AI-driven drug repurposing and binding pose meta dynamics identifies novel targets for monkeypox virus

[1]  V. Garg,et al.  Tecovirimat as a Potential Bioavailable inhibitor against MPXVgp158 Established through Molecular Dynamic Simulations and Docking Studies , 2022, Journal of Pure and Applied Microbiology.

[2]  R. P. Vivek-Ananth,et al.  In silico identification of potential inhibitors of vital monkeypox virus proteins from FDA approved drugs , 2022, Molecular Diversity.

[3]  Guizhong Zhang,et al.  Network Pharmacology and Molecular Docking Analysis Reveal Insights into the Molecular Mechanism of Shengma-Gegen Decoction on Monkeypox , 2022, Pathogens.

[4]  Taher Entezari-Maleki,et al.  Monkeypox treatment: Current evidence and future perspectives , 2022, Journal of medical virology.

[5]  C. H. Chong,et al.  Molecular Docking and In-Silico Analysis of Natural Biomolecules against Dengue, Ebola, Zika, SARS-CoV-2 Variants of Concern and Monkeypox Virus , 2022, International journal of molecular sciences.

[6]  J. Brooks,et al.  Tecovirimat and the Treatment of Monkeypox - Past, Present, and Future Considerations. , 2022, The New England journal of medicine.

[7]  A. Rodríguez-Morales,et al.  Monkeypox and Its Possible Sexual Transmission: Where Are We Now with Its Evidence? , 2022, Pathogens.

[8]  M. Ordobás Gavín,et al.  Monkeypox outbreak predominantly affecting men who have sex with men, Madrid, Spain, 26 April to 16 June 2022 , 2022, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

[9]  Olivier Uwishema,et al.  The burden of monkeypox virus amidst the Covid-19 pandemic in Africa: A double battle for Africa , 2022, Annals of Medicine and Surgery.

[10]  Y. Xiang,et al.  Monkeypox virus emerges from the shadow of its more infamous cousin: family biology matters , 2022, Emerging microbes & infections.

[11]  R. Kakkar,et al.  A combination strategy of structure-based virtual screening, MM-GBSA, cross docking, molecular dynamics and metadynamics simulations used to investigate natural compounds as potent and specific inhibitors of tumor linked human carbonic anhydrase IX , 2022, Journal of biomolecular structure & dynamics.

[12]  J. Kong,et al.  Epidemiological trends and clinical features of the ongoing monkeypox epidemic: A preliminary pooled data analysis and literature review , 2022, Journal of medical virology.

[13]  A. Rodríguez-Morales,et al.  Human monkeypox preparedness in Latin America – Are we ready for the next viral zoonotic disease outbreak after COVID-19? , 2022, The Brazilian Journal of Infectious Diseases.

[14]  Saniya M. Ansari,et al.  Re‐emerging human monkeypox: A major public‐health debacle , 2022, Journal of medical virology.

[15]  H. Gendelman,et al.  The 2022 outbreak and the pathobiology of the monkeypox virus , 2022, Journal of autoimmunity.

[16]  A. Cameron-Smith.  Expunging Variola: The Control and Eradication of Smallpox in India, 1947-1977 by Sanjoy Bhattacharya (review) , 2022, Health and History.

[17]  H. Pandya,et al.  Identification of antiviral phytochemicals as a potential SARS-CoV-2 main protease (Mpro) inhibitor using docking and molecular dynamics simulations , 2021, Scientific Reports.

[18]  M. Tutone,et al.  Evaluation of the IKKβ Binding of Indicaxanthin by Induced-Fit Docking, Binding Pose Metadynamics, and Molecular Dynamics , 2021, Frontiers in Pharmacology.

[19]  P. Cramer.  AlphaFold2 and the future of structural biology , 2021, Nature Structural & Molecular Biology.

[20]  H. Pandya,et al.  Repurposing of anticancer phytochemicals for identifying potential fusion inhibitor for SARS-CoV-2 using molecular docking and molecular dynamics (MD) simulations , 2021, Journal of biomolecular structure & dynamics.

[21]  Yonghua Wang,et al.  Crystal Structure of a Phospholipase D from the Plant-Associated Bacteria Serratia plymuthica Strain AS9 Reveals a Unique Arrangement of Catalytic Pocket , 2021, International journal of molecular sciences.

