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

Cited by (1,010)

Items 401–500 of 1,010

1. Molecular Interactions of Nucleic Acid Bases. A Review of Quantum-Chemical Studies
   Jiřı́ Šponer, Pavel Hobza · 2003 · Collection of Czechoslovak Chemical Communications
2. Refinement and Rescoring of Virtual Screening Results
   Giulio Rastelli, Luca Pinzi · 2019 · Frontiers in Chemistry
3. Accurate prediction of protonation state as a prerequisite for reliable MM‐PB(GB)SA binding free energy calculations of HIV‐1 protease inhibitors
   Kitiyaporn Wittayanarakul, Supot V. Hannongbua, Michael Feig · 2007 · Journal of Computational Chemistry
4. Mechanism of MicroRNA-Target Interaction: Molecular Dynamics Simulations and Thermodynamics Analysis
   Yonghua Wang, Yan Li, Zhi Ma, Wei Yang, Chun‐Zhi Ai · 2010 · PLoS Computational Biology
5. Quantitative Prediction of Fold Resistance for Inhibitors of EGFR
   Trent E. Balius, Robert C. Rizzo · 2009 · Biochemistry
6. Computational prediction of drug binding and rationalisation of selectivity towards cytochromes P450
   Eva Stjernschantz, Nico P.E. Vermeulen, Chris Oostenbrink · 2008 · Expert Opinion on Drug Metabolism & Toxicology
7. Fast and accurate determination of the relative binding affinities of small compounds to HIV-1 protease using non-equilibrium work
   Sơn Tùng Ngô, Huynh Minh Hung, Minh Tho Nguyen · 2016 · Journal of Computational Chemistry
8. Homology modeling, molecular docking, and molecular dynamics simulations elucidated α-fetoprotein binding modes
   Jie Shen, Wenqian Zhang, Hong Fang, Roger Perkins, Weida Tong, Huixiao Hong · 2013 · BMC Bioinformatics
9. Exploring the physicochemical profile and the binding patterns of selected novel anticancer Himalayan plant derived active compounds with macromolecular targets
   Arun Bahadur Gurung, Atanu Bhattacharjee, Mohammad Ajmal Ali · 2016 · Informatics in Medicine Unlocked
10. Drug binding dynamics of the dimeric SARS-CoV-2 main protease, determined by molecular dynamics simulation
    Teruhisa Komatsu, Noriaki Okimoto, Yohei M. Koyama, Yoshinori Hirano, Gentaro Morimoto, Yousuke Ohno, Makoto Taiji · 2020 · Scientific Reports
11. Targeting the 3CLpro and RdRp of SARS-CoV-2 with phytochemicals from medicinal plants of the Andean Region: molecular docking and molecular dynamics simulations
    Francisco Mosquera-Yuqui, Nicolas Lopez-Guerra, Eduardo A. Moncayo · 2020 · Journal of Biomolecular Structure and Dynamics
12. Molecular docking and dynamics simulation analyses unraveling the differential enzymatic catalysis by plant and fungal laccases with respect to lignin biosynthesis and degradation
    Manika Awasthi, Nivedita Jaiswal, Swati Singh, Veda Prakash Pandey, Upendra Nath Dwivedi · 2014 · Journal of Biomolecular Structure and Dynamics
13. Atomic and Dynamic Insights into the Beneficial Effect of the 1,4-Naphthoquinon-2-yl- l -tryptophan Inhibitor on Alzheimer’s Aβ1–42 Dimer in Terms of Aggregation and Toxicity
    Tong Zhang, Weixin Xu, Yuguang Mu, Philippe Derreumaux · 2013 · ACS Chemical Neuroscience
14. Molecular Determinants of Epidermal Growth Factor Binding: A Molecular Dynamics Study
    Jeffrey M. Sanders, Matthew E. Wampole, Mathew L. Thakur, Eric Wickstrom · 2013 · PLoS ONE
15. Recent advances in user-friendly computational tools to engineer protein function
    Carlos Eduardo Sequeiros-Borja, Bartłomiej Surpeta, Jan Brezovský · 2020 · Briefings in Bioinformatics
