stanislav Cherepanov, Sang‐Jun Park, Malini Raghavan, Wonpil Im, Andrei L. Lomize · 2023 · Journal of Chemical Information and Modeling
71. Heterogeneous and Allosteric Role of Surface Hydration for Protein–Ligand Binding
    Jie Shi, Jae-Hyun Cho, W. Hwang · 2023 · Journal of Chemical Theory and Computation
72. Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches
    Phillip S. Hudson, Félix Aviat, R. Meana-Pañeda, Luke C Warrensford, B. C. Pollard, Samarjeet Prasad, Michael R. Jones, H. Woodcock, B. Brooks · 2022 · Journal of Computer-Aided Molecular Design
73. Molecular Determinants for Rate Acceleration in the Claisen Rearrangement Reaction.
    Sebastian Brickel, M. Meuwly · 2018 · Journal of Physical Chemistry B
74. Generating reservoir conformations for replica exchange through the use of the conformational space annealing method
    Asim Okur, Benjamin T. Miller, K. Joo, Jooyoung Lee, B. Brooks · 2013 · Journal of Chemical Theory and Computation
75. Effect of flanking residues on the conformational sampling of the internal fusion peptide from Ebola virus
    Adam J. Jaskierny, Afra Panahi, M. Feig · 2011 · Proteins: Structure, Function, and Bioinformatics
76. Generalizing the Discrete Gibbs Sampler-based λ-Dynamics Approach for Multisite Sampling of Many Ligands
    Jonah Z. Vilseck, Xin-Qiang Ding, Ryan L. Hayes, C. Brooks · 2021 · Journal of Chemical Theory and Computation
77. Mechanisms of negative membrane curvature sensing and generation by ESCRT III subunit Snf7
    B. Nepal, A. Sepehri, T. Lazaridis · 2020 · Protein Science
78. Endoglucanase peripheral loops facilitate complexation of glucan chains on cellulose via adaptive coupling to the emergent substrate structures.
    Yuchun Lin, G. Beckham, M. Himmel, M. Crowley, J. Chu · 2013 · Journal of Physical Chemistry B
79. CIFDock : A novel CHARMM ‐based flexible receptor–flexible ligand docking protocol
    Sai Lakshmana Vankayala, Luke C. Warrensford, Amanda R. Pittman, Benjamin C. Pollard, Fiona L. Kearns, Joseph D. Larkin, H. Lee Woodcock · 2021 · Journal of Computational Chemistry
80. Simulations suggest a scaffolding mechanism of membrane deformation by the caveolin 8S complex
    Sayyid Yobhel Vasquez Rodriguez, T. Lazaridis · 2023 · bioRxiv
81. The emergence of protein dynamics simulations: how computational statistical mechanics met biochemistry
    Daniele Macuglia, B. Roux, G. Ciccotti · 2022 · The European Physical Journal H
82. Entropy Hotspots for the Binding of Intrinsically Disordered Ligands to a Receptor Domain.
    Jie Shi, Q. Shen, Jae-Hyun Cho, W. Hwang · 2020 · Biophysical Journal
83. Multiple Time-Step Dual-Hamiltonian Hybrid Molecular Dynamics — Monte Carlo Canonical Propagation Algorithm
    Yunjie Chen, Seyit Kale, J. Weare, A. Dinner, B. Roux · 2016 · Journal of Chemical Theory and Computation
84. Molecular Multipole Potential Energy Functions for Water.
    M. Tan, Kelly N. Tran, Frank C. Pickard, Andrew C. Simmonett, B. Brooks, T. Ichiye · 2016 · Journal of Physical Chemistry B
85. Effect of multiple symmetries on the association of R67 DHFR subunits bearing interfacial complementing mutations
    J. Dam, A. Blondel · 2004 · Protein Science
86. A thermodynamic approach to alamethicin pore formation.
    A. Rahaman, T. Lazaridis · 2014 · Biochimica et Biophysica Acta
87. Balancing Group I Monatomic Ion-Polar Compound Interactions for Condensed Phase Simulation in the Polarizable Drude Force Field
