済無No Title No Title

  • Wendy S. Garrett
  • , Cathy Lordan
  • , Dinesh Thapa
  • , R. Paul Ross
  • , Paul D. Cotter
  • , 马树庆
  • , 王琪
  • , 罗新兰
  • , emadwiandr
  • , Muhamad Hanif Rawi
  • , Siti Aisyah Zaman
  • , Khairul Faizal Pa’ee
  • , Sui Sien Leong
  • , S.R. Shahrul Razid S.R. Shahrul Razid Sarbini
  • , Dorna Davani-Davari
  • , Manica Negahdaripour
  • , Iman Karimzadeh
  • , Mostafa Seifan
  • , Milad Mohkam
  • , Seyed Jalil Masoumi
  • Aydin Berenjian, Younes Ghasemi, Shuping Long, Yi Yang, Chengpin Shen, Yiwen Wang, Anmei Deng, Qin Qin, Liang Qiao, Yoshitaro Heshiki, Ruben Vazquez-Uribe, Jin Jun Li, Yueqiong Ni, Scott Quainoo, Lejla Imamovic, Jin Jun Li, Maria Sørensen, Billy K.C. Chow, Glen J. Weiss, Aimin Xu, Morten O.A. Sommer, Gianni Panagiotou, Dan M Livovsky, Teorora Pribic, Fernando Azpiroz, Universidade Federal, D E Minas Gerais, Roberta Figueiredo, Resende Riquette, E. Rackaityte, J. Halkias, E. M. Fukui, V. F. Mendoza, C. Hayzelden, E. D. Crawford, K. E. Fujimura, T. D. Burt, S. V. Lynch, Eamonn M M Quigley, Prianka Gajula, Tom Van De Wiele Belgium, Hosptial Val D'hebron, Burkhardt Flemer, Denise B. Lynch, Jillian M.R. Brown, Ian B. Jeffery, Feargal J. Ryan, Marcus J. Claesson, Micheal O'Riordain, Fergus Shanahan, Paul W. O'Toole, Luana Katzuke Wendling, Simone Weschenfelder, Johan Gagnière, Jennifer Raisch, Julie Veziant, Nicolas Barnich, Richard Bonnet, Emmanuel Buc, Marie Agnès Bringer, Denis Pezet, Mathilde Bonnet, Ana Carolina Couto Silva, Nayara Aparecida Silva, Mônica Cecília Santana Pereira, Helena Siqueira Vassimon, Lara Costantini, Romina Molinari, Barbara Farinon, Nicolò Merendino, K.P. Scott, R. Grimaldi, M. Cunningham, S.R. Shahrul Razid S.R. Shahrul Razid Sarbini, A. Wijeyesekera, M.L.K. Tang, J.C.‐Y. Lee, Y.F. Yau, J. Ansell, S. Theis, K. Yang, R. Menon, J. Arfsten, S. Manurung, V. Gourineni, G.R. Glenn R. Gibson, Gabriele Berg, Daria Rybakova, Doreen Fischer, Tomislav Cernava, Marie-Christine Champomier Vergès, Trevor Charles, Xiaoyulong Chen, Luca Cocolin, Kellye Eversole, Gema Herrero Corral, Maria Kazou, Linda Kinkel, Lene Lange, Nelson Lima, Alexander Loy, James A Macklin, Emmanuelle Maguin, Tim Mauchline, Ryan McClure, Birgit Mitter, Matthew Ryan, Inga Sarand, Hauke Smidt, Bettina Schelkle, Hugo Roume, G Seghal Kiran, Joseph Selvin, Rafael Soares Correa de Souza, Leo van Overbeek, Brajesh K Singh, Michael Wagner, Aaron Walsh, Angela Sessitsch, Michael Schloter, Giovanni Gasbarrini, Fiorenza Bonvicini, Annagiulia Gramenzi, Josie Libertucci, Vincent B. Young, Eamonn M M Quigley, Prianka Gajula, Tom Van De Wiele Belgium, Hosptial Val D'hebron, K.P. Scott, R. Grimaldi, M. Cunningham, S.R. Shahrul Razid S.R. Shahrul Razid Sarbini, A. Wijeyesekera, M.L.K. Tang, J.C.‐Y. Lee, Y.F. Yau, J. Ansell, S. Theis, K. Yang, R. Menon, J. Arfsten, S. Manurung, V. Gourineni, G.R. Glenn R. Gibson, K. M. Nampoothiri, D. J. Beena, D. S. Vasanthakumari, B. Ismail, Luana Katzuke Wendling, Simone Weschenfelder, Hakan Ak, Nurdan To, emadwiandr, 马树庆, 王琪, 罗新兰, Beatriz Mothe, Christian Brander, Lara Costantini, Romina Molinari, Barbara Farinon, Nicolò Merendino, i gede wisnu paramadita, Dorna Davani-Davari, Manica Negahdaripour, Iman Karimzadeh, Mostafa Seifan, Milad Mohkam, Seyed Jalil Masoumi, Aydin Berenjian, Younes Ghasemi, Eirini Dimidi, Selina Cox, Megan