16. How accurate are continuum solvation models for drug-like molecules?
    Jacob Kongsted, Pär Söderhjelm, Ulf Ryde · 2009 · Journal of Computer-Aided Molecular Design
17. How broadly tuned olfactory receptors equally recognize their agonists. Human OR1G1 as a test case
    Landry Charlier, Jérémie Topin, Cathérine Ronin, Soo‐Kyung Kim, William A. Goddard, Roman G. Efremov, Jérôme Golebiowski · 2012 · Cellular and Molecular Life Sciences
18. Choline Ion Interactions with DNA Atoms Explain Unique Stabilization of A–T Base Pairs in DNA Duplexes: A Microscopic View
    Miki Nakano, Hisae Tateishi‐Karimata, Shigenori Tanaka, Naoki Sugimoto · 2013 · The Journal of Physical Chemistry B
19. Rapid and Reliable Binding Affinity Prediction of Bromodomain Inhibitors: A Computational Study
    Shunzhou Wan, Agastya P. Bhati, Stefan J. Zasada, Ian D. Wall, Darren V. S. Green, Paul Bamborough, Peter V. Coveney · 2016 · Journal of Chemical Theory and Computation
20. Theoretical Studies on the Susceptibility of Oseltamivir against Variants of 2009 A/H1N1 Influenza Neuraminidase
    Lin Li, Youyong Li, Liling Zhang, Tingjun Hou · 2012 · Journal of Chemical Information and Modeling
21. Processive chitinase is Brownian monorail operated by fast catalysis after peeling rail from crystalline chitin
    Akihiko Nakamura, Kei-ichi Okazaki, Tadaomi Furuta, Minoru Sakurai, Ryota Iino · 2018 · Nature Communications
22. Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4
    Léa El Khoury, Diogo Santos‐Martins, Sukanya Sasmal, Jérôme Eberhardt, Giulia Bianco, Francesca Alessandra Ambrosio, Leonardo Solis-Vasquez, Andreas Koch, Stefano Forli, David L. Mobley · 2019 · Journal of Computer-Aided Molecular Design
23. Interactions between Curcumin Derivatives and Amyloid-β Fibrils: Insights from Molecular Dynamics Simulations
    Joseph M. Jakubowski, Asuka A. Orr, Doan A. Le, Phanourios Tamamis · 2019 · Journal of Chemical Information and Modeling
24. Automated, Accurate, and Scalable Relative Protein–Ligand Binding Free-Energy Calculations Using Lambda Dynamics
    E. Prabhu Raman, Thomas J. Paul, Ryan L. Hayes, Charles L. Brooks · 2020 · Journal of Chemical Theory and Computation
25. Improving the Performance of MM/PBSA in Protein–Protein Interactions via the Screening Electrostatic Energy
    Yan-jing Sheng, Yue‐wen Yin, Yu‐qiang Ma, Hong‐Ming Ding · 2021 · Journal of Chemical Information and Modeling
26. A Contribution to the Drug Resistance Mechanism of Darunavir, Amprenavir, Indinavir, and Saquinavir Complexes with HIV-1 Protease Due to Flap Mutation I50V: A Systematic MM–PBSA and Thermodynamic Integration Study
    Georgios Leonis, Thomas B. Steinbrecher, Μάνθος Γ. Παπαδόπουλος · 2013 · Journal of Chemical Information and Modeling
27. Dynamics of Hydration Water Plays a Key Role in Determining the Binding Thermodynamics of Protein Complexes
    S. Chong, S. Ham · 2017 · Scientific Reports
28. Molecular modelling in structural biology
    Mark J. Forster · 2002 · Micron
29. Calculations of the Absolute Free Energies of Binding between RNA and Metal Ions Using Molecular Dynamics Simulations and Continuum Electrostatics
    Vickie Tsui, David Andrew Case · 2001 · The Journal of Physical Chemistry B
30. Molecular Basis of SARS-CoV‑2 Infection and Rational Design of Potential Antiviral Agents: Modeling and Simulation Approaches
    Antonio Francés‐Monerris, Cécilia Hognon, Tom Miclot, Cristina García‐Iriepa, Isabel Iriepa, Alessio Terenzi, Stéphanie Grandemange, Giampaolo Barone, Marco Marazzi, Antonio Monari · 2020 · Journal of Proteome Research
31. Wedelolactone alleviates cholestatic liver injury by regulating FXR-bile acid-NF-κB/NRF2 axis to reduce bile acid accumulation and its subsequent inflammation and oxidative stress.
