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

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1. Postprocessing of Docked Protein−Ligand Complexes Using Implicit Solvation Models
   Anton Lindström, Lotta Edvinsson, Andreas Johansson, C. David Andersson, Ida E. Andersson, Florian Raubacher, Anna Linusson · 2011 · Journal of Chemical Information and Modeling
2. Mechanisms of DNA methyltransferase–inhibitor interactions: Procyanidin B2 shows new promise for therapeutic intervention of cancer
   Arunima Shilpi, Sabnam Parbin, Dipta Sengupta, Swayamsiddha Kar, Moonmoon Deb, Sandip Kumar Rath, Nibedita Pradhan, Madhumita Rakshit, Samir Kumar Patra · 2015 · Chemico-Biological Interactions
3. Calculation of protein–ligand binding affinities based on a fragment quantum mechanical method
   Jinfeng Liu, Xianwei Wang, John Z. H. Zhang, Xiao Dong He · 2015 · RSC Advances
4. Rapid Estimation of Relative Protein−Ligand Binding Affinities Using a High-Throughput Version of MM-PBSA
   Scott P. Brown, Steven W. Muchmore · 2007 · Journal of Chemical Information and Modeling
5. Nanoquinacrine induced apoptosis in cervical cancer stem cells through the inhibition of hedgehog-GLI1 cascade: Role of GLI-1
   Anmada Nayak, Shakti Ranjan Satapathy, Dipon Das, Sumit Siddharth, Neha Tripathi, Prasad V. Bharatam, Chanakya Nath Kundu · 2016 · Scientific Reports
6. Fast Pairwise Approximation of Solvent Accessible Surface Area for Implicit Solvent Simulations of Proteins on CPUs and GPUs
   He Huang, Carlos L. Simmerling · 2018 · Journal of Chemical Theory and Computation
7. Binding of BRACO19 to a Telomeric G-Quadruplex DNA Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent
   Babitha Machireddy, Holli-Joi Sullivan, Chun Fu Wu · 2019 · Molecules
8. Insights into the biased activity of dextromethorphan and haloperidol towards SARS-CoV-2 NSP6: in silico binding mechanistic analysis
   Preeti Pandey, Kartikay Prasad, Amresh Prakash, Vijay Kumar · 2020 · Journal of Molecular Medicine
9. Digestive α‐amylases of the flour moth Ephestia kuehniella– adaptation to alkaline environment and plant inhibitors
   Jana Pytelková, Jan Hubert, Martin Lepšı́k, Jan Šobotník, Radek Sindelka E, Iva Krizkova‐Kudlikova, Martin Horn, Michael A. Mares · 2009 · FEBS Journal
10. Solvent Accessible Surface Area-Based Hot-Spot Detection Methods for Protein–Protein and Protein–Nucleic Acid Interfaces
    Cristian Robert Munteanu, António C. Pimenta, Carlos Fernandez-Lozano, André Melo, M. Natália D. S. Cordeiro, Irina Sousa Moreira · 2015 · Journal of Chemical Information and Modeling
11. Accounting for ligand conformational restriction in calculations of protein-ligand binding affinities.
    Cen Gao, Min-Sun Park, H. A. Stern · 2010 · Biophysical Journal
12. Nanoscale Engineering of Designer Cellulosomes
    Melissabye Gunnoo, Pierre‐André Cazade, Albert Galera‐Prat, Michael A. Nash, Mirjam Czjzek, Marek Cieplak, Beatriz Alvarez, Marina Aguilar, Alon Karpol, Hermann E. Gaub et al. · 2016 · Advanced Materials
13. A New Method for Navigating Optimal Direction for Pulling Ligand from Binding Pocket: Application to Ranking Binding Affinity by Steered Molecular Dynamics
    Van‐Quan Vuong, Tin Trung Nguyen, Mai Suan Li · 2015 · Journal of Chemical Information and Modeling
14. Computational chemical biology and drug design: Facilitating protein structure, function, and modulation studies
    Mingyue Zheng, Jihui Zhao, Chen Cui, Zunyun Fu, Xutong Li, Xiaohong Liu, Xiaoyu Ding, Xiaoqin Tan, Fei Li, Xiaomin Luo et al. · 2018 · Medicinal Research Reviews
15. Improving Protein–Peptide Docking Results via Pose-Clustering and Rescoring with a Combined Knowledge-Based and MM–GBSA Scoring Function
    Huanyu Tao, Yanjun Zhang, Sheng‐You Huang · 2020 · Journal of Chemical Information and Modeling
16. A Computational Study of the Open and Closed Forms of the N-Lobe Human Serum Transferrin Apoprotein
    David Rinaldo, Martin J. Field · 2003 · Biophysical Journal
17. Molecular dynamics simulations of the dinuclear zinc‐β‐lactamase from Bacteroides fragilis complexed with imipenem
    Dimas Suárez, Natalia Díaz, Kenneth M. Merz · 2002 · Journal of Computational Chemistry
18. Importance of polar solvation and configurational entropy for design of antiretroviral drugs targeting HIV-1 protease.