Rossi, Kevin Whelan, Universidade Federal, D E Minas Gerais, Roberta Figueiredo, Resende Riquette, emadwiandr, Raphaël Enaud, Renaud Prevel, Eleonora Ciarlo, Fabien Beaufils, Gregoire Wieërs, Benoit Guery, Laurence Delhaes, Burkhardt Flemer, Denise B. Lynch, Jillian M.R. Brown, Ian B. Jeffery, Feargal J. Ryan, Marcus J. Claesson, Micheal O'Riordain, Fergus Shanahan, Paul W. O'Toole, Johan Gagnière, Jennifer Raisch, Julie Veziant, Nicolas Barnich, Richard Bonnet, Emmanuel Buc, Marie Agnès Bringer, Denis Pezet, Mathilde Bonnet, Wendy S. Garrett, Your Guide, N P D Process, Yoshitaro Heshiki, Ruben Vazquez-Uribe, Jin Jun Li, Yueqiong Ni, Scott Quainoo, Lejla Imamovic, Jin Jun Li, Maria Sørensen, Billy K.C. Chow, Glen J. Weiss, Aimin Xu, Morten O.A. Sommer, Gianni Panagiotou, Kenya Honda, Dan R. Littman, Thergiory Irrazábal, Antoaneta Belcheva, Stephen E. Girardin, Alberto Martin, Dana J. Philpott, Pochanart Kanjan, Neha M. Sahasrabudhe, Bart J. de Haan, Paul de Vos, Dan M Livovsky, Teorora Pribic, Fernando Azpiroz, Petra Louis, Georgina L. Hold, Harry J. Flint, Shuping Long, Yi Yang, Chengpin Shen, Yiwen Wang, Anmei Deng, Qin Qin, Liang Qiao, Cathy Lordan, Dinesh Thapa, R. Paul Ross, Paul D. Cotter, Renzo Garcia V O N Pinho, Victor Do, Nascimento Rodrigues, E. Rackaityte, J. Halkias, E. M. Fukui, V. F. Mendoza, C. Hayzelden, E. D. Crawford, K. E. Fujimura, T. D. Burt, S. V. Lynch, Muhamad Hanif Rawi, Siti Aisyah Zaman, Khairul Faizal Pa’ee, Sui Sien Leong, S.R. Shahrul Razid S.R. Shahrul Razid Sarbini, Michelle G. Rooks, Wendy S. Garrett, Cynthia L. Sears, Wendy S. Garrett, Ana Carolina Couto Silva, Nayara Aparecida Silva, Mônica Cecília Santana Pereira, Helena Siqueira Vassimon, Vera Camargo Prado, Processos Biotecnol, Universidade Federal, Carlos Ricardo Soccol, Campos D O S Goytacazes, R J Abril, Przemysław Tomasik, Henry Watson, Suparna Mitra, Fiona C. Croden, Morag Taylor, Henry M. Wood, Sarah L. Perry, Jade A. Spencer, Phil Quirke, Giles J. Toogood, Clare L. Lawton, Louise Dye, Paul M. Loadman, Mark A. Hull, José Tarcísio De Giffoni De Carvalho, Débora Da Silva Baldivia, Daniel Ferreira Leite, Laura Costa Alves De Araújo, Priscilla Pereira De Toledo Espindola, Katia Avila Antunes, Paola Santos Rocha, Kely De Picoli Souza, Edson Lucas Dos Santos, De Zea, Adriana Santuzza, De Oliveira Duarte, Alana Rodrigues De Melo, Lenice Freiman De Oliveira, Valéria Ruschid, Sete Lagoas, Colin Hill, Francisco Guarner, Gregor Reid, G.R. Glenn R. Gibson, Daniel J. Merenstein, Bruno Pot, Lorenzo Morelli, Roberto Berni Canani, Harry J. Flint, Seppo Salminen, Philip C. Calder, Mary Ellen Sanders, A. Korniluk, O. Koper, H. Kemona, V. Dymicka-Piekarska, Chaelin Lee, Hien Thi Thu Do, Junhyeok Her, Yeonjae Kim, Dongkyu Seo, Inmoo Rhee, Yanqun Li, Dexin Kong, Ying Fu, Michael R. Sussman, Hong Wu, Serviço Nacional de Aprendizagem Rural, Grace L. Su, Cynthia W. Ko, Premysl Bercik, Yngve Falck-Ytter, Shahnaz Sultan, Adam V. Weizman, Rebecca L. Morgan, Abhimanu Pandey, Chengpin Shen, Si Ming Man, Thaís A. Pedrete, Rachel A. Hauser-Davis, Josino C. Moreira, Saúde Em, Produtos Lácteos, Carlos Alberto Scapim, Claudio Guilherme Portela de Carvalho, Cosme Damião Cruz, Alessandra Cardozo Medeiros, Lves De, Rosângela Aquino Da Rosa, Diego Oliveira Miranda, Diego Oliveira Miranda, Estágios Da, Terapia Antitumoral

