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

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Items 801–900 of 1,010

1. Relating repair susceptibility of carcinogen-damaged DNA with structural distortion and thermodynamic stability
   Min Wu · 2002 · Nucleic Acids Research
2. Guiding graphene derivatization for covalent immobilization of aptamers
   Maxim K. Rabchinskii, Sergei A. Ryzhkov, Nadezhda A. Besedina, Maria M. Brzhezinskaya, Maxim N. Malkov, Dina Yu. Stolyarova, Albert F. Arutyunyan, Nikolai S. Struchkov, Svyatoslav D. Saveliev, Igor D. Diankin et al. · 2022 · Carbon
3. Superimmunity by pan-sarbecovirus nanobodies
   Yufei Xiang, Wei Huang, Hejun Liu, Zhe Sang, Sham Nambulli, Jérôme Tubiana, Kevin L. Williams, William Paul Duprex, Dina Schneidman‐Duhovny, Ian A. Wilson et al. · 2022 · Cell Reports
4. Dissecting the molecular mechanism of cepharanthine against COVID-19, based on a network pharmacology strategy combined with RNA-sequencing analysis, molecular docking, and molecular dynamics simulation
   Jiaqin Liu, Taoli Sun, Sa Liu, Jian Liu, Senbiao Fang, Shengyu Tan, Yucheng Zeng, Bikui Zhang, Wenqun Li · 2022 · Computers in Biology and Medicine
5. The Structures of the E22Δ Mutant-Type Amyloid-β Alloforms and the Impact of E22Δ Mutation on the Structures of the Wild-Type Amyloid-β Alloforms
   Orkid Coskuner‐Weber, Olivia Wise-Scira, George L. Perry, Taizo Kitahara · 2012 · ACS Chemical Neuroscience
6. Origins of Resistance to the HIVgp41 Viral Entry Inhibitor T20
   Brian E. McGillick, Trent E. Balius, Sudipto Mukherjee, Robert C. Rizzo · 2010 · Biochemistry
7. Comparative insights into the saccharification potentials of a relatively unexplored but robust Penicillium funiculosum glycoside hydrolase 7 cellobiohydrolase
   Funso Emmanuel Ogunmolu, Navya Bhatt Kammachi Jagadeesha, Rakesh Kumar, Pawan Kumar, Dinesh Kumar Gupta, Syed Shams Yazdani · 2017 · Biotechnology for Biofuels
8. QTAIM and NCI analysis of intermolecular interactions in steroid ligands binding a cytochrome P450 enzyme – Beyond the most obvious interactions
   Caio Lima Firme, Norberto de Kássio Vieira Monteiro, Sérgio Ruschi Bergamachi Silva · 2017 · Computational and Theoretical Chemistry
9. Tyrosine Regulates β-Sheet Structure Formation in Amyloid-β42: A New Clustering Algorithm for Disordered Proteins
   Orkid Coskuner‐Weber, Vladimir Nikolaevich Uversky · 2017 · Journal of Chemical Information and Modeling
10. Peptide Inhibitors Targeting the Neisseria gonorrhoeae Pivotal Anaerobic Respiration Factor AniA
    Aleksandra E. Sikora, Robert H. Mills, Jacob V. Weber, Adel Hamza, Bryan W. Passow, Andrew Romaine, Zachary A. Williamson, Robert W. Reed, Ryszard A. Zielke, Konstantin V. Korotkov · 2017 · Antimicrobial Agents and Chemotherapy
11. Insights into the inhibitory mechanism of a resveratrol and clioquinol hybrid against Aβ42 aggregation and protofibril destabilization: A molecular dynamics simulation study
    Rajneet Kaur Saini, Suniba Shuaib, Deepti Goyal, Bhupesh Goyal · 2018 · Journal of Biomolecular Structure and Dynamics
