Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

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1. Impact of Cu(II) Binding on Structures and Dynamics of Aβ42 Monomer and Dimer: Molecular Dynamics Study
   Pham Dinh Quoc Huy, Van‐Quan Vuong, Giovanni La Penna, Peter Faller, Mai Suan Li · 2016 · ACS Chemical Neuroscience
2. The Molecular Basis of the Sodium Dodecyl Sulfate Effect on Human Ubiquitin Structure: A Molecular Dynamics Simulation Study
   Majid Jafari, Faramarz Mehrnejad, Fereshteh Rahimi, Seyed Mohsen Asghari · 2018 · Scientific Reports
3. Rapid Evolution of Reduced Susceptibility against a Balanced Dual-Targeting Antibiotic through Stepping-Stone Mutations
   Petra Éva Szili, Gábor Draskovits, Tamas Revesz, Ferenc Bogár, Dávid Balogh, Tamás A. Martinek, Lejla Daruka, Réka Spohn, Bálint Márk Vásárhelyi, Márton Simon Czikkely et al. · 2019 · Antimicrobial Agents and Chemotherapy
4. Development and Evaluation of MM/GBSA Based on a Variable Dielectric GB Model for Predicting Protein-Ligand Binding Affinities
   Ercheng Wang, Hui Liu, Jun-Mei Wang, Gao-Qi Weng, Hui-Yong Sun, Zhe Wang, Yu Kang, Ting-Jun Hou · 2020 · Journal of Chemical Information and Modeling
5. Structure based virtual screening: Fast and slow
   Alejandro Varela‐Rial, Maciej Majewski, Gianni De Fabritiis · 2021 · Wiley Interdisciplinary Reviews Computational Molecular Science
6. Activity of Mannich bases of 7-hydroxycoumarin against Flaviviridae
   Mauro Mazzei, Erika Nieddu, Mariangela Miele, ALESSANDRO BALBI, Marco L. Ferrone, Maurizio Fermeglia, Marco T. Mazzei, Sabrina Pricl, Paolo La Colla, Fabio Marongiu et al. · 2007 · Bioorganic & Medicinal Chemistry
7. Therapeutic strategies underpinning the development of novel techniques for the treatment of HIV infection
   Jianjun Tan, Xiao J. Cong, Li Hu, Cun X. Wang, Lee Jia, Xing‐Jie Liang · 2010 · Drug Discovery Today
8. Case-specific performance of MM-PBSA, MM-GBSA, and SIE in virtual screening
   Salla I. Virtanen, Sanna P. Niinivehmas, Olli T. Pentikäinen · 2015 · Journal of Molecular Graphics and Modelling
9. The challenge of intracellular antibiotic accumulation, a function of fluoroquinolone influx versus bacterial efflux
   Julia Vergalli, Alessio Atzori, Jelena D. Pajović, Estelle Dumont, Giuliano Malloci, Muriel Masi, Attilio Vittorio Vargiu, Mathias Winterhalter, Matthieu Réfrégiers, Paolo Ruggerone et al. · 2020 · Communications Biology
10. Efficiency of a second‐generation HIV‐1 protease inhibitor studied by molecular dynamics and absolute binding free energy calculations
    Martin Lepšı́k, Zdeněk Křı́ž, Zdeněk Havlas · 2004 · Proteins Structure Function and Bioinformatics
11. Polarizable Force Fields for Biomolecular Modeling
    Yue Shi, Peng-Yu Y. Ren, M. Schnieders, Jean-Philip Piquemal · 2015 · Reviews in computational chemistry
12. Key Binding and Susceptibility of NS3/4A Serine Protease Inhibitors against Hepatitis C Virus
    Arthitaya Meeprasert, Supot V. Hannongbua, Thanyada Rungrotmongkol · 2014 · Journal of Chemical Information and Modeling
13. QM/MM−PBSA Method To Estimate Free Energies for Reactions in Proteins
    Markus Kaukonen, Pär Söderhjelm, Jimmy Heimdal, Ulf Ryde · 2008 · The Journal of Physical Chemistry B
14. Alchemical free energy simulations for biological complexes: powerful but temperamental …
    Alexey V. Aleksandrov, Damien Thompson, Thomas Simonson · 2009 · Journal of Molecular Recognition