    Kar, Parimal, Lipowsky, Reinhard, Knecht, Volker · 2013 · The Journal of Physical Chemistry B
19. Insights into the missing apiosylation step in flavonoid apiosides biosynthesis of Leguminosae plants
    Wang, Hao-Tian, Wang, Zi-Long, Chen, Kuan, Yao, Ming-Ju, Zhang, Meng, Wang, Rong-Shen, Zhang, Jia-He, Ågren, Hans, Li, Fu-Dong, Li, Junhao et al. · 2023 · Nature Communications
20. Amyloid-β peptide structure in aqueous solution varies with fragment size
    Olivia Wise-Scira, Liang Xu, Taizo Kitahara, George L. Perry, Orkid Coskuner‐Weber · 2011 · The Journal of Chemical Physics
21. Structure-Based Function Prediction of Uncharacterized Protein Using Binding Sites Comparison
    Janez Konc, Milan Hodošček, Mitja Ogrizek, Joanna Trykowska Konc, Dušanka Janežič · 2013 · PLoS Computational Biology
22. Absolute binding free energy calculations of sparsomycin analogs to the bacterial ribosome.
    Xiaoxia Ge, B. Roux · 2010 · Journal of Physical Chemistry B
23. Structure-based discovery of the first allosteric inhibitors of cyclin-dependent kinase 2
    Giulio Rastelli, Andrew Anighoro, Martina Chripková, Laura Carrassa, Massimo Broggini · 2014 · Cell Cycle
24. Simulating electrostatic energies in proteins: Perspectives and some recent studies of p K a s, redox, and other crucial functional properties
    Arieh Warshel, Anatoly Dryga · 2011 · Proteins Structure Function and Bioinformatics
25. Design, synthesis, anti-tumor activity, and molecular modeling of quinazoline and pyrido[2,3-d]pyrimidine derivatives targeting epidermal growth factor receptor
    Ju Hou, Shanhe Wan, Guangfa Wang, Tingting Zhang, Zhonghuang Li, Yuanxin Tian, Yonghuan Yu, Xiaoyun Wu, Jiajie Zhang · 2016 · European Journal of Medicinal Chemistry
26. Can We Rely on Computational Predictions To Correctly Identify Ligand Binding Sites on Novel Protein Drug Targets? Assessment of Binding Site Prediction Methods and a Protocol for Validation of Predicted Binding Sites
    Neal K. Broomhead, Mahmoud E. S. Soliman · 2016 · Cell Biochemistry and Biophysics
27. New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein–Protein Interfaces
    Inês C. M. Simões, Inês P. D. Costa, João T. S. Coimbra, Maria João Ramos, Pedro Alexandrino Fernandes · 2016 · Journal of Chemical Information and Modeling
28. In silico identification of potential inhibitors targeting Streptococcus mutans sortase A
    Hao Luo, Danfeng Liang, Minyue Bao, Rong Sun, Yuanyuan Li, Jian-Zong Li, Xin Wang, Kaimin Lu, Jinku Bao · 2017 · International Journal of Oral Science
29. Targeting Tumor Associated Carbonic Anhydrases IX and XII: Highly Isozyme Selective Coumarin and Psoralen Inhibitors
    Claudia Melis, Simona Distinto, Giulia Bianco, Rita Meleddu, Filippo Cottiglia, Benedetta Fois, Domenico Taverna, Rossella Angius, Stefano Alcaro, Francesco Ortuso et al. · 2018 · ACS Medicinal Chemistry Letters
30. Experimentally guided computational antibody affinity maturation with de novo docking, modelling and rational design