12. PD-1-Targeted Discovery of Peptide Inhibitors by Virtual Screening, Molecular Dynamics Simulation, and Surface Plasmon Resonance
    Yuanqiang Wang, Haiqiong Guo, Zhiwei Feng, Siyi Wang, Yuxuan Wang, Qingxiu He, Guangping Li, Zhihua Lin, Xiang‐Qun Xie, Zhihua Lin · 2019 · Molecules
13. Understanding the Pyrimethamine Drug Resistance Mechanism via Combined Molecular Dynamics and Dynamic Residue Network Analysis
    Arnold Amusengeri, Rolland Bantar Tata, Özlem Taştan Bishop · 2020 · Molecules
14. Mechanism of self/nonself-discrimination in Brassica self-incompatibility
    Kohji Murase, Yoshitaka Moriwaki, Tomoyuki Mori, Xiao Liu, Chiho Masaka, Yoshinobu Takada, Ryoko Maesaki, Masaki Mishima, Sota Fujii, Yoshinori Hirano et al. · 2020 · Nature Communications
15. Dietary stigmastane-type saponins as promising dual-target directed inhibitors of SARS-CoV-2 proteases: a structure-based screening
    Oludare Michael Ogunyemi, Gideon Ampoma Gyebi, Ibrahim M. Ibrahim, Charles O. Olaiya, Joshua Omaojo Ocheje, Modupe M. Fabusiwa, Joseph Oluwatope Adebayo · 2021 · RSC Advances
16. Molecular modelling of the FOXO4-TP53 interaction to design senolytic peptides for the elimination of senescent cancer cells
    Hillary H. Le, Süleyman Selim Çınaroğlu, Elise C. Manalo, Aysegul Ors, Michelle M. Gomes, Burcin Duan Sahbaz, Karla Bonic, Carlos A. Origel Marmolejo, Arnaud Quentel, Justin S. Plaut et al. · 2021 · EBioMedicine
17. Recent development of two chitinase inhibitors, Argifin and Argadin, produced by soil microorganisms
    Tomoyasu Hirose, Toshiaki Sunazuka, Satoshi Ōmura · 2010 · Proceedings of the Japan Academy Series B
18. Structures and Free Energy Landscapes of the Wild-Type and A30P Mutant-Type α-Synuclein Proteins with Dynamics
    Olivia Wise-Scira, Ahmet Kemal Aloglu, Aquila Dunn, Isin T. Sakallioglu, Orkid Coskuner‐Weber · 2013 · ACS Chemical Neuroscience
19. Crystal structure of the human TLR2-Diprovocim complex
    H. Zhang, Bruce Beutler, Diana R. Tomchick, Lijing Su · 2018 · Worldwide Protein Data Bank
20. Pharmacophore-Based Screening and Identification of Novel Human Ligase I Inhibitors with Potential Anticancer Activity
    Shagun Krishna, Deependra Kumar Singh, Sanjeev Meena, Dipak B. Datta, Mohammad Imran Siddiqi, Dibyendu Banerjee · 2014 · Journal of Chemical Information and Modeling
21. Reliable molecular simulations of solute-solvent systems with a minimum number of solvent shells
    Giuseppe Brancato, Nadia Rega, Vincenzo Barone · 2006 · The Journal of Chemical Physics
22. Thermochemical Fragment Energy Method for Biomolecules: Application to a Collagen Model Peptide
    Ernesto Suárez, Natalia Díaz, Dimas Suárez · 2009 · Journal of Chemical Theory and Computation
23. Optimized Potential of Mean Force Calculations for Standard Binding Free Energies
    Ignasi Buch, S. Kashif Sadiq, Gianni De Fabritiis · 2011 · Journal of Chemical Theory and Computation
24. RNA pentaloop structures as effective targets of regulators belonging to the RsmA/CsrA protein family
    Karine Lapouge, Remo Perozzo, Justyna Iwaszkiewicz, Claire Bertelli, Vincent Zoete, Olivier Alain Michielin, Léonardo Scapozza, Dieter Haas · 2013 · RNA Biology
