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

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Items 901–1,000 of 1,010

1. Atomic decomposition of the protein solvation free energy and its application to amyloid-beta protein in water
   Song‐Ho Chong, Sihyun Ham · 2011 · The Journal of Chemical Physics
2. Relative free energy of binding and binding mode calculations of HIV‐1 RT inhibitors based on dock‐MM‐PB/GS
   Zhigang Zhou, Jeffry D. Madura · 2004 · Proteins Structure Function and Bioinformatics
3. Molecular Basis of Bcl-XL-p53 Interaction: Insights from Molecular Dynamics Simulations
   Nagakumar Bharatham, Seung‐Wook Chi, Ho Sup Yoon · 2011 · PLoS ONE
4. An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN Internal Loops Studied by Molecular Dynamics Methods.
   Kamila Réblová, Zora Střelcová, Petr Kulhánek, Ivana Beššeová, David H. Mathews, Keith P. Van Nostrand, Ilyas Yildirim, Douglas H. Turner, Jiřı́ Šponer · 2010 · PubMed
5. Fast and reliable prediction of domain–peptide binding affinity using coarse-grained structure models
   Feifei Tian, Rui Tan, Tailin Guo, Peng Zhou, Yang Li · 2013 · Biosystems
6. Entropy in bimolecular simulations: A comprehensive review of atomic fluctuations-based methods
   Summer M Kassem, Marawan Ahmed, Salah El-Sheikh, Khaled Barakat · 2015 · Journal of Molecular Graphics and Modelling
7. Application of a novel in silico high-throughput screen to identify selective inhibitors for protein–protein interactions
   Catherine Joce, Joshua A. Stahl, Mitesh Shridhar, Mark Rowland Hutchinson, Linda R. Watkins, Peter O. Fedichev, Hang Hubert Yin · 2010 · Bioorganic & Medicinal Chemistry Letters
8. Structure-Based Design of Short Peptide Ligands Binding onto the E. coli Processivity Ring
   Philippe Wolff, Vincent Oliéric, Jean Paul Briand, Olivier Chaloin, Annick P. Dejaegere, Philippe Dumas, Eric Ennifar, Gilles Guichard, Jérôme E. Wagner, Dominique Burnouf · 2011 · Journal of Medicinal Chemistry
9. Targeting Promoter G‐Quadruplex DNAs by Indenopyrimidine‐Based Ligands
   K. V. Diveshkumar, Saaz Sakrikar, S. Harikrishna, V. Dhamodharan, Pushpangadan Indira Pradeepkumar · 2014 · ChemMedChem
10. Bioassay-guided identification of an anti-inflammatory prenylated acylphloroglucinol from Melicope ptelefolia and molecular insights into its interaction with 5-lipoxygenase
    Khozirah Shaari, Velan Suppaiah, Lam Kok Wai, Johnson Stanslas, Bimo Ario Tejo, Daud Ahmad Israf, Faridah Abas, Intan Safinar Ismail, Nor Hasifi Shuaib, Seema Zareen et al. · 2011 · Bioorganic & Medicinal Chemistry
11. Rational design of biaryl pharmacophore inserted noscapine derivatives as potent tubulin binding anticancer agents
    Seneha Santoshi, Naresh Kumar Manchukonda, Charu Suri, Manya Sharma, Balasubramanian Sridhar, Silja Joseph, Manu Lopus, Srinivas Kantevari, Iswar Baitharu, Pradeep Kumar Naik · 2014 · Journal of Computer-Aided Molecular Design
12. The binding mechanism, multiple binding modes, and allosteric regulation of Staphylococcus aureus Sortase A probed by molecular dynamics simulations
    Kalli Kappel, Jeff Wereszczynski, Robert Clubb, James Andrew McCammon · 2012 · Protein Science
13. Improving the Scoring of Protein–Ligand Binding Affinity by Including the Effects of Structural Water and Electronic Polarization
    Jinfeng Liu, Xiao Dong He, John Z. H. Zhang · 2013 · Journal of Chemical Information and Modeling
14. Targeting Truncated Retinoid X Receptor-α by CF31 Induces TNF-α–Dependent Apoptosis
    Guanghui Wang, Fuquan Jiang, Yinghui Duan, Zhiping Zeng, Fan Chen, Yi Dai, Jiebo Chen, Jin‐Xing Liu, Jie Liu, Hu Zhou et al. · 2012 · Cancer Research