    Mei-Qi Wang, Kai-Hui Zhang, Fang-Le Liu, Rui Zhou, Yu Zeng, Ali Chen, Yang Yu, Quan Xia, Chen-Chen Zhu, Chao-Zhan Lin · 2023 · Phytomedicine
32. Practical Considerations in Virtual Screening and Molecular Docking
    Michael J. Berry, Burtram Clinton Fielding, Junaid Gamieldien · 2015 · Elsevier eBooks
33. Flexible receptor docking for drug discovery
    Chung F. Wong · 2015 · Expert Opinion on Drug Discovery
34. Effect of a Bound Non-Nucleoside RT Inhibitor on the Dynamics of Wild-Type and Mutant HIV-1 Reverse Transcriptase
    Zhigang Zhou, Marcela Madrid, Jeffrey D. Evanseck, Jeffry D. Madura · 2005 · Journal of the American Chemical Society
35. Exploring the Molecular Mechanism of Cross-Resistance to HIV-1 Integrase Strand Transfer Inhibitors by Molecular Dynamics Simulation and Residue Interaction Network Analysis
    Weiwei Xue, Xiaojie Jin, Lulu Ning, Meixia Wang, Huanxiang Liu, Xiaojun Yao · 2012 · Journal of Chemical Information and Modeling
36. The Role of Methylation in the Intrinsic Dynamics of B- and Z-DNA
    Nuri A. Temiz, Duncan E. Donohue, Albino Bacolla, Brian T. Luke, Jack Collins · 2012 · PLoS ONE
37. Distinct Glycan Topology for Avian and Human Sialopentasaccharide Receptor Analogues upon Binding Different Hemagglutinins: A Molecular Dynamics Perspective
    Dong Xu, E. Irene Newhouse, Rommie E. Amaro, Hsing C. Pao, Lily S. Cheng, Phineus R. L. Markwick, James Andrew McCammon, Wilfred W. Li, PETER W. ARZBERGER · 2009 · Journal of Molecular Biology
38. Synergy between trastuzumab and pertuzumab for human epidermal growth factor 2 (Her2) from colocalization: an in silicobased mechanism
    Gloria Fuentes, Maurizio Scaltriti, Jose M Baselga, Chandra Shekhar Verma · 2011 · Breast Cancer Research
39. Generation of Receptor Structural Ensembles for Virtual Screening Using Binding Site Shape Analysis and Clustering
    David J. Osguthorpe, Woody Sherman, A. T. Hagler · 2012 · Chemical Biology & Drug Design
40. Ligand Selectivity Mechanism and Conformational Changes in Guanine Riboswitch by Molecular Dynamics Simulations and Free Energy Calculations
    Guodong Hu, Aijing Ma, Jihua Wang · 2017 · Journal of Chemical Information and Modeling
41. Chemical profile of Lippia thymoides, evaluation of the acetylcholinesterase inhibitory activity of its essential oil, and molecular docking and molecular dynamics simulations
    Sebastião Gomes Silva, Renato Araújo da Costa, Mozaniel Santana de Oliveira, Jorddy Neves Cruz, Pablo Luis B. Figueiredo, Davi do Socorro Barros Brasil, Lidiane Diniz do Nascimento, Antônio Maia de Jesus Chaves Neto, Raul Nunes de Carvalho, Eloísa Helena de Aguiar Andrade · 2019 · PLoS ONE
42. Potential inhibitors of the enzyme acetylcholinesterase and juvenile hormone with insecticidal activity: study of the binding mode via docking and molecular dynamics simulations
    Ryan da Silva Ramos, Williams Jorge da Cruz Macêdo, Josivan S. Costa, Carlos H. T. de P. da Silva, Joaquín M. Campos Rosa, Jorddy Neves Cruz, Mozaniel Santana de Oliveira, Eloísa Helena de Aguiar Andrade, Raullyan B. L. e Silva, Raimundo Nonato Picanço Souto et al. · 2019 · Journal of Biomolecular Structure and Dynamics
43. Entropic contributions and the influence of the hydrophobic environment in promiscuous protein–protein association