15. Thermodynamic and Structural Basis of Phosphorylation-Induced Disorder-to-Order Transition in the Regulatory Light Chain of Smooth Muscle Myosin
    Michel Espinoza-Fonseca, David J.E. Kast, David Dale Thomas · 2008 · Journal of the American Chemical Society
16. Importance of Ligand Reorganization Free Energy in Protein−Ligand Binding-Affinity Prediction
    Chao‐Yie Yang, Haiying Sun, Jianyong Chen, Zaneta Nikolovska‐Coleska, Shaomeng Wang · 2009 · Journal of the American Chemical Society
17. A novelO-linked glycan modulatesCampylobacter jejunimajor outer membrane protein-mediated adhesion to human histo-blood group antigens and chicken colonization
    Jafar Mahdavi, Necmettin Pirinççioğlu, Neil J. Oldfield, Elisabet Carlsohn, Jeroen Stoof, Akhmed Aslam, Tim J. Self, Shaun A. Cawthraw, Liljana Petrovska, Natalie Colborne et al. · 2014 · Open Biology
18. Topology Specific Stabilization of Promoter over Telomeric G-Quadruplex DNAs by Bisbenzimidazole Carboxamide Derivatives
    V. Dhamodharan, S. Harikrishna, Achikanath C. Bhasikuttan, Pushpangadan Indira Pradeepkumar · 2014 · ACS Chemical Biology
19. Molecular Mechanism of the Affinity Interactions between Protein A and Human Immunoglobulin G1 Revealed by Molecular Simulations
    Bo Huang, Fufeng Liu, Xiaoyan Dong, Yan Ping Sun · 2011 · The Journal of Physical Chemistry B
20. In Silico Predictions of Endocrine Disruptors Properties
    Melanie Schneider, Jean-Luc Pons, Gilles Labesse, William Bourguet · 2019 · Endocrinology
21. Theoretical Investigation of the Binding Free Energies and Key Substrate-Recognition Components of the Replication Fidelity of Human DNA Polymerase β
    Jan Florián, Myron F. Goodman, Arieh Warshel · 2002 · The Journal of Physical Chemistry B
22. Origin of Decrease in Potency of Darunavir and Two Related Antiviral Inhibitors against HIV-2 Compared to HIV-1 Protease
    Parimal Kar, Volker Knecht · 2012 · The Journal of Physical Chemistry B
23. Quantifying the Effect of Surface Ligands on Dendron–DNA Interactions: Insights into Multivalency through a Combined Experimental and Theoretical Approach
    Simon P. Jones, Giovanni Maria Pavan, Andrea Danani, Sabrina Pricl, David K. Smith · 2010 · Chemistry - A European Journal
24. Molecular Dynamics Simulations of Wild Type and Mutants of SAPAP in Complexed with Shank3
    Lianhua Piao, Zhou Chen, Qiuye Li, Ranran Liu, Wei Song, Ren Kong, Shan Chang · 2019 · International Journal of Molecular Sciences
25. Computational targeting of allosteric site of MEK1 by quinoline‐based molecules
    Rahul Singh, Vijay Kumar Bhardwaj, Rituraj Purohit · 2022 · Cell Biochemistry and Function
26. Computational Study on the Drug Resistance Mechanism against HCV NS3/4A Protease Inhibitors Vaniprevir and MK-5172 by the Combination Use of Molecular Dynamics Simulation, Residue Interaction Network, and Substrate Envelope Analysis
    Weiwei Xue, Yihe Ban, Huanxiang Liu, Xiaojun Yao · 2013 · Journal of Chemical Information and Modeling
27. Structure-Based, Rational Design of T Cell Receptors
    Vincent Zoete, Melita B. Irving, Mathias Ferber, Michel A. Cuendet, Olivier Alain Michielin · 2013 · Frontiers in Immunology
28. A STRUCTURAL BIOINFORMATICS APPROACH TO THE ANALYSIS OF NONSYNONYMOUS SINGLE NUCLEOTIDE POLYMORPHISMS (nsSNPs) AND THEIR RELATION TO DISEASE
    Catherine L. Worth, G. Richard Bickerton, Adrian M. Schreyer, Julia Forman, Tammy M. K. Cheng, Semin Lee, Sungsam Gong, David F. Burke, Tom L. Blundell · 2007 · Journal of Bioinformatics and Computational Biology