15. Computational Alanine Scanning Mutagenesis—An Improved Methodological Approach for Protein–DNA Complexes
    Rui Miguel Ramos, Irina Sousa Moreira · 2013 · Journal of Chemical Theory and Computation
16. Differential regulation of baicalin and scutellarin on AMPK and Akt in promoting adipose cell glucose disposal
    Lele Yang, Na Xiao, Jinfeng Liu, Kang Liu, Baolin Liu, Ping Li, Lian‐Wen Qi · 2016 · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease
17. Molecular dynamics and MM/GBSA-integrated protocol probing the correlation between biological activities and binding free energies of HIV-1 TAR RNA inhibitors
    Saikiran Reddy Peddi, Sree Kanth Sivan, Vijjulatha Manga · 2017 · Journal of Biomolecular Structure and Dynamics
18. Molecular dynamics simulation, binding free energy calculation and unbinding pathway analysis on selectivity difference between FKBP51 and FKBP52: Insight into the molecular mechanism of isoform selectivity
    Danfeng Shi, Qifeng Bai, Shuangyan Zhou, Xue‐Wei Liu, Huanxiang Liu, Xiaojun Yao · 2017 · Proteins Structure Function and Bioinformatics
19. Novel Consensus Docking Strategy to Improve Ligand Pose Prediction
    Xiaodong Ren, Yu-Sheng Shi, Yan Zhang, Bin Liu, Li-Hong Zhang, Yu-Bo Peng, Rui Zeng · 2018 · Journal of Chemical Information and Modeling
20. Molecular Dynamics Simulation reveals the mechanism by which the Influenza Cap-dependent Endonuclease acquires resistance against Baloxavir marboxil
    Ryunosuke Yoshino, Nobuaki Yasuo, Masakazu Sekijima · 2019 · Scientific Reports
21. Exploring the potency of currently used drugs against HIV-1 protease of subtype D variant by using multiscale simulations
    Md Fulbabu Sk, Rajarshi Roy, Parimal Kar · 2020 · Journal of Biomolecular Structure and Dynamics
22. Discovery of novel dual adenosine A1/A2A receptor antagonists using deep learning, pharmacophore modeling and molecular docking
    Mukuo Wang, Shujing Hou, Yu Wei, Dongmei Li, Jianping Lin · 2021 · PLoS Computational Biology
23. Advances in Implicit Models of Water Solvent to Compute Conformational Free Energy and Molecular Dynamics of Proteins at Constant pH
    Yury N. Vorobjev · 2011 · Advances in protein chemistry and structural biology
24. Conformational Transitions in RNA Single Uridine and Adenosine Bulge Structures: A Molecular Dynamics Free Energy Simulation Study
    André Barthel, Martin Zacharias · 2006 · Biophysical Journal
25. Key Amino Acid Associated with Acephate Detoxification by Cydia pomonella Carboxylesterase Based on Molecular Dynamics with Alanine Scanning and Site-Directed Mutagenesis
    Xue Yang, Ji Yuan Liu, Xian Chun Li, Mao Hua Chen, Ya Lin Zhang · 2014 · Journal of Chemical Information and Modeling
26. Antiviral Activity of (+)-Rutamarin against Kaposi's Sarcoma-Associated Herpesvirus by Inhibition of the Catalytic Activity of Human Topoisomerase II
    Bo Xu, Ling Wang, Lorenzo González-Molleda, Yan Wang, Jun Xu, Yan Yuan · 2013 · Antimicrobial Agents and Chemotherapy
27. Molecular Mechanism of the Effects of Salt and pH on the Affinity 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
28. Reduction Potentials and Acidity Constants of Mn Superoxide Dismutase Calculated by QM/MM Free‐Energy Methods
    Jimmy Heimdal, Markus Kaukonen, Martin Srnec, Lubomı́r Rulı́šek, Ulf Ryde · 2011 · ChemPhysChem
29. Computational Approaches to Model Ligand Selectivity in Drug Design
    Angel Ortiz, Paulino Gómez‐Puertas, Alejandra Leo‐Macías, Pedro López‐Romero, Eduardo López‐Viñas, Antonio Morreale, Marta Murcia, Kun Wang · 2005 · Current Topics in Medicinal Chemistry
30. Theoretical Studies on the Mechanism of Thioesterase-Catalyzed Macrocyclization in Erythromycin Biosynthesis