    Chia‐en A. Chang, William A. McLaughlin, Riccardo Baron, Wei Wang, James Andrew McCammon · 2008 · Proceedings of the National Academy of Sciences
44. Discovery of Tertiary Amine and Indole Derivatives as Potent RORγt Inverse Agonists
    Ting Yang, Qian Liu, Yaobang Cheng, Wei Cai, Yingli Ma, Liuqing Yang, Qianqian Wu, Lisa A. Orband‐Miller, Ling Zhou, Zhijun Xiang et al. · 2013 · ACS Medicinal Chemistry Letters
45. Comparing sixteen scoring functions for predicting biological activities of ligands for protein targets
    Weijun Xu, Andrew J. Lucke, David P. Fairlie · 2015 · Journal of Molecular Graphics and Modelling
46. A computational analysis of the binding affinities of FKBP12 inhibitors using the MM‐PB/SA method
    Yong Xu, Renxiao Wang · 2006 · Proteins Structure Function and Bioinformatics
47. Computational Alanine Scanning Mutagenesis: MM-PBSA vs TI
    Martins, Sílvia A., Perez, Marta A. S., Moreira, Irina S., Sousa, Sérgio F., Ramos, M. J., Fernandes, P. A. · 2013 · Journal of Chemical Theory and Computation
48. How Can (−)-Epigallocatechin Gallate from Green Tea Prevent HIV-1 Infection? Mechanistic Insights from Computational Modeling and the Implication for Rational Design of Anti-HIV-1 Entry Inhibitors
    Adel Hamza, Chang‐Guo Zhan · 2006 · The Journal of Physical Chemistry B
49. Dynamic mechanisms for pre-miRNA binding and export by Exportin-5
    Xia Wang, Xue Jun Xu, Zhi Ma, Yingqiu Huo, Zhengtao Xiao, Yan Li, Yonghua Wang · 2011 · RNA
50. Explicit solvent dynamics and energetics of HIV‐1 protease flap opening and closing
    S. Kashif Sadiq, Gianni De Fabritiis · 2010 · Proteins Structure Function and Bioinformatics
51. The molecular organization of the beta-sheet region in Corneous beta-proteins (beta-keratins) of sauropsids explains its stability and polymerization into filaments
    Matteo Calvaresi, Leopold Eckhart, Lorenzo Alibardi · 2016 · Journal of Structural Biology
52. Selective G-quadruplex DNA stabilizing agents based on bisquinolinium and bispyridinium derivatives of 1,8-naphthyridine.
    V. Dhamodharan, S. Harikrishna, C. Jagadeeswaran, K. Halder, P. Pradeepkumar · 2012 · Journal of Organic Chemistry
53. Atomic Radii for Continuum Electrostatics Calculations on Nucleic Acids
    Nilesh K. Banavali, Benoı̂t Roux · 2002 · The Journal of Physical Chemistry B
54. Natural analogues inhibiting selective cyclin-dependent kinase protein isoforms: a computational perspective
    Rahul Singh, Vijay Kumar Bhardwaj, Pralay Das, Rituraj Purohit · 2019 · Journal of Biomolecular Structure and Dynamics
55. Vibrational Circular Dichroism Absolute Configuration Determination of Natural Products
    Pedro Joseph‐Nathan, Bárbara Gordillo-Román · 2014 · Fortschritte der Chemie Organischer Naturstoffe/Fortschritte der Chemie organischer Naturstoffe/Progress in the chemistry of organic natural products
56. iAPBS: a programming interface to the adaptive Poisson–Boltzmann solver
    Robert Konečný, Nathan Baker, James Andrew McCammon · 2012 · Computational Science & Discovery
57. Implicit solvent methods for free energy estimation
    Sergio Decherchi, Matteo Masetti, Ivan Vyalov, Walter Rocchia · 2014 · European Journal of Medicinal Chemistry
58. CXC and CC Chemokines Form Mixed Heterodimers
    Irina V. Nesmelova, Yuk Yin Sham, Jiali Gao, Kevin H. Mayo · 2008 · Journal of Biological Chemistry