Research output: Chapter in Book/Report/Conference proceedingsChapterpeer-review

Abstract

Predicting the binding mode of flexible polypeptides to proteins is an important task that falls outside the domain of applicability of most small molecule and protein−protein docking tools. Here, we test the small molecule flexible ligand docking program Glide on a set of 19 non-α-helical peptides and systematically improve pose prediction accuracy by enhancing Glide sampling for flexible polypeptides. In addition, scoring of the poses was improved by post-processing with physics-based implicit solvent MM- GBSA calculations. Using the best RMSD among the top 10 scoring poses as a metric, the success rate (RMSD ≤ 2.0 Å for the interface backbone atoms) increased from 21% with default Glide SP settings to 58% with the enhanced peptide sampling and scoring protocol in the case of redocking to the native protein structure. This approaches the accuracy of the recently developed Rosetta FlexPepDock method (63% success for these 19 peptides) while being over 100 times faster. Cross-docking was performed for a subset of cases where an unbound receptor structure was available, and in that case, 40% of peptides were docked successfully. We analyze the results and find that the optimized polypeptide protocol is most accurate for extended peptides of limited size and number of formal charges, defining a domain of applicability for this approach.
Original languageEnglish (Ireland)
Title of host publicationGut
Pages2020
Publication statusPublished - 2020

Publication series

NameGut
Volume11

Keywords

  • 08
  • 12
  • 18
  • 20
  • 2015
  • 3 e cândido a
  • Acute inflammation
  • Adhesion molecules
  • Anakinra (PubChem CID: 90470007)
  • BAY-11-7082 (PubChem CID: 5353431)
  • Behavioral disorders
  • Cancer
  • Chronic inflammation
  • Colitis
  • Colonic fermentation
  • Colorectal cancer
  • Cyclomodulin
  • DHA
  • Dectin-1
  • Diabetes
  • Dietary fiber
  • Dysbiosis
  • EPA
  • Environmental factors
  • Fructo-oligosaccharides
  • Galacto-oligosaccharides
  • Glyburide (PubChem CID: 3488)
  • Growth and development
  • Gut microbiota
  • Gut-Lung Axis
  • Hydroxybutyrate (PubChem CID: 441)
  • ISAPP
  • Inflammasome
  • Inflammasomes
  • Inflammation
  • Inhibitors
  • Innate immunity
  • MCC950 (PubChem CID: 9910393)
  • Machine learning
  • Medicinal plant
  • Medicinal plants
  • Microbiome
  • Microbiota
  • Mycobiota
  • N-acetyl Cysteine (PubChem CID: 12035)
  • NLRP
  • Oligosaccharide
  • Omega-3 PUFAs
  • Organelle
  • Oxidative stress
  • Prebiotic
  • Prebiotics
  • Probiotic
  • Proteomics
  • Respiratory disease
  • Ritonavir (PubChem CID: 392622)
  • Secondary metabolites
  • Short chain fatty acids
  • Short-chain fatty acids
  • THP-1 macrophage
  • TLRs
  • Thalidomide (PubChem CID: 5426)
  • Therapeutics
  • Therapy
  • Treatment outcome
  • VX-740 (PubChem CID: 153270)
  • VX-765 (PubChem CID: 11398092)
  • Zea mays
  • altura da inserção da espiga
  • altura da planta
  • anna christina de almeida
  • antibiotic
  • aprovado para publicação em
  • autor para correspondência
  • bacteria
  • beneficial microbes
  • colorectal cancer
  • consumer preferences
  • convencional
  • da costa 4
  • de cultivo orgânico e
  • diet
  • digestion
  • digestive well-being
  • dysbiosis
  • fatty acid
  • fecal microbiota transplantation
  • fermented food
  • fermented milk
  • food ingestion
  • functional food
  • grãos
  • gut fermentation
  • health benefits
  • health-promoting gut bacteria
  • icle
  • kefir
  • kimchi
  • kombucha
  • lucinéia de pinho 1
  • maria cristina d
  • melhoramento genético
  • microbiome
  • microbiota
  • microorganisms
  • miso
  • natto
  • nutraceuticals
  • nutritional supplement
  • omega-3
  • organic production
  • paes 2
  • pharmabiotic
  • prebiotic
  • prebiotics
  • probiosis
  • probiotic
  • prolificidade
  • recebido para publicação em
  • satiety
  • sauerkraut
  • sourdough
  • soy
  • spikelets
  • study
  • taste
  • tempeh
  • β-glucan
  • Киари

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