25. Stability and bioactivity of thrombin binding aptamers modified with d -/ l -isothymidine in the loop regions
    Baobin Cai, Xiantao Yang, Lidan Sun, Xinmeng Fan, Liyu Li, Hongwei Jin, Yun Wu, Zhu Guan, Liangren Zhang, Lihe Zhang et al. · 2014 · Organic & Biomolecular Chemistry
26. Understanding the Basis of Drug Resistance of the Mutants of αβ-Tubulin Dimer via Molecular Dynamics Simulations
    Kathiresan Natarajan, Sanjib Senapati · 2012 · PLoS ONE
27. Active-State Models of Ternary GPCR Complexes: Determinants of Selective Receptor-G-Protein Coupling
    Ralf Christian Kling, Harald Lanig, Timothy Clark, Peter Gmeiner · 2013 · PLoS ONE
28. Computational and statistical study on the molecular interaction between antigen and antibody
    Tomonori Osajima, Masaaki Suzuki, Saburo Neya, Tyuji Hoshino · 2014 · Journal of Molecular Graphics and Modelling
29. Antimycobacterial activity of new 3,5-disubstituted 1,3,4-oxadiazol-2(3H)-one derivatives. Molecular modeling investigations
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30. Different Molecular Mechanisms of Inhibition of Bovine Viral Diarrhea Virus and Hepatitis C Virus RNA-Dependent RNA Polymerases by a Novel Benzimidazole
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31. Two novel antimicrobial defensins from rice identified by gene coexpression network analyses
    Supaluk Tantong, Onanong Pringsulaka, Kamonwan Weerawanich, Arthitaya Meeprasert, Thanyada Rungrotmongkol, Rakrudee Sarnthima, Sittiruk Roytrakul, Supaart Sirikantaramas · 2016 · Peptides
32. Anti-arrhythmic Medication Propafenone a Potential Drug for Alzheimer’s Disease Inhibiting Aggregation of Aβ: In Silico and in Vitro Studies
    Sơn Tùng Ngô, Shang-Ting Fang, Shu-Hsiang Huang, Chao‐Liang Chou, Pham Dinh Quoc Huy, Mai Suan Li, Yi-Cheng Chen · 2016 · Journal of Chemical Information and Modeling
33. What a Difference a Methyl Group Makes: The Selectivity of Monoamine Oxidase B Towards Histamine and N‐Methylhistamine
    Aleksandra Maršavelski, Robert Vianello · 2017 · Chemistry - A European Journal
34. Chemical affinity of 10-methacryloyloxydecyl dihydrogen phosphate to dental zirconia: Effects of molecular structure and solvents
    Ying Chen, Zhicen Lu, Mengke Qian, Huaiqin Zhang, Chen Chen, Haifeng Xie, Franklin R. Tay · 2017 · Dental Materials
35. PLVAP and GKN3 Are Two Critical Host Cell Receptors Which Facilitate Japanese Encephalitis Virus Entry Into Neurons
    Sriparna Mukherjee, Nabonita Sengupta, Ankur Chaudhuri, Irshad Akbar, Noopur Singh, Sibani Sen Chakraborty, Amol Ratnakar Suryawanshi, Arindam Bhattacharyya, Anirban Basu · 2018 · Scientific Reports
36. Oversampling Free Energy Perturbation Simulation in Determination of the Ligand‐Binding Free Energy
    Sơn Tùng Ngô, Trung Hai Nguyen, Nguyễn Thanh Tùng, Pham Cam Nam, Khanh Bao Vu, Van V. Vu · 2019 · Journal of Computational Chemistry
37. Anti-HIV potential of diarylpyrimidine derivatives as non-nucleoside reverse transcriptase inhibitors: design, synthesis, docking, TOPKAT analysis and molecular dynamics simulations