59. Virtual Screening and Biological Evaluation of Inhibitors Targeting the XPA-ERCC1 Interaction
    Khaled Barakat, Lars Petter Jordheim, Rolando Pérez, David Scott Wishart, Charles Dumontet, Jack A. Tuszyński · 2012 · PLoS ONE
60. Effective Estimation of Ligand-Binding Affinity Using Biased Sampling Method
    Sơn Tùng Ngô, Khanh Bao Vu, Le Minh Bui, Van V. Vu · 2019 · ACS Omega
61. Atomistic mechanism of polyphenol amyloid aggregation inhibitors: molecular dynamics study of Curcumin, Exifone, and Myricetin interaction with the segment of tau peptide oligomer
    Workalemahu Mikre Berhanu, Artëm E. Masunov · 2014 · Journal of Biomolecular Structure and Dynamics
62. Unraveling the Importance of Protein−Protein Interaction: Application of a Computational Alanine-Scanning Mutagenesis to the Study of the IgG1 Streptococcal Protein G (C2 Fragment) Complex
    Irina Sousa Moreira, Pedro Alexandrino Fernandes, Maria João Ramos · 2006 · The Journal of Physical Chemistry B
63. Identification of naturally originated molecules as γ-aminobutyric acid receptor antagonist
    Jatin Sharma, Vijay Kumar Bhardwaj, Pralay Das, Rituraj Purohit · 2020 · Journal of Biomolecular Structure and Dynamics
64. A Molecular Basis for the Selectivity of Thiadiazole Urea Inhibitors with Stromelysin-1 and Gelatinase-A from Generalized Born Molecular Dynamics Simulations
    Robert C. Rizzo, Samuel Toba, Irwin D. Kuntz · 2004 · Journal of Medicinal Chemistry
65. Implicit Solvent Simulations of DNA and DNA−Protein Complexes: Agreement with Explicit Solvent vs Experiment
    Jana Vacek Chocholoušová, Michael Feig · 2006 · The Journal of Physical Chemistry B
66. Solvated Interaction Energy (SIE) for Scoring Protein–Ligand Binding Affinities. 2. Benchmark in the CSAR-2010 Scoring Exercise
    Traian I. Sulea, Qizhi Cui, Enrico O. Purisima · 2011 · Journal of Chemical Information and Modeling
67. Structure-Dependent Charge Density as a Determinant of Antimicrobial Activity of Peptide Analogues of Defensin
    Yang Bai, Shouping Liu, Ping Jiang, Lei Zhou, Jing Li, Charles Tang, Chandra Shekhar Verma, Yuguang Mu, Roger Wilmer Beuerman, Konstantin V. Pervushin · 2009 · Biochemistry
68. Discovery and optimization of triazine derivatives as ROCK1 inhibitors: molecular docking, molecular dynamics simulations and free energy calculations
    Mingyun Shen, Shunye Zhou, Youyong Li, Peichen Pan, Liling Zhang, Tingjun Hou · 2012 · Molecular BioSystems
69. Conformational Stability of Fibrillar Amyloid-Beta Oligomers via Protofilament Pair Formation – A Systematic Computational Study
    Anna Kahler, Heinrich Sticht, Anselm H. C. Horn · 2013 · PLoS ONE
70. Hierarchical Modeling of Activation Mechanisms in the ABL and EGFR Kinase Domains: Thermodynamic and Mechanistic Catalysts of Kinase Activation by Cancer Mutations
    Anshuman Dixit, Gennady M. Verkhivker · 2009 · PLoS Computational Biology
71. An Efficient Implementation of the Nwat-MMGBSA Method to Rescore Docking Results in Medium-Throughput Virtual Screenings
    Irene Maffucci, Xiao Hu, Valentina Fumagalli, Alessandro Contini · 2018 · Frontiers in Chemistry
72. Entropic Cost of Protein−Ligand Binding and Its Dependence on the Entropy in Solution
    Sheeba Jem Irudayam, Richard Humfry Henchman · 2009 · The Journal of Physical Chemistry B