    Xiong-Ping Chen, Ting Shi, Xiaolei Wang, Jitao Wang, Qihua Chen, Linquan Bai, Yi‐Lei Zhao · 2016 · ACS Catalysis
31. Molecular Dynamics, Free Energy, and SPR Analyses of the Interactions between the SH2 Domain of Grb2 and ErbB Phosphotyrosyl Peptides
    Atsushi Suenaga, Mio Ichikawa, Mariko Okada, Xiaomei Yu, Noriyuki Futatsugi, Tetsu Narumi, Kazuhiko Fukui, Takaho Terada, Makoto Taiji, Mikako Shirouzu et al. · 2003 · Biochemistry
32. Structure of human NaV1.6 channel reveals Na+ selectivity and pore blockade by 4,9-anhydro-tetrodotoxin
    Yue Li, Tian Yuan, Bo Huang, Feng Zhou, Chao Peng, Xiaojing Li, Yunlong Qiu, Bei Yang, Yan Zhao, Zhuo Huang et al. · 2023 · Nature Communications
33. Ligand and structure-based virtual screening approaches in drug discovery: minireview
    Matheus Nunes da Rocha, Damião Sampaio de Sousa, Francisco Rogênio da Silva Mendes, Hélcio Silva dos Santos, Gabrielle Silva Marinho, Márcia Machado Marinho, Emmanuel Silva Marinho · 2024 · Molecular Diversity
34. Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution
    Amanda Tse, Gennady M. Verkhivker · 2015 · PLoS ONE
35. Understanding the drug resistance mechanism of hepatitis C virus NS3/4A to ITMN-191 due to R155K, A156V, D168A/E mutations: A computational study
    Dabo Pan, Weiwei Xue, Wenqi Zhang, Huanxiang Liu, Xiaojun Yao · 2012 · Biochimica et Biophysica Acta (BBA) - General Subjects
36. A QM/MM study of the binding of RAPTA ligands to cathepsin B
    Antonella Ciancetta, Samuel Genheden, Ulf Ryde · 2011 · Journal of Computer-Aided Molecular Design
37. Fluorescence Detection of KRAS2 mRNA Hybridization in Lung Cancer Cells with PNA-Peptides Containing an Internal Thiazole Orange
    Mahesh V. Sonar, Matthew E. Wampole, Yuanyuan Jin, Chang-Po Chen, Mathew L. Thakur, Eric Wickstrom · 2014 · Bioconjugate Chemistry
38. Unravelling Hot Spots: a comprehensive computational mutagenesis study
    Irina Sousa Moreira, Pedro Alexandrino Fernandes, Maria João Ramos · 2006 · Theoretical Chemistry Accounts
39. Molecular Determinants of Bim(BH3) Peptide Binding to Pro-Survival Proteins
    Laura Delgado-Soler, Marta Pinto, Kaori Tanaka-Gil, J. Rubio · 2012 · Journal of Chemical Information and Modeling
40. Understanding microscopic binding of macrophage migration inhibitory factor with phenolic hydrazones by molecular docking, molecular dynamics simulations and free energy calculations
    Lei Xu, Youyong Li, Lin Li, Shunye Zhou, Tingjun Hou · 2012 · Molecular BioSystems
41. Molecular dynamic simulation of wild type and mutants of the polymorphic amyloid NNQNTF segments of elk prion: Structural stability and thermodynamic of association
    Workalemahu Mikre Berhanu, Artëm E. Masunov · 2011 · Biopolymers
42. Protein Interface Pharmacophore Mapping Tools for Small Molecule Protein: Protein Interaction Inhibitor Discovery
    Arnout R. D. Voet, Eleanor F. Banwell, Kamlesh Kumar Sahu, Jonathan G. Heddle, Kam Y. J. Zhang · 2013 · Current Topics in Medicinal Chemistry
43. FabSim: Facilitating computational research through automation on large-scale and distributed e-infrastructures
    Derek Groen, Agastya P. Bhati, James L. Suter, James Hetherington, Stefan J. Zasada, Peter V. Coveney · 2016 · Computer Physics Communications
44. In Silicoandin VitroStudy of Binding Affinity of Tripeptides to Amyloid β Fibrils: Implications for Alzheimer’s Disease
    Viet Hoang Man, Katarína Šipošová, Zuzana Bednáriková, Andrea Antošová, Truc Trang Nguyen, Zuzana Gažová, Mai Suan Li · 2015 · The Journal of Physical Chemistry B
45. Modeling Membrane Protein–Ligand Binding Interactions: The Human Purinergic Platelet Receptor
    D’Artagnan Greene, Wesley M. Botello‐Smith, Alec H. Follmer, Li Xiao, Eleftherios Lambros, Ray Luo · 2016 · The Journal of Physical Chemistry B