29. The Interaction of Heparin Tetrasaccharides with Chemokine CCL5 Is Modulated by Sulfation Pattern and pH
    Arunima Singh, Warren C. Kett, India C. Severin, Isaac Agyekum, Jiana Duan, I. Jonathan Amster, Amanda E. I. Proudfoot, Deirdre R. Coombe, Robert J. Woods · 2015 · Journal of Biological Chemistry
30. Effect of atomic charge, solvation, entropy, and ligand protonation state on MM‐PB(GB)SA binding energies of HIV protease
    Daniel P. Oehme, Robert T. C. Brownlee, David J. D. Wilson · 2012 · Journal of Computational Chemistry
31. The adsorption mechanism and induced conformational changes of three typical proteins with different secondary structural features on graphene
    Jingjing Guo, Xiaojun Yao, Lulu Ning, Qianqian Wang, Huanxiang Liu · 2013 · RSC Advances
32. Design, synthesis, biological evaluation, and molecular modeling studies of chalcone-rivastigmine hybrids as cholinesterase inhibitors
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33. Interaction entropy for computational alanine scanning in protein–protein binding
    Linqiong Qiu, Yuna Yan, Zhaoxi Sun, Jianing Song, John Z. H. Zhang · 2017 · Wiley Interdisciplinary Reviews Computational Molecular Science
34. Recent advances inde novodesign strategy for practical lead identification
    Teruki Honma · 2003 · Medicinal Research Reviews
35. Molecular Dynamics
    Xiaolin Cheng, Ivaylo N. Ivanov · 2012 · Methods in molecular biology
36. Probing the Effect of Point Mutations at Protein-Protein Interfaces with Free Energy Calculations
    Martin Almlöf, Johan Åqvist, Arne Oskar Smalås, Bjørn Olav Brandsdal · 2005 · Biophysical Journal
37. HER2 Targeting Peptides Screening and Applications in Tumor Imaging and Drug Delivery
    Lingling Geng, Zihua Wang, Xiangqian Jia, Qiuju Han, Zhichu Xiang, Dan Li, Xiaoliang Yang, Di Zhang, Xiangli Bu, Weizhi Wang et al. · 2016 · Theranostics
38. In silico methods for design of biological therapeutics
    Ankit Roy, Sanjana Anilkumar Nair, Neeladri Sen, Neelesh Soni, Mallur Srivatsan Madhusudhan · 2017 · Methods
39. Computational Characterization of Structural Role of the Non-active Site Mutation M36I of Human Immunodeficiency Virus Type 1 Protease
    Hirotaka Ode, Shou Matsuyama, Masayuki Hata, Saburo Neya, Junko Kakizawa, Wataru Sugiura, Tyuji Hoshino · 2007 · Journal of Molecular Biology
40. In Silico Discovery of Potential VEGFR-2 Inhibitors from Natural Derivatives for Anti-Angiogenesis Therapy
    Jing Li, Nan Zhou, Kun Luo, Wei Zhang, Xinru Li, Chuanfang Wu, Jinku Bao · 2014 · International Journal of Molecular Sciences
41. Ensemble-based virtual screening reveals dual-inhibitors for the p53–MDM2/MDMX interactions
    Khaled Barakat, Jonathan Y. Mane, Douglas E. Friesen, Jack A. Tuszyński · 2009 · Journal of Molecular Graphics and Modelling
42. Reorganization Energy for Internal Electron Transfer in Multicopper Oxidases
    LiHong Hu, Maryam Farrokhnia, Jimmy Heimdal, Sergey Shleev, Lubomı́r Rulı́šek, Ulf Ryde · 2011 · The Journal of Physical Chemistry B
43. Accurate and Efficient Calculation of Protein–Protein Binding Free Energy-Interaction Entropy with Residue Type-Specific Dielectric Constants
    Xiao Liu, Long Peng, John Z. H. Zhang · 2018 · Journal of Chemical Information and Modeling
44. Why the first self-binding peptide of human c-Src kinase does not contain class II motif but can bind to its cognate Src homology 3 domain in class II mode?