73. Isatin thiazoline hybrids as dual inhibitors of HIV-1 reverse transcriptase
    Rita Meleddu, Simona Distinto, Angela Corona, Enzo Tramontano, Giulia Bianco, Claudia Melis, Filippo Cottiglia, Elias Maccioni · 2016 · Journal of Enzyme Inhibition and Medicinal Chemistry
74. Cheminformatics-aided discovery of small-molecule Protein-Protein Interaction (PPI) dual inhibitors of Tumor Necrosis Factor (TNF) and Receptor Activator of NF-κB Ligand (RANKL)
    Georgia Melagraki, Evangelos Ntougkos, Vagelis E. Rinotas, Christos P. Papaneophytou, Georgios Leonis, Thomas Mavromoustakos, George A. Kontopidis, Eleni K. Douni, Antreas Afantitis, George A. Kollias · 2017 · PLoS Computational Biology
75. Genome-wide functional analyses of plant coiled–coil NLR-type pathogen receptors reveal essential roles of their N-terminal domain in oligomerization, networking, and immunity
    Tadeusz Wróblewski, Laurentiu N. Spiridon, Eliza Cristina Martin, Andrei‐José Petrescu, Keri Cavanaugh, María José Truco, Huaqin Xu, Dariusz Gozdowskı, Krzysztof Pawłowski, Richard W. Michelmore et al. · 2018 · PLoS Biology
76. Identification of broadly conserved cross-species protective Leishmania antigen and its responding CD4 + T cells
    Zhirong Mou, Jintao Li, Thouraya Boussoffara, Hiroyuki Kishi, Hiroshi Hamana, Peyman Ezzati, Chuanmin Hu, Weijing Yi, Dong Liu, Forough Khadem et al. · 2015 · Science Translational Medicine
77. Common and Selective Molecular Determinants Involved in Metabotopic Glutamate Receptor Agonist Activity
    Hugues‐Olivier Bertrand, Anne‐Sophie Bessis, Jean‐Philippe Pin, Francine Acher · 2002 · Journal of Medicinal Chemistry
78. Evaluation of Poisson Solvation Models Using a Hybrid Explicit/Implicit Solvent Method
    Michael S. Lee, Mark A. Olson · 2005 · The Journal of Physical Chemistry B
79. Coarse-Grained Models for Protein-Cell Membrane Interactions
    Ryan P. Bradley, Ravi Radhakrishnan · 2013 · Polymers
80. Molecular Dynamics Simulations of the Human Glucose Transporter GLUT1
    Minsun Park · 2015 · PLoS ONE
81. A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations
    S. Genheden, U. Ryde · 2011 · Journal of Computational Chemistry
82. Origins of Resistance Conferred by the R292K Neuraminidase Mutation via Molecular Dynamics and Free Energy Calculations
    Ricky Chachra, Robert C. Rizzo · 2008 · Journal of Chemical Theory and Computation
83. From Drug Target to Leads-Sketching A Physicochemical Pathway for Lead Molecule Design In Silico
    Saher Afshan Shaikh, T. Jain, Gurvisha Sandhu, N. Latha, Bhyravabhotla Jayaram · 2007 · Current Pharmaceutical Design
84. Improved Computation of Protein–Protein Relative Binding Energies with the Nwat-MMGBSA Method
    Irene Maffucci, Alessandro Contini · 2016 · Journal of Chemical Information and Modeling
85. Allosteric Communication across the Native and Mutated KIT Receptor Tyrosine Kinase
    Élodie Laine, Christian Auclair, Luba Tchertanov · 2012 · PLoS Computational Biology
86. A cationic polymethacrylate-copolymer acts as an agonist for β-amyloid and an antagonist for amylin fibrillation
    Bikash Ranjan Sahoo, Takuya Genjo, Takahiro Watanabe‐Nakayama, Andrea K. Stoddard, Toshio Ando, Kazuma Yasuhara, Carol A. Fierke, Ayyalusamy Ramamoorthy · 2019 · Chemical Science