    Yiling Nan, A. MacKerell · 2024 · Journal of Chemical Theory and Computation
88. CHARMM-GUI LBS Finder & Refiner for Ligand Binding Site Prediction and Refinement
    H. Guterres, Sang-Jun Park, Han Zhang, W. Im · 2021 · Journal of Chemical Information and Modeling
89. Multi-State VALBOND for Atomistic Simulations of Hypervalent Molecules, Metal Complexes, and Reactions.
    Maurus H Schmid, A. K. Das, C. Landis, M. Meuwly · 2018 · Journal of Chemical Theory and Computation
90. Time reversible and phase‐space conserving molecular dynamics at constant temperature
    R. Winkler, V. Kraus, P. Reineker · 1995 · The Journal of Chemical Physics
91. Doubly Polarized QM/MM with Machine Learning Chaperone Polarizability
    Bryant Kim, Yihan Shao, Jingzhi Pu · 2021 · Journal of Chemical Theory and Computation
92. Ion channel selectivity through ion-modulated changes of selectivity filter pKa values
    Ada Y Chen, B. Brooks, A. Damjanovic · 2023 · Proceedings of the National Academy of Sciences of the United States of America
93. O to bR transition in bacteriorhodopsin occurs through a proton hole mechanism
    Denis Maag, Thilo Mast, M. Elstner, Q. Cui, T. Kubař · 2021 · Proceedings of the National Academy of Sciences of the United States of America
94. Heterogeneous Dielectric Generalized Born model with a van der Waals Term (HDGBvdW) Provides Improved Association Energetics of Membrane-Embedded Transmembrane Helices
    Bercem Dutagaci, M. Sayadi, M. Feig · 2017 · Journal of Computational Chemistry
95. Solid-State NMR-Restrained Ensemble Dynamics of a Membrane Protein in Explicit Membranes.
    Xi Cheng, Sunhwan Jo, Yifei Qi, F. Marassi, W. Im · 2015 · Biophysical Journal
96. Beta‐hairpin restraint potentials for calculations of potentials of mean force as a function of beta‐hairpin tilt, rotation, and distance
    Jinhyuk Lee, S. Ham, W. Im · 2009 · Journal of Computational Chemistry
97. Protein Conformational Transitions from All-atom Adaptively Biased Path Optimization (ABPO)
    Heng Wu, C. Post · 2018 · Journal of Chemical Theory and Computation
98. Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model
    Bercem Dutagaci, M. Feig · 2017 · Journal of Chemical Information and Modeling
99. Computational prediction of the optimal oligomeric state for membrane‐inserted β ‐barrels of protegrin‐1 and related mutants
    Richard B. Lipkin, Themis Lazaridis · 2017 · Journal of Peptide Science
100. Multi-ion distributions in the cytoplasmic domain of inward rectifier potassium channels.
     J. Robertson, L. G. Palmer, B. Roux · 2012 · Biophysical Journal
101. Selection pressures on evolution of ribonuclease H explored with rigorous free–energy–based design
     Ryan L. Hayes, Charlotte F. Nixon, Susan Marqusee, Charles L. Brooks · 2024 · Proceedings of the National Academy of Sciences
102. Training machine learning potentials for reactive systems: A Colab tutorial on basic models
     Xiaoliang Pan, Ryan Snyder, Jianing Wang, Chance Lander, Carly Wickizer, Richard S. Van, Andrew D. Chesney, Yuanfei Xue, Yuezhi Mao, Ye Mei et al. · 2023 · Journal of Computational Chemistry
103. Putative Pore Structures of Amyloid β 25-35 in Lipid Bilayers.
     Ankita Dutta, A. Sepehri, T. Lazaridis · 2023 · Biochemistry
104. Exploring Routes to Enhance the Calculation of Free Energy Differences via Non-Equilibrium Work SQM/MM Switching Simulations Using Hybrid Charge Intermediates between MM and SQM Levels of Theory or Non-Linear Switching Schemes
     A. Schöller, H. Woodcock, S. Boresch · 2023 · Molecules
105. ppdx: Automated modeling of protein–protein interaction descriptors for use with machine learning
     Simone Conti, V. Ovchinnikov, M. Karplus · 2022 · Journal of Computational Chemistry
106. Simulations of Diabetic and Non-Diabetic Peripheral Nerve Myelin Lipid Bilayers.
     Yi-Ding Yuan, Yalun Yu, Jeffery B. Klauda · 2021 · Journal of Physical Chemistry B
107. All-atom adaptively biased path optimization of Src kinase conformational inactivation: Switched electrostatic network in the concerted motion of αC helix and the activation loop.