[22]  Raghvendra Mall,et al.  A Modelling Framework for Embedding-based Predictions for Compound-Viral Protein Activity , 2021, Bioinform..

[23]  H. Pandya,et al.  Pinpointing the potential hits for hindering interaction of SARS-CoV-2 S-protein with ACE2 from the pool of antiviral phytochemicals utilizing molecular docking and molecular dynamics (MD) simulations , 2021, Journal of Molecular Graphics and Modelling.

[24]  Abu Montakim Tareq,et al.  Drug Repurposing Approach against Novel Coronavirus Disease (COVID-19) through Virtual Screening Targeting SARS-CoV-2 Main Protease , 2020, Biology.

[25]  U. Moens,et al.  Monkeypox Virus in Nigeria: Infection Biology, Epidemiology, and Evolution , 2020, Viruses.

[26]  David J. Baumler,et al.  In silico screening of hundred phytocompounds of ten medicinal plants as potential inhibitors of nucleocapsid phosphoprotein of COVID-19: an approach to prevent virus assembly , 2020, Journal of biomolecular structure & dynamics.

[27]  Kai Zhao,et al.  A pneumonia outbreak associated with a new coronavirus of probable bat origin , 2020, Nature.

[28]  David S Palmer,et al.  Exploring Ligand Stability in Protein Crystal Structures Using Binding Pose Metadynamics , 2020, J. Chem. Inf. Model..

[29]  H. Mok.  Vaccinia virus requires heat-shock proteins for genome replication and virion assembly , 2019 .

[30]  Zhou Yin,et al.  Mechanism of Small Molecules Inhibiting Activator Protein-1 DNA Binding Probed with Induced Fit Docking and Metadynamics Simulations , 2019, J. Chem. Inf. Model..

[31]  Raghvendra Mall,et al.  BCrystal: an interpretable sequence-based protein crystallization predictor , 2019, Bioinform..

[32]  Y. Nakazawa,et al.  Monkeypox re-emergence in Africa: a call to expand the concept and practice of One Health , 2019, Expert review of anti-infective therapy.

[33]  Raghvendra Mall,et al.  DeepCrystal: A Deep Learning Framework for Sequence-based Protein Crystallization Prediction , 2018, 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

[34]  M. E. El Zowalaty,et al.  A review of the monkeypox virus and a recent outbreak of skin rash disease in Nigeria , 2018, Journal of medical virology.

[35]  Raghvendra Mall,et al.  DeepSol: a deep learning framework for sequence‐based protein solubility prediction , 2018, Bioinform..

[36]  Raghvendra Mall,et al.  PaRSnIP: sequence-based protein solubility prediction using gradient boosting machine , 2018, Bioinform..

[37]  Pietro Liò,et al.  Graph Attention Networks , 2017, ICLR.

[38]  Raudah Lazim,et al.  Application of conventional molecular dynamics simulation in evaluating the stability of apomyoglobin in urea solution , 2017, Scientific Reports.

[39]  Aaron C. Courville,et al.  Professor Forcing: A New Algorithm for Training Recurrent Networks , 2016, NIPS.

[40]  B. Moss,et al.  Retrograde Transport from Early Endosomes to the trans-Golgi Network Enables Membrane Wrapping and Egress of Vaccinia Virus Virions , 2016, Journal of Virology.

[41]  Pratyush Tiwary,et al.  Prediction of Protein-Ligand Binding Poses via a Combination of Induced Fit Docking and Metadynamics Simulations. , 2016, Journal of chemical theory and computation.

[42]  R. Kennedy,et al.  Defending against smallpox: a focus on vaccines , 2016, Expert review of vaccines.

[43]  Tianqi Chen,et al.  XGBoost: A Scalable Tree Boosting System , 2016, KDD.

[44]  L. Nolen,et al.  Introduction of Monkeypox into a Community and Household: Risk Factors and Zoonotic Reservoirs in the Democratic Republic of the Congo. , 2015, The American journal of tropical medicine and hygiene.

[45]  Johan A. K. Suykens,et al.  Very Sparse LSSVM Reductions for Large-Scale Data , 2015, IEEE Transactions on Neural Networks and Learning Systems.