    Vishal Kumar Singh, Ritika Srivastava, Parth Sarthi Sen Gupta, Farha Naaz, Himani Chaurasia, Richa Mishra, Malay Kumar Rana, Ramendra Kumar Singh · 2020 · Journal of Biomolecular Structure and Dynamics
38. Identifying structural–functional analogue of GRL0617, the only well-established inhibitor for papain-like protease (PLpro) of SARS-CoV2 from the pool of fungal metabolites using docking and molecular dynamics simulation
    Priyashi Rao, Rohit Patel, Arpit Shukla, Paritosh Parmar, Rakesh Rawal, Meenu S Saraf, Dweipayan Goswami · 2021 · Molecular Diversity
39. The similarity of class II HLA genotypes defines patterns of autoreactivity in idiopathic bone marrow failure disorders
    Simona Pagliuca, Carmelo Gurnari, Hassan K. Awada, Ashwin Kishtagari, Sunisa Kongkiatkamon, Laila Terkawi, Misam Zawit, Yihong Guan, Thomas LaFramboise, Babal Kant Jha et al. · 2021 · Blood
40. Mechanisms of distinctive mismatch tolerance between Rad51 and Dmc1 in homologous recombination
    Jingfei Xu, Lingyun Zhao, Sijia Peng, Huiying Chu, Rui Liang, Meng Tian, Philip P. Connell, Guohui Li, Chunlai Chen, Hongwei Wang · 2021 · Nucleic Acids Research
41. Affinity and Specificity of Protein U1A-RNA Complex Formation Based on an Additive Component Free Energy Model
    Bethany L. Kormos, Yulia Benitex, Anne M. Baranger, David L. Beveridge · 2007 · Journal of Molecular Biology
42. Computational study of bindings of olive leaf extract (OLE) to HIV‐1 fusion protein gp41
    J. Bao, D.W. Zhang, J.Z.H. Zhang, P. Lee Huang, P. Lin Huang, Sylvia Lee‐Huang · 2007 · FEBS Letters
43. 3-Aryl-2-[1H-benzotriazol-1-yl]acrylonitriles: A novel class of potent tubulin inhibitors
    Antonio Carta, Irene Briguglio, Sandra Piras, Gianpiero Boatto, Paolo La Colla, Roberta Loddo, Manlio Tolomeo, Stefania Grimaudo, Antonietta Di Cristina, Rosaria Maria Pipitone et al. · 2011 · European Journal of Medicinal Chemistry
44. Synthesis and biological evaluation of phenolic 4,5-dihydroisoxazoles and 3-hydroxy ketones as estrogen receptor α and β agonists
    Pekka Poutiainen, Tuomas Venäläinen, Mikael Peräkylä, Juha M. Matilainen, Sami Vaïsänen, Paavo Honkakoski, Reino Laatikainen, Juha T. Pulkkinen · 2010 · Bioorganic & Medicinal Chemistry
45. Study of Tamiflu Sensitivity to Variants of A/H5N1 Virus Using Different Force Fields
    Trang Truc Nguyen, Binh Khanh Mai, Mai Suan Li · 2011 · Journal of Chemical Information and Modeling
46. Overcoming the Inadequacies or Limitations of Experimental Structures as Drug Targets by Using Computational Modeling Tools and Molecular Dynamics Simulations
    Esther Marco, Federico Gago · 2007 · ChemMedChem
47. New Insights into the Structures of Ligand−Quadruplex Complexes from Molecular Dynamics Simulations
    Jinqiang Hou, Shuo-Bin Chen, Jia‐Heng Tan, Tian‐Miao Ou, Hai‐Bin Luo, Ding Li, Jun Xu, Lian‐Quan Gu, Zhi‐Shu Huang · 2010 · The Journal of Physical Chemistry B
48. Application of MM/PBSA colony free energy to loop decoy discrimination: Toward correlation between energy and root mean square deviation