87. A breakthrough on Amanita phalloides poisoning: an effective antidotal effect by polymyxin B
    Juliana Garcia, Vera Marisa Costa, Alexandra T. P. Carvalho, Ricardo Silvestre, José Alberto Duarte, Daniel F. A. R. Dourado, Marcelo Dutra Arbo, Teresa Baltazar, Ricardo Jorge Dinis‐Oliveira, Paula C. Baptista et al. · 2015 · Archives of Toxicology
88. Molecular Dynamics Simulation and Free Energy Calculation Studies of the Binding Mechanism of Allosteric Inhibitors with p38α MAP Kinase
    Ying Yang, Yulin Shen, Huanxiang Liu, Xiaojun Yao · 2011 · Journal of Chemical Information and Modeling
89. Effects of Water Models on Binding Affinity: Evidence from All-Atom Simulation of Binding of Tamiflu to A/H5N1 Neuraminidase
    Trang Truc Nguyen, Viet Hoang Man, Mai Suan Li · 2014 · The Scientific World JOURNAL
90. Prediction of peptides binding to the PKA RIIα subunit using a hierarchical strategy
    Tingjun Hou, Youyong Li, Wei Wang · 2011 · Bioinformatics
91. Binding Modes of Flavones to Human Serum Albumin: Insights from Experimental and Computational Studies
    Hui Liu, Wei Bao, Hanjing Ding, Jongchol Jang, Guolin Zou · 2010 · The Journal of Physical Chemistry B
92. Some Practical Approaches to Treating Electrostatic Polarization of Proteins
    Changge Ji, Ye Mei · 2014 · Accounts of Chemical Research
93. GLUT1 and GLUT3 involvement in anthocyanin gastric transport- Nanobased targeted approach
    Hélder Oliveira, Catarina Roma‐Rodrigues, Ana Isabel Santos, Bruno Veigas, Natércia F. Brás, Ana Faria, Conceição Calhau, Victor Armando Pereira de Freitas, Pedro Viana Baptista, Nuno Filipe da Cruz Batista Mateus et al. · 2019 · Scientific Reports
94. Quercetin Blocks Ebola Virus Infection by Counteracting the VP24 Interferon-Inhibitory Function
    Elisa Fanunza, Mathieu Iampietro, Simona Distinto, Angela Corona, Marina Quartu, Elias Maccioni, Branka Horvat, Enzo Tramontano · 2020 · Antimicrobial Agents and Chemotherapy
95. Assessing the Accuracy and Performance of Implicit Solvent Models for Drug Molecules: Conformational Ensemble Approaches
    Michal H. Kolář, Jindřich Fanfrlík, Martin Lepšı́k, Flavio Forti, Francisco Javier Luque, Pavel Hobza · 2013 · The Journal of Physical Chemistry B
96. Early stage intercalation of doxorubicin to DNA fragments observed in molecular dynamics binding simulations
    Hongxing Lei, Xiaofeng Wang, Chun Fu Wu · 2012 · Journal of Molecular Graphics and Modelling
97. Binding site elucidation and structure guided design of macrocyclic IL-17A antagonists
    Shenping Liu, Leslie A. Dakin, Xing Li, Jane M. Withka, Parag V. Sahasrabudhe, Wei Li, Mary Ellen Banker, Paul Balbo, Suman Shanker, Boris A. Chrunyk et al. · 2016 · Scientific Reports
98. Suitability of MMGBSA for the selection of correct ligand binding modes from docking results
    Mira Ahinko, Sanna P. Niinivehmas, Elmeri M. Jokinen, O. Pentikäinen · 2018 · Chemical Biology and Drug Design
99. Approaches to efficiently estimate solvation and explicit water energetics in ligand binding: the use of WaterMap.
    Yang, Yue, Lightstone, Felice C, Wong, Sergio E · 2013 · Expert Opinion on Drug Discovery
100. Unwrapping of Nucleosomal DNA Ends: A Multiscale Molecular Dynamics Study
     Karine Voltz, Joanna Trylska, Nicolas Calimet, Jeremy C. Smith, Jörg Langowski · 2012 · Biophysical Journal