    Daniel A. Cannon, Lu Shan, Qun Du, Lena Shirinian, Keith W. Rickert, Kim L. Rosenthal, Martin Korade, Lilian E. van Vlerken-Ysla, Andrew G. Buchanan, Tristan J. Vaughan et al. · 2019 · PLoS Computational Biology
31. Binding of Calcium and Other Metal Ions to the EF-Hand Loops of Calmodulin Studied by Quantum Chemical Calculations and Molecular Dynamics Simulations
    Martin Lepšı́k, Martin J. Field · 2007 · The Journal of Physical Chemistry B
32. (3Z)-3-(2-[4-(aryl)-1,3-thiazol-2-yl]hydrazin-1-ylidene)-2,3-dihydro-1H-indol-2-one derivatives as dual inhibitors of HIV-1 reverse transcriptase
    Rita Meleddu, Simona Distinto, Angela Corona, Giulia Bianco, Valeria Cannas, Francesca Esposito, Anna Artese, Stefano Alcaro, Péter Mátyus, Dóra Bogdán et al. · 2015 · European Journal of Medicinal Chemistry
33. Oxime-based inhibitors of glucose transporter 1 displaying antiproliferative effects in cancer cells
    Tiziano Tuccinardi, Carlotta Granchi, Jessica Iegre, Ilaria Paterni, Simone Bertini, Marco Macchia, Adriano Martinelli, Yanrong Qian, Xiaozhuo Chen, Filippo Minutolo · 2013 · Bioorganic & Medicinal Chemistry Letters
34. Mechanism of Drug Resistance Due to N88S in CRF01_AE HIV-1 Protease, Analyzed by Molecular Dynamics Simulations
    Hirotaka Ode, Shou Matsuyama, Masayuki Hata, Tyuji Hoshino, Junko Kakizawa, Wataru Sugiura · 2007 · Journal of Medicinal Chemistry
35. Effect of the English Familial Disease Mutation (H6R) on the Monomers and Dimers of Aβ40 and Aβ42
    Viet Hoang Man, Phuong Hoang Nguyen, Philippe Derreumaux, Mai Suan Li · 2014 · ACS Chemical Neuroscience
36. Computational inhibitor design against malaria plasmepsins
    Sinisa Bjelic, Martin Nervall, Hugo Gutiérrez‐de‐Terán, Karolina Ersmark, Anders Hallberg, Johan Åqvist · 2007 · Cellular and Molecular Life Sciences
37. γ-Cyclodextrin capped silver nanoparticles for molecular recognition and enhancement of antibacterial activity of chloramphenicol
    Ramesh Gannimani, Muthusamy Ramesh, Sphamandla E. Mtambo, Karen Pillay, Mahmoud E. S. Soliman, Patrick Govender · 2016 · Journal of Inorganic Biochemistry
38. Impact of a pectic polysaccharide on oenin copigmentation mechanism
    Ana Fernandes, Natércia F. Brás, Joana Oliveira, Nuno Filipe da Cruz Batista Mateus, Victor Armando Pereira de Freitas · 2016 · Food Chemistry
39. A Novel Bromodomain Inhibitor Reverses HIV-1 Latency through Specific Binding with BRD4 to Promote Tat and P-TEFb Association
    Huachao Huang, Shuai Liu, Maxime Junior Jean, Sydney Simpson, He Huang, Mark A. Merkley, Tsuyoshi Hayashi, Weili Kong, Irene Rodríguez-Sánchez, Xiaofeng Zhang et al. · 2017 · Frontiers in Microbiology
40. BiPPred: Combined sequence‐ and structure‐based prediction of peptide binding to the Hsp70 chaperone BiP
    Schneider, Markus, Rosam, Mathias, Glaser, Manuel, Patronov, Atanas, Shah, Harpreet, Back, Katrin Christiane, Daake, Marina Angelika, Buchner, Johannes, Antes, Iris · 2016 · Proteins: Structure, Function, and Bioinformatics
41. The Role of Phe82 and Phe351 in Auxin-Induced Substrate Perception by TIR1 Ubiquitin Ligase: A Novel Insight from Molecular Dynamics Simulations