    Peng Zhou, Fugang Yan, Qingqing Miao, Zheng Chen, Heyi Wang · 2019 · Journal of Biomolecular Structure and Dynamics
45. Structural based study to identify new potential inhibitors for dual specificity tyrosine-phosphorylation- regulated kinase
    Vijay Kumar Bhardwaj, RAHUL KUNWAR SINGH, Jatin Sharma, Pralay Das, Rituraj Purohit · 2020 · Computer Methods and Programs in Biomedicine
46. Molecular Modeling Study of Dihydrofolate Reductase Inhibitors. Molecular Dynamics Simulations, Quantum Mechanical Calculations, and Experimental Corroboration
    Rodrigo D. Tosso, Sebastián A. Andújar, Lucas Joel Gutiérrez, Emilio Angelina, Ricaurte Rodríguez, Manuel Nogueras, Héctor A. Baldoni, Fernando D. Suvire, Justo Cobo, Ricardo Daniel Enriz · 2013 · Journal of Chemical Information and Modeling
47. Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations
    Mauro Lapelosa, Emilio Gallicchio, R. Levy · 2012 · Journal of Chemical Theory and Computation
48. Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculations
    Bernd Kuhn, Peter A. Kollman, Martin Ståhl · 2004 · Journal of Computational Chemistry
49. Molecular insight into the specific binding of ADP-ribose to the nsP3 macro domains of chikungunya and venezuelan equine encephalitis viruses: Molecular dynamics simulations and free energy calculations
    Thanyada Rungrotmongkol, Nadtanet Nunthaboot, Maturos Malaisree, Nopporn Kaiyawet, Pathumwadee Yotmanee, Arthitaya Meeprasert, Supot V. Hannongbua · 2010 · Journal of Molecular Graphics and Modelling
50. Combretastatin A-4 inspired novel 2-aryl-3-arylamino-imidazo-pyridines/pyrazines as tubulin polymerization inhibitors, antimitotic and anticancer agents
    Nitesh Sanghai, Vaibhav Jain, Ranjan Preet, Somnath G. Kandekar, Sarita Das, Neha Trivedi, Purusottam Mohapatra, Garima Priyadarshani, Maneesh Kashyap, Dipon Das et al. · 2014 · MedChemComm
51. Large-scale molecular dynamics simulation of DNA: implementation and validation of the AMBER98 force field in LAMMPS
    Christina Rebecca Grindon, Sarah Anne Harris, Tom Evans, Keir E. Novik, Peter V. Coveney, Charles A. Laughton · 2004 · Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences
52. Phenol Red Interacts with the Protofibril-Like Oligomers of an Amyloidogenic Hexapeptide NFGAIL through Both Hydrophobic and Aromatic Contacts
    Chun Fu Wu, Hongxing Lei, Zhixiang Wang, Wei Zhang, Yong Duan · 2006 · Biophysical Journal
53. Specific Stabilization of c-MYC and c-KIT G-Quadruplex DNA Structures by Indolylmethyleneindanone Scaffolds
    K. V. Diveshkumar, Saaz Sakrikar, Frédéric Rosu, S. Harikrishna, Valérie Gabelica, Pushpangadan Indira Pradeepkumar · 2016 · Biochemistry
54. Structural dynamics of Casein Kinase I (CKI) from malarial parasite Plasmodium falciparum (Isolate 3D7): Insights from theoretical modelling and molecular simulations
    Budheswar Dehury, Santosh Kumar Behera, Namita Mahapatra · 2016 · Journal of Molecular Graphics and Modelling
55. Identification of potential inhibitors ofFasciola giganticathioredoxin1: computational screening, molecular dynamics simulation, and binding free energy studies