     Heng Wu, He Huang, C. Post · 2020 · Journal of Chemical Physics
108. A novel strategy to determine protein structures using exclusively residual dipolar coupling
     Thenmalarchelvi Rathinavelan, W. Im · 2008 · Journal of Computational Chemistry
109. Spontaneous curvature generation by peptides in asymmetric bilayers
     Soohyung Park, Amy Rice, Wonpil Im, R. Pastor · 2023 · Journal of Computational Chemistry
110. Amino acid deprotonation rates from classical force fields.
     T. Lazaridis, A. Sepehri · 2022 · Journal of Chemical Physics
111. Conformational free energy differences of large solvated systems with the focused confinement method.
     Paul B. Orndorff, Sang T. Le Phan, Ka-Ho Li, A. van der Vaart · 2020 · Journal of Chemical Theory and Computation
112. Discrimination of Native-like States of Membrane Proteins with Implicit Membrane-Based Scoring Functions
     Bercem Dutagaci, Kitiyaporn Wittayanarakul, Takaharu Mori, M. Feig · 2017 · Journal of Chemical Theory and Computation
113. Acceleration of Semiempirical Quantum Mechanical Calculations by Extended Lagrangian Molecular Dynamics Approach.
     Kwangho Nam · 2013 · Journal of Chemical Theory and Computation
114. Explicit treatment of force contribution from alignment tensor using overdetermined linear equations and its application in NMR structure determination
     Thenmalarchelvi Rathinavelan, W. Im · 2007 · Journal of Computational Chemistry
115. Expanding the CHARMM36 United Atom Chain Model for the Inclusion of Sphingolipids.
     J. Lucker, Michael Kio, Jeffery B. Klauda · 2024 · Journal of Physical Chemistry B
116. FASTDock: A Pipeline for Allosteric Drug Discovery
     Furyal Ahmed, Carl L. Brooks · 2023 · Journal of Chemical Information and Modeling
117. Proton Paths in Models of the Hv1 Proton Channel.
     T. Lazaridis · 2023 · Journal of Physical Chemistry B
118. Alchemical free energy simulations without speed limits. A generic framework to calculate free energy differences independent of the underlying molecular dynamics program
     M. Wieder, Markus Fleck, Benedict Braunsfeld, S. Boresch · 2022 · Journal of Computational Chemistry
119. Calculation of conformational free energies with the focused confinement method.
     A. van der Vaart, Paul B. Orndorff, Sang T. Le Phan · 2019 · Journal of Chemical Theory and Computation
120. (Ala)4-X-(Ala)4 as a model system for the optimization of the χ1 and χ2 amino acid side-chain dihedral empirical force field parameters
     Jihyun Shim, Xiao Zhu, R. Best, Alexander D. MacKerell · 2012 · Journal of Computational Chemistry
121. Path‐integral calculations of heavy atom kinetic isotope effects in condensed phase reactions using higher‐order trotter factorizations
     Alexandra Vardi-Kilshtain, Asaf Azuri, D. Major · 2012 · Journal of Computational Chemistry
122. Enhanced Sampling of Buried Charges in Free Energy Calculations using Replica Exchange with Charge Tempering
     Xiaorong Liu, Charles L. Brooks · 2024 · Journal of Chemical Theory and Computation
123. Transmembrane β-Barrel Models of α-Synuclein Oligomers
     Manuela Maurer, T. Lazaridis · 2023 · Journal of Chemical Information and Modeling
124. Molecular origins of asymmetric proton conduction in the influenza M2 channel
     T. Lazaridis · 2022 · bioRxiv
125. Calculation of conformational free energies by confinement simulations in explicit water with implicit desolvation
     François Villemot, Alfredo Peguero-Tejada, A. van der Vaart · 2018
126. Extension of the FACTS Implicit Solvation Model to Membranes.
     Martín Carballo-Pacheco, I. Vancea, B. Strodel · 2014 · Journal of Chemical Theory and Computation
127. Refinement of the primary hydration shell model for molecular dynamics simulations of large proteins
     M. Hamaneh, M. Buck · 2009 · Journal of Computational Chemistry
128. Mechanical couplings of protein backbone and side chains exhibit scale-free network properties and specific hotspots for function
     N. Raj, T. Click, Haw Yang, J. Chu · 2021 · Computational and Structural Biotechnology Journal
129. The Extended Eighth‐Shell method for periodic boundary conditions with rotational symmetry
     Samarjeet Prasad, Andrew C. Simmonett, R. Meana-Pañeda, B. Brooks · 2021 · Journal of Computational Chemistry
130. Secondary structure of peptides mimicking the Gly-rich regions of major ampullate spidroin protein 1 and 2.
     Geoffrey M. Gray, Brittany Thiessen, A. van der Vaart · 2022 · Biophysical Chemistry
131. Multistate multiscale docking study of the hydrolysis of toxic nerve agents by phosphotriesterase
     P. Gupta, Naziha Tarannam, Shani Zev, D. Major · 2023 · Electronic Structure
132. Development of CHARMM Additive Potential Energy Parameters for α-Methyl Amino Acids
     A. Pane, Wen-Bo Yu, Asaminew H. Aytenfisu, Jude Tunyi, R. Venable, Alexander D. MacKerell, R. Pastor · 2021 · Journal of Physical Chemistry B