    Ge‐Fei Hao, Guang‐Fu Yang · 2010 · PLoS ONE
42. Reversible Self-Assembly of Nanoprobes in Live Cells for Dynamic Intracellular pH Imaging
    Bo Dong, Shuangli Du, Chunxiao Wang, Haohao Fu, Qiang Li, Nannan Xiao, Jie An Yang, Xue Xue, Wensheng Cai, Dingbin Liu · 2019 · ACS Nano
43. Identification of Potential Inhibitors against Epstein–Barr Virus Nuclear Antigen 1 (EBNA1): An Insight from Docking and Molecular Dynamic Simulations
    Shweta Jakhmola, Nisha Amarnath Jonniya, Md Fulbabu Sk, Annu Rani, Parimal Kar, Hem Chandra Jha · 2021 · ACS Chemical Neuroscience
44. A chimeric peptide promotes immune surveillance of senescent cells in injury, fibrosis, tumorigenesis and aging
    Xinliang Ming, Ze Ran Yang, Yuqiao Huang, Zhiguo Wang, Qingyan Zhang, Changchang Lu, Yandi Sun, Yuanhao Chen, Liang Zhang, Jicheng Wu et al. · 2024 · Nature Aging
45. Novel human mPGES-1 inhibitors identified through structure-based virtual screening
    Adel Hamza, Xinyun Zhao, Min Tong, Hsin‐Hsiung Tai, Chang‐Guo Zhan · 2011 · Bioorganic & Medicinal Chemistry
46. Computational Methods of Studying the Binding of Toxins From Venomous Animals to Biological Ion Channels: Theory and Applications
    Dan Gordon, Rong Chen, Shin‐Ho Chung · 2013 · Physiological Reviews
47. Energetic basis for drug resistance of HIV-1 protease mutants against amprenavir
    Parimal Kar, Volker Knecht · 2012 · Journal of Computer-Aided Molecular Design
48. Importance of protein flexibility in ranking inhibitor affinities: modeling the binding mechanisms of piperidine carboxamides as Type I1/2 ALK inhibitors
    Xiaotian Kong, Peichen Pan, Dan Li, Sheng Tian, Youyong Li, Tingjun Hou · 2015 · Physical Chemistry Chemical Physics
49. Synthesis, biological evaluation and molecular modeling study of 5-trifluoromethyl-Δ2-pyrazoline and isomeric 5/3-trifluoromethylpyrazole derivatives as anti-inflammatory agents
    Ranjana Aggarwal, Anshul Bansal, Isabel Rozas, Brendan Kelly, Pawan Kaushik, Dhirender Kaushik · 2013 · European Journal of Medicinal Chemistry
50. An Efficient Computational Method for Calculating Ligand Binding Affinities
    Atsushi Suenaga, Noriaki Okimoto, Yoshinori Hirano, Kazuhiko Fukui · 2012 · PLoS ONE
51. A Combined Crystallographic and Theoretical Study Explains the Capability of Carboxylic Acids to Adopt Multiple Binding Modes in the Active Site of Carbonic Anhydrases
    Emma Langella, Katia D’Ambrosio, Melissa D’Ascenzio, Simone Carradori, Simona Maria Monti, Claudiu Trandafir Supuran, Giuseppina De Simone · 2015 · Chemistry - A European Journal
52. Exploring the Inhibitory Mechanism of Approved Selective Norepinephrine Reuptake Inhibitors and Reboxetine Enantiomers by Molecular Dynamics Study
    Guoxun Zheng, Weiwei Xue, Panpan Wang, Fengyuan Yang, Bo Li, Xiaofeng Li, Yinghong Li, Xiaojun Yao, Feng Zhu · 2016 · Scientific Reports
53. Insights into the binding interaction of substrate with catechol 2,3-dioxygenase from biophysics point of view
    Xian-Hong Zeng, Huan Du, Hai-Ming Zhao, Lei Xiang, Nai-Xian Feng, Hui Li, Yanwen Li, Quan-Ying Cai, Ce-Hui Mo, Ming Hung Wong et al. · 2020 · Journal of Hazardous Materials