    Rohit Shukla, Harish Shukla, Parismita Kalita, Amit Kumar Sonkar, Tripti Pandey, Dev Bukhsh Singh, Awanish Kumar, Timir Tripathi · 2017 · Journal of Biomolecular Structure and Dynamics
56. In Silico Identification of the Potential Drug Resistance Sites over 2009 Influenza A (H1N1) Virus Neuraminidase
    Huanxiang Liu, Xiaojun Yao, Chengqi C. Q. Wang, Jian Han · 2010 · Molecular Pharmaceutics
57. Identification of a repurposed drug as an inhibitor of Spike protein of human coronavirus SARS-CoV-2 by computational methods
    Sruthi Unni, Snehal Aouti, Saravanamuthu Thiyagarajan, Balasundaram Padmanabhan · 2020 · Journal of Biosciences
58. In-silico identification of new inhibitors for Low-density lipoprotein receptor-related protein6 (LRP6)
    Maryam Enayatkhani, Mona Salimi, Kayhan Azadmanesh, Ladan Teimoori‐Toolabi · 2020 · Journal of Biomolecular Structure and Dynamics
59. Protein-Triggered Supramolecular Disassembly: Insights Based on Variations in Ligand Location in Amphiphilic Dendrons
    Diego Amado Torres, Matteo Garzoni, Ayyagari V. Subrahmanyam, Giovanni Maria Pavan, S. Thayumanavan · 2014 · Journal of the American Chemical Society
60. Assessing the differential action on cancer cells of LDH-A inhibitors based on the N-hydroxyindole-2-carboxylate (NHI) and malonic (Mal) scaffolds
    Carlotta Granchi, Emilia C. Calvaresi, Tiziano Tuccinardi, Ilaria Paterni, Marco Macchia, Adriano Martinelli, Paul J. Hergenrother, Filippo Minutolo · 2013 · Organic & Biomolecular Chemistry
61. Mapping the Structural and Dynamical Features of Multiple p53 DNA Binding Domains: Insights into Loop 1 Intrinsic Dynamics
    Suryani Lukman, David Philip Lane, Chandra Shekhar Verma · 2013 · PLoS ONE
62. An integrated molecular dynamics, principal component analysis and residue interaction network approach reveals the impact of M184V mutation on HIV reverse transcriptase resistance to lamivudine
    Soumendranath Bhakat, Alberto J. M. Martín, Mahmoud E. S. Soliman · 2014 · Molecular BioSystems
63. Investigation of the Interactions of Silibinin with 2-Hydroxypropyl-β-cyclodextrin through Biophysical Techniques and Computational Methods
    Tahsin F. Kellici, Dimitrios Ntountaniotis, Georgios Leonis, Μaria V. Chatziathanasiadou, Alexandra V. Chatzikonstantinou, Johanna Becker‐Baldus, Clemens Glaubitz, Andreas G. Tzakos, Kyriakos G. Viras, Petros Chatzigeorgiou et al. · 2015 · Molecular Pharmaceutics
64. Mapping the interactions and bioactivity of quercetin(2-hydroxypropyl)-β-cyclodextrin complex
    Tahsin F. Kellici, Μaria V. Chatziathanasiadou, Dimitris Diamantis, Alexandra V. Chatzikonstantinou, Ioannis Andreadelis, Eirini Christodoulou, Georgia N. Valsami, Thomas Mavromoustakos, Andreas G. Tzakos · 2016 · International Journal of Pharmaceutics
65. Investigating Phosphorylation-Induced Conformational Changes in WNK1 Kinase by Molecular Dynamics Simulations
    Nisha Amarnath Jonniya, Md Fulbabu Sk, Parimal Kar · 2019 · ACS Omega