    Federico Fogolari, Silvio C. E. Tosatto · 2005 · Protein Science
49. From structure to chemical shift and vice-versa
    Christopher A. Hunter, Martin J. Packer, Cristiano Zonta · 2005 · Progress in Nuclear Magnetic Resonance Spectroscopy
50. The Vitamin D Receptor as a Potential Target for the Toxic Effects of Per- and Polyfluoroalkyl Substances (Pfass)
    Ettayapuram Ramaprasad Azhagiya Singam, Kathleen A. Durkin, Michele Andrea La Merrill, J. David Furlow, Jen-Chywan Wang, Martyn T. Smith · 2022 · Environmental Research
51. Computing the relative binding affinity of ligands based on a pairwise binding comparison network
    Jie Yu, Zhaojun Steven Li, Geng Chen, Xiangtai Kong, Jie Hu, Dingyan Wang, Duanhua Cao, Yanbei Li, Ruifeng Huo, Gang Wang et al. · 2023 · Nature Computational Science
52. Structure-based Design of Peptides with High Affinity and Specificity to HER2 Positive Tumors
    Lingling Geng, Zihua Wang, Xiaoliang Yang, Dan Li, Wenxi Lian, Zhichu Xiang, Weizhi Wang, Xiangli Bu, Wenjia Lai, Zhiyuan Hu et al. · 2015 · Theranostics
53. Characterization of an inhibitory dynamic pharmacophore for the ERCC1–XPA interaction using a combined molecular dynamics and virtual screening approach
    Khaled Barakat, J. Torin Huzil, Tyler Luchko, Lars Petter Jordheim, Charles Dumontet, Jack A. Tuszyński · 2009 · Journal of Molecular Graphics and Modelling
54. Insights into Ligand Selectivity in Estrogen Receptor Isoforms: Molecular Dynamics Simulations and Binding Free Energy Calculations
    Juan Zeng, Weihua Li, Yaxue Zhao, Guixia Liu, Yun Tang, Hualiang Jiang · 2008 · The Journal of Physical Chemistry B
55. Structures and free energy landscapes of aqueous zinc(II)-bound amyloid-β(1–40) and zinc(II)-bound amyloid-β(1–42) with dynamics
    Olivia Wise-Scira, Liang Xu, George L. Perry, Orkid Coskuner‐Weber · 2012 · JBIC Journal of Biological Inorganic Chemistry
56. Computational Studies of the Regioselectivities of COMT-CatalyzedMeta-/Para-O Methylations of Luteolin and Quercetin
    Yang Cao, Zhongjian Chen, Huidi Jiang, Jianzhong Chen · 2013 · The Journal of Physical Chemistry B
57. Including Explicit Water Molecules as Part of the Protein Structure in MM/PBSA Calculations
    Yongliang Zhu, Paul Beroza, Dean R. Artis · 2013 · Journal of Chemical Information and Modeling
58. Binding of pyrazole-based inhibitors to Mycobacterium tuberculosis pantothenate synthetase: docking and MM-GB(PB)SA analysis
    Fidele Ntie‐Kang, Srinivasaraghavan Kannan, Kanin Wichapong, L. C. Owono Owono, Wolfgang Sippl, Eugène Megnassan · 2013 · Molecular BioSystems
59. General van der Waals potential for common organic molecules
    Rui Qi, Qiantao Wang, Pengyu Y. Ren · 2016 · Bioorganic & Medicinal Chemistry
60. Molecular Dynamics Studies on the Enzalutamide Resistance Mechanisms Induced by Androgen Receptor Mutations
    Hongli Liu, Lingyan Wang, Jiaqi Tian, Jiazhong Li, Huanxiang Liu · 2017 · Journal of Cellular Biochemistry
61. Lumican Peptides: Rational Design Targeting ALK5/TGFBRI