54. Recent advances in computational methods for biosensor design
    Zahra Khoshbin, Mohammad Reza Housaindokht, Mohammad Izadyar, Mohammad Reza Bozorgmehr, Asma Verdian · 2020 · Biotechnology and Bioengineering
55. Native or Non-Native Protein–Protein Docking Models? Molecular Dynamics to the Rescue
    Zuzana Jandová, Attilio Vittorio Vargiu, Alexandre M. J. J. Bonvin · 2021 · Journal of Chemical Theory and Computation
56. A mean field approach for molecular simulations of fluid systems
    Giuseppe Brancato, Alfredo Di Nola, Vincenzo Barone, Andrea Amadei · 2005 · The Journal of Chemical Physics
57. Context contribution to the intermolecular recognition of human ACE2-derived peptides by SARS-CoV-2 spike protein: implications for improving the peptide affinity but not altering the peptide specificity by optimizing indirect readout
    Peng Zhou, Heyi Wang, Zheng Chen, Qian Liu · 2020 · Molecular Omics
58. Computational investigation of natural compounds as potential main protease (Mpro) inhibitors for SARS-CoV-2 virus
    Chirag Patel, Siddhi P. Jani, Sivakumar Prasanth Kumar, Krunal Modi, Yogesh Kumar · 2022 · Computers in Biology and Medicine
59. Structural insights into the mechanism of GTP initiation of microtubule assembly
    Ju Zhou, Anhui Wang, Yin-Long Song, Nan Liu, Jia Wang, Yan Li, Xin Liang, Guohui Li, Huiying Chu, Hongwei Wang · 2023 · Nature Communications
60. Selective and Brain‐Permeable Polo‐like Kinase‐2 (Plk‐2) Inhibitors That Reduce α‐Synuclein Phosphorylation in Rat Brain
    Danielle L. Aubele, Roy K. Hom, Marc Adler, Robert A. Galemmo, Simeon Bowers, Anh P. Truong, Hu Pan, Paul Beroza, R. Jeffrey Neitz, Nanhua Yao et al. · 2013 · ChemMedChem
61. A Refined Model of the HCV NS5A Protein Bound to Daclatasvir Explains Drug-Resistant Mutations and Activity against Divergent Genotypes
    Khaled Barakat, Anwar Anwar‐Mohamed, Jack A. Tuszyński, Morris J. Robins, D. Lorne Tyrrell, Michael Houghton · 2014 · Journal of Chemical Information and Modeling
62. Insights into amprenavir resistance in E35D HIV-1 protease mutation from molecular dynamics and binding free-energy calculations
    Heike Meiselbach, Anselm H. C. Horn, Thomas Harrer, Heinrich Sticht · 2006 · Journal of Molecular Modeling
63. Binding affinities in the SAMPL3 trypsin and host–guest blind tests estimated with the MM/PBSA and LIE methods
    Paulius Mikulskis, Samuel Genheden, Patrik Rydberg, Lars Sandberg, Lars Olsen, Ulf Ryde · 2011 · Journal of Computer-Aided Molecular Design
64. Oligomer Formation of Amyloid-β(29–42) from Its Monomers Using the Hamiltonian Replica-Permutation Molecular Dynamics Simulation
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65. The identification of novel Mycobacterium tuberculosis DHFR inhibitors and the investigation of their binding preferences by using molecular modelling
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66. Accurate Prediction of Complex Structure and Affinity for a Flexible Protein Receptor and Its Inhibitor.