46. Replica exchange molecular dynamics study of the truncated amyloid beta (11–40) trimer in solution
    Sơn Tùng Ngô, Huynh Minh Hung, Duc Toan Truong, Minh Tho Nguyen · 2016 · Physical Chemistry Chemical Physics
47. Molecular Dynamics Simulation of a RNA Aptasensor
    Min Ruan, Mahamadou Seydou, Vincent Noël, Benoı̂t Piro, François Maurel, Florent Barbault · 2017 · The Journal of Physical Chemistry B
48. Molecular docking, molecular dynamics and MM/PBSA studies of FDA approved drugs for protein kinase a of Mycobacterium tuberculosis; application insights of drug repurposing
    Shobana Sundar, Lokesh Thangamani, Gowdham Manivel, Praveen Kumar, Shanmughavel Piramanayagam · 2019 · Informatics in Medicine Unlocked
49. Harmicines − harmine and cinnamic acid hybrids as novel antiplasmodial hits
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50. Predicting and designing therapeutics against the Nipah virus
    Neeladri Sen, Tejashree Rajaram Kanitkar, Ankit Roy, Neelesh Soni, Kaustubh Amritkar, Shreyas Supekar, Sanjana Anilkumar Nair, Gulzar Singh, Mallur Srivatsan Madhusudhan · 2019 · PLoS neglected tropical diseases
51. Cryptic Sites in Tau Fibrils Explain the Preferential Binding of the AV-1451 PET Tracer toward Alzheimer’s Tauopathy
    N. Arul Murugan, Agneta K. Nordberg, Hans Ågren · 2021 · ACS Chemical Neuroscience
52. Arginine and Disordered Amyloid-β Peptide Structures: Molecular Level Insights into the Toxicity in Alzheimer’s Disease
    Orkid Coskuner‐Weber, Olivia Wise-Scira · 2013 · ACS Chemical Neuroscience
53. Construction and Validation of a RET TK Catalytic Domain by Homology Modeling
    Tiziano Tuccinardi, Fabrizio Manetti, Silvia Schenone, Adriano Martinelli, Maurizio Botta · 2007 · Journal of Chemical Information and Modeling
54. Molecular interaction of PCB153 to human serum albumin: Insights from spectroscopic and molecular modeling studies
    Chao Han, Senbiao Fang, Huiming Cao, Yan Lü, Yaqiong Ma, Dongfeng Wei, Xiaoyun Xie, Xiaohua Liu, Xin Li, Dong‐Qing Fei et al. · 2013 · Journal of Hazardous Materials
55. Biological and Computational Evaluation of Resveratrol Inhibitors against Alzheimer's Disease
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56. Omicron BA.1 and BA.2 variants increase the interactions of SARS-CoV-2 spike glycoprotein with ACE2
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57. Fragment Linker Prediction Using the Deep Encoder-Decoder Network for PROTACs Drug Design
    Chien‐Ting Kao, Chieh‐Te Lin, Cheng-Li Chou, Chu‐Chung Lin · 2023 · Journal of Chemical Information and Modeling
58. Ultrafast protein structure-based virtual screening with Panther
    Sanna P. Niinivehmas, Kari Salokas, Sakari Lätti, Hannu Raunio, Olli T. Pentikäinen · 2015 · Journal of Computer-Aided Molecular Design
59. Structure-based virtual screening of novel, high-affinity BRD4 inhibitors
    Charuvaka Muvva, Ettayapuram Ramaprasad Azhagiya Singam, S. Sundar Raman, V. Subramanian · 2014 · Molecular BioSystems
60. Conformational Plasticity of an Enzyme during Catalysis: Intricate Coupling between Cyclophilin A Dynamics and Substrate Turnover
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61. Molecular modeling and residue interaction network studies on the mechanism of binding and resistance of the HCV NS5B polymerase mutants to VX-222 and ANA598
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62. Molecular mechanism of HIV‐1 integrase–vDNA interactions and strand transfer inhibitor action: A molecular modeling perspective
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63. Does water drive protein folding?