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62. Synthesis, antiviral evaluation and molecular docking studies of N4-aryl substituted/unsubstituted thiosemicarbazones derived from 1-indanones as potent anti-bovine viral diarrhea virus agents
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63. A molecular dynamics investigation into the mechanisms of alectinib resistance of three ALK mutants
    Muyang He, Weikang Li, Qing‐Chuan Zheng, Hong‐Xing Zhang · 2018 · Journal of Cellular Biochemistry
64. PD-L1 Nanobody Competitively Inhibits the Formation of the PD-1/PD-L1 Complex: Comparative Molecular Dynamics Simulations
    Xin Sun, Xiao Hong Yan, Wei Zhuo, Jinke Gu, Ke Zuo, Wei Liu, Li Liang, Ya Gan, Gang He, Hua Wan et al. · 2018 · International Journal of Molecular Sciences
65. Binding of Telomestatin, TMPyP4, BSU6037, and BRACO19 to a Telomeric G-Quadruplex–Duplex Hybrid Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent
    Holli-Joi Sullivan, Carolyn Readmond, Christina Radicella, Victoria Persad, Thomas J. Fasano, Chun Wu · 2018 · ACS Omega
66. Probing the Structural and Energetic Basis of Kinesin–Microtubule Binding Using Computational Alanine-Scanning Mutagenesis
    Minghui Li, Wenjun Zheng · 2011 · Biochemistry
67. Investigating the binding affinity, interaction, and structure-activity-relationship of 76 prescription antiviral drugs targeting RdRp and Mpro of SARS-CoV-2
    Sinthyia Ahmed, Rumana Mahtarin, Sayeda Samina Ahmed, Shaila Akter, Md. Shamiul Islam, Abdulla Al Mamun, Rajib Islam, Md Nayeem Hossain, Muhammad Ali, Mossammad Umme Chand Sultana et al. · 2020 · Journal of Biomolecular Structure and Dynamics
68. Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population
    Yudibeth Sixto‐López, José Correa‐Basurto, Martiniano Bello, Bruno Landeros‐Rivera, José Antonio Garzón Tiznado, Sarita Montaño · 2021 · Scientific Reports
69. Relaxed complex scheme suggests novel inhibitors for the lyase activity of DNA polymerase beta
    Khaled Barakat, Jack A. Tuszyński · 2010 · Journal of Molecular Graphics and Modelling
70. Modulation of the p53-MDM2 Interaction by Phosphorylation of Thr18: A Computational Study
    Hui Jun Lee, Deepa Srinivasan, David Coomber, David Philip Lane, Chandra Shekhar Verma · 2007 · Cell Cycle
71. Theoretical Study of a New DNA Structure: The Antiparallel Hoogsteen Duplex
    Elena Cubero, Nicola G. A. Abrescia, Juan A. Subirana, Francisco Javier Luque, Modesto Orozco · 2003 · Journal of the American Chemical Society
72. Structural insights by molecular dynamics simulations into specificity of the major human AP endonuclease toward the benzene-derived DNA adduct, pBQ-C
    Anton B. Guliaev · 2004 · Nucleic Acids Research
73. Design, asymmetric synthesis, and evaluation of pseudosymmetric sulfoximine inhibitors against HIV-1 protease
    Lu Ding, Yuk Yin Sham, Robert Vince · 2010 · Bioorganic & Medicinal Chemistry
74. Homology Modeling of NR2B Modulatory Domain of NMDA Receptor and Analysis of Ifenprodil Binding
    Luciana Marinelli, Sandro Cosconati, Thomas B. Steinbrecher, Vittorio Limongelli, Alessia Bertamino, Ettore Novellino, David Andrew Case · 2007 · ChemMedChem