    G. Bekker, N. Kamiya, M. Araki, I. Fukuda, Y. Okuno, Haruki Nakamura · 2017 · Journal of Chemical Theory and Computation
67. Combating Drug-Resistant Mutants of Anaplastic Lymphoma Kinase with Potent and Selective Type-I1/2 Inhibitors by Stabilizing Unique DFG-Shifted Loop Conformation
    Peichen Pan, Huidong Yu, Qinglan Liu, Xiaotian Kong, Hu Chen, Jiean Chen, Qi Liu, Dan Li, Yu Kang, Huiyong Sun et al. · 2017 · ACS Central Science
68. Design, synthesis, biological evaluation and molecular modeling of novel 1H-pyrazolo[3,4-d]pyrimidine derivatives as BRAFV600E and VEGFR-2 dual inhibitors
    Yuanyuan Wang, Shanhe Wan, Zhonghuang Li, Yu Fu, Guangfa Wang, Jiajie Zhang, Xiaoyun Wu · 2018 · European Journal of Medicinal Chemistry
69. Structure-Based Optimization of N-Substituted Oseltamivir Derivatives as Potent Anti-Influenza A Virus Agents with Significantly Improved Potency against Oseltamivir-Resistant N1-H274Y Variant
    Jian Zhang, N. Arul Murugan, Ye Tian, Chiara Bertagnin, Zengjun Fang, Dongwei Kang, Xiujie Kong, Haiyong Jia, Zhuosen Sun, Ruifang Jia et al. · 2018 · Journal of Medicinal Chemistry
70. Conformational preferences of substituted prolines in the collagen triple helix
    Sean David Mooney, Peter A. Kollman, Teri E. Klein · 2002 · Biopolymers
71. An Improved PMF Scoring Function for Universally Predicting the Interactions of a Ligand with Protein, DNA, and RNA
    Xiaoyu Zhao, Xiaofeng Liu, Yuanyuan Wang, Zhi Chen, Ling Kang, Hailei Zhang, Xiaomin Luo, Weiliang Zhu, Kaixian Chen, Honglin Li et al. · 2008 · Journal of Chemical Information and Modeling
72. Importance of individual side chains for the stability of a protein fold: Computational alanine scanning of the insulin monomer
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73. Protein–ligand free energies of binding from full-protein DFT calculations: convergence and choice of exchange–correlation functional
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74. Substrate Promiscuity, Crystal Structure, and Application of a Plant UDP-Glycosyltransferase UGT74AN3
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75. Physical scoring function based on AMBER force field and Poisson–Boltzmann implicit solvent for protein structure prediction
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76. Analysis of the Strength of Interfacial Hydrogen Bonds between Tubulin Dimers Using Quantum Theory of Atoms in Molecules
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77. Discovery of N-benzoxazol-5-yl-pyrazole-4-carboxamides as nanomolar SQR inhibitors
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78. Diarylaniline Derivatives as a Distinct Class of HIV-1 Non-nucleoside Reverse Transcriptase Inhibitors
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79. Lactose binding to human galectin-7 (p53-induced gene 1) induces long-range effects through the protein resulting in increased dimer stability and evidence for positive cooperativity
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80. Molecular Dynamics Simulations of Binding Modes between Methylene Blue and DNA with Alternating GC and AT Sequences
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81. Combination of Repurposed Drug Diosmin with Amoxicillin-Clavulanic acid Causes Synergistic Inhibition of Mycobacterial Growth
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82. Cheminformatics-Based Identification of Potential Novel Anti-SARS-CoV-2 Natural Compounds of African Origin
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83. Binding energy analysis for wild‐type and Y181C mutant HIV‐1 RT/8‐Cl TIBO complex structures: Quantum chemical calculations based on the ONIOM method
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84. Exploring the Anticancer Activity of Tamoxifen-Based Metal Complexes Targeting Mitochondria
    Valeria Scalcon, Riccardo Bonsignore, Jana Aupič, Sophie R. Thomas, Alessandra Folda, Alexandra A. Heidecker, Alexander Pöthig, Alessandra Magistrato, Angela Casini, Maria Pia Rigobello · 2023 · Journal of Medicinal Chemistry
85. Computational Modeling of Structurally Conserved Cancer Mutations in the RET and MET Kinases: The Impact on Protein Structure, Dynamics, and Stability
    Anshuman Dixit, Ali Torkamani, Nicholas J. Schork, Gennady M. Verkhivker · 2009 · Biophysical Journal
86. Biomolecular electrostatics—I want your solvation (model)
    Jaydeep P. Bardhan · 2012 · Computational Science & Discovery
87. Amyloid peptide Aβ40 inhibits aggregation of Aβ42: Evidence from molecular dynamics simulations
    Viet Hoang Man, Mai Suan Li · 2012 · The Journal of Chemical Physics
88. Understanding the molecular basis of MK2–p38α signaling complex assembly: insights into protein–protein interaction by molecular dynamics and free energy studies