[46]  J. Lloyd-Smith.  Vacated niches, competitive release and the community ecology of pathogen eradication , 2013, Philosophical Transactions of the Royal Society B: Biological Sciences.

[47]  P. Kerr.  Myxomatosis in Australia and Europe: a model for emerging infectious diseases. , 2012, Antiviral research.

[48]  Leiliang Zhang,et al.  Poxvirus Proteomics and Virus-Host Protein Interactions , 2009, Microbiology and Molecular Biology Reviews.

[49]  Christoph J. Burckhardt,et al.  Virus Movements on the Plasma Membrane Support Infection and Transmission between Cells , 2009, PLoS pathogens.

[50]  Simone Marsili,et al.  ORAC: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level , 2009, J. Comput. Chem..

[51]  W. Muraskin.  Expunging Variola: The Control and Eradication of Smallpox in India 1947–1977 , 2007 .

[52]  Tom Halgren,et al.  New Method for Fast and Accurate Binding‐site Identification and Analysis , 2007, Chemical biology & drug design.

[53]  V. Ryabov.  Constant pressure-temperature molecular dynamics on a torus , 2006 .

[54]  Xiaojie Xu,et al.  Recent Advances in Free Energy Calculations with a Combination of Molecular Mechanics and Continuum Models , 2006 .

[55]  J. Melski,et al.  Monkeypox: An epidemiologic and clinical comparison of African and US disease , 2006, Journal of the American Academy of Dermatology.

[56]  Chung-Lin Liao,et al.  Vaccinia Virus Proteome: Identification of Proteins in Vaccinia Virus Intracellular Mature Virion Particles , 2006, Journal of Virology.

[57]  J. Seward,et al.  Smallpox , 2006, The Lancet.

[58]  Richard A. Friesner,et al.  Integrated Modeling Program, Applied Chemical Theory (IMPACT) , 2005, J. Comput. Chem..

[59]  K. Travis,et al.  A configurational temperature Nosé-Hoover thermostat. , 2005, The Journal of chemical physics.

[60]  K. Reimann,et al.  Smallpox vaccine–induced antibodies are necessary and sufficient for protection against monkeypox virus , 2005, Nature Medicine.

[61]  David Baker,et al.  Protein structure prediction and analysis using the Robetta server , 2004, Nucleic Acids Res..

[62]  P. Earl,et al.  Immunogenicity of a highly attenuated MVA smallpox vaccine and protection against monkeypox , 2004, Nature.

[63]  Hege S. Beard,et al.  Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. , 2004, Journal of medicinal chemistry.

[64]  Matthew P. Repasky,et al.  Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. , 2004, Journal of medicinal chemistry.

[65]  Marc A. Martí-Renom,et al.  Tools for comparative protein structure modeling and analysis , 2003, Nucleic Acids Res..

[66]  G. Hankins,et al.  Smallpox and Pregnancy: From Eradicated Disease to Bioterrorist Threat , 2002, Obstetrics and gynecology.

[67]  S. Shchelkunov,et al.  Species-Specific Differences in Organization of Orthopoxvirus Kelch-Like Proteins , 2002, Virus Genes.

[68]  P. Kollman,et al.  Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding , 2000 .

[69]  S. Hammond,et al.  Mutagenesis of phospholipase D defines a superfamily including a trans‐Golgi viral protein required for poxvirus pathogenicity , 1997, The EMBO journal.

[70]  W. L. Jorgensen,et al.  Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .

[71]  T. Darden,et al.  A smooth particle mesh Ewald method , 1995 .

[72]  W. L. Jorgensen,et al.  The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. , 1988, Journal of the American Chemical Society.

[73]  P. Leggat,et al.  Human Monkeypox: Current State of Knowledge and Implications for the Future , 2016, Tropical medicine and infectious disease.

[74]  Guigang Zhang,et al.  Deep Learning , 2016, Int. J. Semantic Comput..

[75]  Vladimir Vapnik,et al.  Support-vector networks , 2004, Machine Learning.

[76]  B. Sodeik,et al.  Assembly of vaccinia virus revisited: de novo membrane synthesis or acquisition from the host? , 2002, Trends in microbiology.

[77]  G. Langlet,et al.  International Tables for Crystallography , 2002 .

[78]  P. Kollman,et al.  Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. , 2001, Annual review of biophysics and biomolecular structure.