75. Design of protein-ligand binding based on the molecular-mechanics energy model.
    F. Boas, P. Harbury · 2008 · Journal of Molecular Biology
76. Exploring the Interaction of N/S Compounds with a Dicopper Center: Tyrosinase Inhibition and Model Studies
    Elina Buitrago, Alexandra Vuillamy, Ahcène Boumendjel, Wei Yi, Gisèle Gellon, Renaud Hardré, Christian Philouze, Guy Serratrice, Hélène Jamet, Marius Réglier et al. · 2014 · Inorganic Chemistry
77. Comparative molecular dynamics simulations of HIV‐1 integrase and the T66I/M154I mutant: Binding modes and drug resistance to a diketo acid inhibitor
    Alessandro Brigo, Keun Woo Lee, Federico Fogolari, Gabriela Iurcu Mustata, James M. Briggs · 2005 · Proteins Structure Function and Bioinformatics
78. Evading the proofreading machinery of a replicative DNA polymerase: induction of a mutation by an environmental carcinogen
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79. Gain-of-Function SHP2 E76Q Mutant Rescuing Autoinhibition Mechanism Associated with Juvenile Myelomonocytic Leukemia
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80. Phloretin and phlorizin mitigates inflammatory stress and alleviate adipose and hepatic insulin resistance by abrogating PPARγ S273-Cdk5 interaction in type 2 diabetic mice
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81. Structural Insight into the Role of Thrombospondin-1 Binding to Calreticulin in Calreticulin-Induced Focal Adhesion Disassembly
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82. Mutation-Induced Loop Opening and Energetics for Binding of Tamiflu to Influenza N8 Neuraminidase
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83. Why OppA protein can bind sequence-independent peptides? A combination of QM/MM, PB/SA, and structure-based QSAR analyses
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84. A Biophysical Study with Carbohydrate Derivatives Explains the Molecular Basis of Monosaccharide Selectivity of the Pseudomonas aeruginosa Lectin LecB
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85. A systematic profile of clinical inhibitors responsive to EGFR somatic amino acid mutations in lung cancer: implication for the molecular mechanism of drug resistance and sensitivity
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86. Importance of Polar Solvation for Cross-Reactivity of Antibody and Its Variants with Steroids
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87. Theoretical Studies on Inclusion Complexes of Cyclodextrins
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88. Ferric uptake regulator protein: Binding free energy calculations and per‐residue free energy decomposition
    Rafi Ahmad, Bjørn Olav Brandsdal, Isabelle Michaud‐Soret, Nils Peder Willassen · 2008 · Proteins Structure Function and Bioinformatics
89. An optimized MM/PBSA virtual screening approach applied to an HIV‐1 gp41 fusion peptide inhibitor
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90. Thermodynamics of Binding Between Proteins and Carbon Nanoparticles: The Case of C60@Lysozyme
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91. In silico study on anti-Chikungunya virus activity of hesperetin
    Adrian Oo, Pouya Hassandarvish, Sek Peng Chin, Vannajan Sanghiran Lee, Sazaly AbuBakar, Keivan Zandi · 2016 · PeerJ
92. SAT2 Foot-and-Mouth Disease Virus Structurally Modified for Increased Thermostability
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93. Discovery of High Affinity Receptors for Dityrosine through Inverse Virtual Screening and Docking and Molecular Dynamics
    Fangfang Wang, Wei Yang, Xiaojun Hu · 2018 · International Journal of Molecular Sciences
94. Alanine Scanning Effects on the Biochemical and Biophysical Properties of Intrinsically Disordered Proteins: A Case Study of the Histidine to Alanine Mutations in Amyloid-β 42
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95. An in-silico study on selected organosulfur compounds as potential drugs for SARS-CoV-2 infection via binding multiple drug targets
    Liya Thurakkal, Satyam Kumar Singh, Rajarshi Roy, Parimal Kar, Sushabhan Sadhukhan, Mintu Porel · 2020 · Chemical Physics Letters
96. Allosteric mechanism for KCNE1 modulation of KCNQ1 potassium channel activation
    Georg Kuenze, Carlos G. Vanoye, Reshma R. Desai, Sneha Adusumilli, Kathryn R. Brewer, Hope Woods, Eli Fritz McDonald, Charles R. Sanders, Alfred L. George, Jens Meiler · 2020 · eLife
97. Purple passion fruit seeds (Passiflora edulis f. edulis Sims) as a promising source of skin anti-aging agents: Enzymatic, antioxidant and multi-level computational studies
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98. MMPBSA Decomposition of the Binding Energy throughout a Molecular Dynamics Simulation of Amyloid-Beta (Aß10−35) Aggregation
    Josep M. Campanera, R. Pouplana · 2010 · Molecules
99. Conformational flexibility of N-glycans in solution studied by REMD simulations
    Suyong Re, Wataru Nishima, Naoyuki Miyashita, Yuji Sugita · 2012 · Biophysical Reviews
100. Role of Water Molecules in Structure and Energetics of Pseudomonas aeruginosa Lectin I Interacting with Disaccharides
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