66. Pinpointing the potential hits for hindering interaction of SARS-CoV-2 S-protein with ACE2 from the pool of antiviral phytochemicals utilizing molecular docking and molecular dynamics (MD) simulations
    Chirag Patel, Dweipayan Goswami, Dharmesh G. Jaiswal, Robin M. Parmar, Hitesh Solanki, Himanshu A. Pandya · 2021 · Journal of Molecular Graphics and Modelling
67. Biomolecular Applications of Poisson–Boltzmann Methods
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68. New anti-viral drugs for the treatment of COVID-19 instead of favipiravir
    Ahmet Aktaş, Burak Tüzün, Rukiye Aslan, Koray Sayın, Hilmi Ataseven · 2020 · Journal of Biomolecular Structure and Dynamics
69. The beginning and the end: flanking nucleotides induce a parallel G-quadruplex topology
    Jielin Chen, Mingpan Cheng, Gilmar F. J. Salgado, Petr Stadlbauer, Xiaobo Zhang, Samir Amrane, Aurore Guédin, Fangni He, Jiřı́ Šponer, Huangxian Ju et al. · 2021 · Nucleic Acids Research
70. Continuum Solvation Models in the Linear Interaction Energy Method
    Jens Carlsson, Martin Andér, Martin Nervall, Johan Åqvist · 2006 · The Journal of Physical Chemistry B
71. Multiscale molecular dynamics using the matched interface and boundary method
    Weihua Geng, Guo‐Wei Wei · 2010 · Journal of Computational Physics
72. Insights into Saquinavir Resistance in the G48V HIV-1 Protease: Quantum Calculations and Molecular Dynamic Simulations
    Kitiyaporn Wittayanarakul, Ornjira Aruksakunwong, Suwipa Saen‐oon, Wasun Chantratita, Vudhichai Parasuk, Pornthep Sompornpisut, Supot V. Hannongbua · 2004 · Biophysical Journal
73. Binding of curcumin with glyoxalase I: Molecular docking, molecular dynamics simulations, and kinetics analysis
    Ming Liu, Minggui Yuan, Minxian Luo, Xianzhang Bu, Hai‐Bin Luo, Xiaopeng Hu · 2009 · Biophysical Chemistry
74. A detailed binding free energy study of 2 : 1 ligand–DNA complex formation by experiment and simulation
    Witcha Treesuwan, Kitiyaporn Wittayanarakul, Nahoum G. Anthony, Guillaume Huchet, Hasan Yaser Alniss, Supa Hannongbua, Abedawn I. Khalaf, Colin J. Suckling, John A. Parkinson, Simon Paul Mackay · 2009 · Physical Chemistry Chemical Physics
75. Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site
    Gilad Wainreb, Lior Wolf, Haim Ashkenazy, Yves Dehouck, Nir Ben‐Tal · 2011 · Bioinformatics
76. Evaluation of Predicted Protein–Protein Complexes by Binding Free Energy Simulations
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77. A FABP4-PPARγ signaling axis regulates human monocyte responses to electrophilic fatty acid nitroalkenes
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78. Insights into the Acylation Mechanism of Class A β-Lactamases from Molecular Dynamics Simulations of the TEM-1 Enzyme Complexed with Benzylpenicillin
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79. Accurate Predictions of Nonpolar Solvation Free Energies Require Explicit Consideration of Binding-Site Hydration
    Samuel Genheden, Paulius Mikulskis, LiHong Hu, Jacob Kongsted, Pär Söderhjelm, Ulf Ryde · 2011 · Journal of the American Chemical Society