    Ying Yang, Huanxiang Liu, Xiaojun Yao · 2012 · Molecular BioSystems
89. Solvent‐accessible surface area: How well can be applied to hot‐spot detection?
    João Miguel da Silva Martins, Rui Miguel Ramos, António C. Pimenta, Irina Sousa Moreira · 2013 · Proteins Structure Function and Bioinformatics
90. Structural characterization of Lyn‐SH3 domain in complex with a herpesviral protein reveals an extended recognition motif that enhances binding affinity
    Finn Bauer, Kristian Schweimer, Heike Meiselbach, Silke Hoffmann, PAUL J. ROSCH, Heinrich Sticht · 2005 · Protein Science
91. Binding free energy based analysis of arsenic (+ 3 oxidation state) methyltransferase with S-adenosylmethionine
    Asma Abro, Syed Sikander Azam · 2016 · Journal of Molecular Liquids
92. Exploring Molecular Mechanisms of Paradoxical Activation in the BRAF Kinase Dimers: Atomistic Simulations of Conformational Dynamics and Modeling of Allosteric Communication Networks and Signaling Pathways
    Amanda Tse, Gennady M. Verkhivker · 2016 · PLoS ONE
93. Spectroscopic profiling (FT-IR, FT-Raman, NMR and UV-Vis), autoxidation mechanism (H-BDE) and molecular docking investigation of 3-(4-chlorophenyl)-N,N-dimethyl-3-pyridin-2-ylpropan-1-amine by DFT/TD-DFT and molecular dynamics: A potential SSRI drug
    Christina Susan Abraham, S. Muthu, Johanan Christian Prasana, Sanja J. Armaković, Stevan Armaković, Fathima Rizwana B, Ben Geoffrey A S · 2018 · Computational Biology and Chemistry
94. Molecular dynamics simulation reveals the possible druggablehot-spotsof USP7
    Mitul Srivastava, Charu Suri, Mrityunjay Singh, Rajani Mathur, Shailendra Asthana · 2018 · Oncotarget
95. Computational Investigation of Structural Dynamics of SARS-CoV-2 Methyltransferase-Stimulatory Factor Heterodimer nsp16/nsp10 Bound to the Cofactor SAM
    Md Fulbabu Sk, Nisha Amarnath Jonniya, Rajarshi Roy, Sayan Poddar, Parimal Kar · 2020 · Frontiers in Molecular Biosciences
96. Dynamics-Based Discovery of Novel, Potent Benzoic Acid Derivatives as Orally Bioavailable Selective Estrogen Receptor Degraders for ERα+ Breast Cancer
    Xiaomeng Zhang, Yazhou Wang, Xue Li, Jie Wu, Liwen Zhao, Wei Li, Jian Liu · 2021 · Journal of Medicinal Chemistry
97. Differential Nucleotide Excision Repair Susceptibility of Bulky DNA Adducts in Different Sequence Contexts: Hierarchies of Recognition Signals
    Yuqin Cai, Dinshaw J. Patel, Nicholas E. Geacintov, Suse B. Broyde · 2008 · Journal of Molecular Biology
98. Novel Mechanism of Interaction of p85 Subunit of Phosphatidylinositol 3-Kinase and ErbB3 Receptor-derived Phosphotyrosyl Peptides
    Atsushi Suenaga, Naoki Takada, Mariko Okada, Mio Ichikawa, Xiaomei Yu, Kentaro Tomii, Noriaki Okimoto, Noriyuki Futatsugi, Tetsu Narumi, Mikako Shirouzu et al. · 2004 · Journal of Biological Chemistry
99. Physics-based methods for studying protein-ligand interactions.
    Niu Huang, Matthew P. Jacobson · 2007 · PubMed
100. A human ether-á-go-go-related (hERG) ion channel atomistic model generated by long supercomputer molecular dynamics simulations and its use in predicting drug cardiotoxicity
     Anwar Anwar‐Mohamed, Khaled Barakat, Rakesh Kumar Bhat, Sergei Yu. Noskov, D. Lorne Tyrrell, Jack A. Tuszyński, Michael Houghton · 2014 · Toxicology Letters