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64. Mutatomics analysis of the systematic thermostability profile of Bacillus subtilis lipase A
    Feifei Tian, Cao Yang, Congcong Wang, Tailin Guo, Peng Zhou · 2014 · Journal of Molecular Modeling
65. Comparison of the Molecular Dynamics and Calculated Binding Free Energies for Nine FDA‐Approved HIV‐1 PR Drugs Against Subtype B and C‐SA HIV PR
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66. Cooperativity and Specificity of Cys2His2 Zinc Finger Protein−DNA Interactions: A Molecular Dynamics Simulation Study
    Juyong Lee, Jin‐Soo Kim, Chaok Seok · 2010 · The Journal of Physical Chemistry B
67. Evaluation and Characterization of Trk Kinase Inhibitors for the Treatment of Pain: Reliable Binding Affinity Predictions from Theory and Computation
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68. Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson–Boltzmann Equation: Implementation and DNA Study
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69. Unpicking the Cause of Stereoselectivity in Actinorhodin Ketoreductase Variants with Atomistic Simulations
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70. Molecular dynamics of C99-bound γ-secretase reveal two binding modes with distinct compactness, stability, and active-site retention: implications for Aβ production
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71. Gas-phase stability of G-quadruplex DNA determined by electrospray ionization tandem mass spectrometry and molecular dynamics simulations
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72. Comparison of computational approaches for predicting the effects of missense mutations on p53 function
    Lillian T. Chong, Jed W. Pitera, William C. Swope, Vijay S. Pande · 2008 · Journal of Molecular Graphics and Modelling
73. A statistical rescoring scheme for protein–ligand docking: Consideration of entropic effect
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74. Docking Applied to the Prediction of the Affinity of Compounds to P-Glycoprotein
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75. Interaction identification of Zif268 and TATAZF proteins with GC‐/AT‐rich DNA sequence: A theoretical study
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76. Toward a Computational Tool Predicting the Stereochemical Outcome of Asymmetric Reactions. 1. Application to Sharpless Asymmetric Dihydroxylation
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77. Understanding the specificity of a docking interaction between JNK1 and the scaffolding protein JIP1
    Yan, Chunli, Kaoud, Tamer, Lee, Sunbae, Dalby, Kevin N., Ren, Pengyu · 2011 · The Journal of Physical Chemistry B
78. Allosteric Cross-Talk among Spike’s Receptor-Binding Domain Mutations of the SARS-CoV-2 South African Variant Triggers an Effective Hijacking of Human Cell Receptor
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79. Functional characterization, structural basis, and protein engineering of a rare flavonoid 2′-O-glycosyltransferase from Scutellaria baicalensis
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80. Exploring the binding of BACE-1 inhibitors using comparative binding energy analysis (COMBINE)
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81. The Lipopolysaccharide from Capnocytophaga canimorsus Reveals an Unexpected Role of the Core-Oligosaccharide in MD-2 Binding
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82. Correlation Analyses on Binding Affinity of Sialic Acid Analogues and Anti-Influenza Drugs with Human Neuraminidase Using ab Initio MO Calculations on Their Complex Structures – LERE-QSAR Analysis (IV)
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83. Effect of explicit water molecules on ligand-binding affinities calculated with the MM/GBSA approach
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84. Test MM-PB/SA on True Conformational Ensembles of Protein−Ligand Complexes
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85. Using Free Energy of Binding Calculations to Improve the Accuracy of Virtual Screening Predictions
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86. Virtual Screening of PRK1 Inhibitors: Ensemble Docking, Rescoring Using Binding Free Energy Calculation and QSAR Model Development
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87. Cyclodextrin Complexes of Reduced Bromonoscapine in Guar Gum Microspheres Enhance Colonic Drug Delivery
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88. Neutron structure of human carbonic anhydrase II in complex with methazolamide: mapping the solvent and hydrogen-bonding patterns of an effective clinical drug
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89. The Effect of Conformational Flexibility on Binding Free Energy Estimation between Kinases and Their Inhibitors
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90. Characterization of the Saffron Derivative Crocetin as an Inhibitor of Human Lactate Dehydrogenase 5 in the Antiglycolytic Approach against Cancer
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91. A novel flavanone derivative inhibits dengue virus fusion and infectivity
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92. A Synthetic Oxygen Sensor for Plants Based on Animal Hypoxia Signaling
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93. Drug repurposing against arabinosyl transferase (EmbC) of Mycobacterium tuberculosis: Essential dynamics and free energy minima based binding mechanics analysis
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94. Identification of promising anti-DNA gyrase antibacterial compounds using de novo design, molecular docking and molecular dynamics studies
    Md Ataul Islam, Tahir S. Pillay · 2019 · Journal of Biomolecular Structure and Dynamics
95. Structural, functional, and stability change predictions in human telomerase upon specific point mutations
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96. Coumarins from Magydaris pastinacea as inhibitors of the tumour-associated carbonic anhydrases IX and XII: isolation, biological studies and in silico evaluation
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97. A Halogen Bonding Perspective on Iodothyronine Deiodinase Activity
    Eric S. Marsan, Craig A. Bayse · 2020 · Molecules
98. Docking studies and molecular dynamics simulations of the binding characteristics of waldiomycin and its methyl ester analog to Staphylococcus aureus histidine kinase
    Awwad A. Radwan, Gamal Mohamed Mahrous · 2020 · PLoS ONE
99. Structural insight into the recognition of S -adenosyl-L-homocysteine and sinefungin in SARS-CoV-2 Nsp16/Nsp10 RNA cap 2′-O-Methyltransferase
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100. Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2
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