80. Can MM‐PBSA calculations predict the specificities of protein kinase inhibitors?
    Christopher S. Page, Paul A. Bates · 2006 · Journal of Computational Chemistry
81. Free energy calculations of glycosaminoglycan–protein interactions
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82. Small-Angle Neutron Scattering Study of a Monoclonal Antibody Using Free-Energy Constraints
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83. Ribonuclease H/DNA Polymerase HIV-1 Reverse Transcriptase Dual Inhibitor: Mechanistic Studies on the Allosteric Mode of Action of Isatin-Based Compound RMNC6
    Angela Corona, Rita Meleddu, Francesca Esposito, Simona Distinto, Giulia Bianco, Takashi Masaoka, Elias Maccioni, Luis Menéndez‐Arias, Stefano Alcaro, Stuart F.J. Le Grice et al. · 2016 · PLoS ONE
84. Hydrophobic Binding Hot Spots of Bcl-xL Protein−Protein Interfaces by Cosolvent Molecular Dynamics Simulation
    Yang, Chao-Yie, Wang, Shaomeng · 2011 · ACS Medicinal Chemistry Letters
85. Computational design and modeling of nanobodies toward SARS‐CoV‐2 receptor binding domain
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86. Rapid and accurate estimation of protein–ligand relative binding affinities using site-identification by ligand competitive saturation
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87. Nucleotide Excision Repair Efficiencies of Bulky Carcinogen–DNA Adducts Are Governed by a Balance between Stabilizing and Destabilizing Interactions
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88. Interaction of nucleic acids with carbon nanotubes and dendrimers
    Bidisha Nandy, Santosh Mogurampelly, Prabal Kumar Maiti · 2012 · Journal of Biosciences
89. Molecular Structures of Quiescently Grown and Brain-Derived Polymorphic Fibrils of the Alzheimer Amyloid Aβ9-40 Peptide: A Comparison to Agitated Fibrils
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90. Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations
    I. Ben-Shalom, Stefania Pfeiffer-Marek, K. Baringhaus, H. Gohlke · 2017 · Journal of Chemical Information and Modeling
91. How accurate are your simulations? Effects of confined aqueous volume and AMBER FF99SB and CHARMM22/CMAP force field parameters on structural ensembles of intrinsically disordered proteins: Amyloid-β42in water
    Orkid Coskuner‐Weber, Vladimir Nikolaevich Uversky · 2017 · Intrinsically Disordered Proteins
92. An electron transfer competent structural ensemble of membrane-bound cytochrome P450 1A1 and cytochrome P450 oxidoreductase
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93. O-GlcNAcylation regulates the stability of transferrin receptor (TFRC) to control the ferroptosis in hepatocellular carcinoma cells
    Xunyu Zhou, Yida Wang, Xiaoyu Li, Jing Zhou, Wanyi Yang, Xin Wang, Sitong Jiao, Weibo Zuo, Ziming You, Wantao Ying et al. · 2024 · Redox Biology
94. Calculation of Protein−Ligand Interaction Energies by a Fragmentation Approach Combining High-Level Quantum Chemistry with Classical Many-Body Effects
    Pär Söderhjelm, Francesco Aquilante, Ulf Ryde · 2009 · The Journal of Physical Chemistry B
95. Molecular dynamics simulation studies of GSK-3β ATP competitive inhibitors: understanding the factors contributing to selectivity
    Minhajul Arfeen, Rahul Patel, Tosif Khan, Prasad V. Bharatam · 2015 · Journal of Biomolecular Structure and Dynamics
96. Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson–Boltzmann Equation: II. Protein and Its Ligand-Binding System Studies
    Yoshio Okiyama, Chiduru Watanabe, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka · 2018 · The Journal of Physical Chemistry B
97. The impact of interior dielectric constant and entropic change on HIV-1 complex binding free energy prediction
    Yuchen Li, Yalong Cong, Guoqiang Feng, Susu Zhong, John Z. H. Zhang, Huiyong Sun, Lili Duan · 2018 · Structural Dynamics
98. Insight into the selective binding mechanism of DNMT1 and DNMT3A inhibitors: a molecular simulation study
    Tianli Xie, Jie Yu, Weitao Fu, Zhe Wang, Lei Xu, Shan Chang, Ercheng Wang, Feng Zhu, Su Zeng, Yu Kang et al. · 2019 · Physical Chemistry Chemical Physics
99. Preclinical Validation of the Heparin-Reactive Peptide p5+14 as a Molecular Imaging Agent for Visceral Amyloidosis
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100. Implicit Solvent Electrostatics in Biomolecular Simulation
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