Abstract
| Original language | English (Ireland) |
|---|---|
| Title of host publication | Gut |
| Pages | 2020 |
| Publication status | Published - 2020 |
Publication series
| Name | Gut |
|---|---|
| Volume | 11 |
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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Gut. 2020. p. 2020 (Gut; Vol. 11).
Research output: Chapter in Book/Report/Conference proceedings › Chapter › peer-review
TY - CHAP
T1 - 済無No Title No Title
AU - Garrett, Wendy S.
AU - Lordan, Cathy
AU - Thapa, Dinesh
AU - Ross, R. Paul
AU - Cotter, Paul D.
AU - 马树庆,
AU - 王琪,
AU - 罗新兰,
AU - emadwiandr,
AU - Rawi, Muhamad Hanif
AU - Zaman, Siti Aisyah
AU - Pa’ee, Khairul Faizal
AU - Leong, Sui Sien
AU - Sarbini, S.R. Shahrul Razid S.R. Shahrul Razid
AU - Davani-Davari, Dorna
AU - Negahdaripour, Manica
AU - Karimzadeh, Iman
AU - Seifan, Mostafa
AU - Mohkam, Milad
AU - Masoumi, Seyed Jalil
AU - Berenjian, Aydin
AU - Ghasemi, Younes
AU - Long, Shuping
AU - Yang, Yi
AU - Shen, Chengpin
AU - Wang, Yiwen
AU - Deng, Anmei
AU - Qin, Qin
AU - Qiao, Liang
AU - Heshiki, Yoshitaro
AU - Vazquez-Uribe, Ruben
AU - Li, Jin Jun
AU - Ni, Yueqiong
AU - Quainoo, Scott
AU - Imamovic, Lejla
AU - Li, Jin Jun
AU - Sørensen, Maria
AU - Chow, Billy K.C.
AU - Weiss, Glen J.
AU - Xu, Aimin
AU - Sommer, Morten O.A.
AU - Panagiotou, Gianni
AU - Livovsky, Dan M
AU - Pribic, Teorora
AU - Azpiroz, Fernando
AU - Federal, Universidade
AU - Gerais, D E Minas
AU - Figueiredo, Roberta
AU - Riquette, Resende
AU - Rackaityte, E.
AU - Halkias, J.
AU - Fukui, E. M.
AU - Mendoza, V. F.
AU - Hayzelden, C.
AU - Crawford, E. D.
AU - Fujimura, K. E.
AU - Burt, T. D.
AU - Lynch, S. V.
AU - Quigley, Eamonn M M
AU - Gajula, Prianka
AU - Van De Wiele Belgium, Tom
AU - Val D'hebron, Hosptial
AU - Flemer, Burkhardt
AU - Lynch, Denise B.
AU - Brown, Jillian M.R.
AU - Jeffery, Ian B.
AU - Ryan, Feargal J.
AU - Claesson, Marcus J.
AU - O'Riordain, Micheal
AU - Shanahan, Fergus
AU - O'Toole, Paul W.
AU - Wendling, Luana Katzuke
AU - Weschenfelder, Simone
AU - Gagnière, Johan
AU - Raisch, Jennifer
AU - Veziant, Julie
AU - Barnich, Nicolas
AU - Bonnet, Richard
AU - Buc, Emmanuel
AU - Bringer, Marie Agnès
AU - Pezet, Denis
AU - Bonnet, Mathilde
AU - Silva, Ana Carolina Couto
AU - Silva, Nayara Aparecida
AU - Pereira, Mônica Cecília Santana
AU - Vassimon, Helena Siqueira
AU - Costantini, Lara
AU - Molinari, Romina
AU - Farinon, Barbara
AU - Merendino, Nicolò
AU - Scott, K.P.
AU - Grimaldi, R.
AU - Cunningham, M.
AU - Sarbini, S.R. Shahrul Razid S.R. Shahrul Razid
AU - Wijeyesekera, A.
AU - Tang, M.L.K.
AU - Lee, J.C.‐Y.
AU - Yau, Y.F.
AU - Ansell, J.
AU - Theis, S.
AU - Yang, K.
AU - Menon, R.
AU - Arfsten, J.
AU - Manurung, S.
AU - Gourineni, V.
AU - Gibson, G.R. Glenn R.
AU - Berg, Gabriele
AU - Rybakova, Daria
AU - Fischer, Doreen
AU - Cernava, Tomislav
AU - Champomier Vergès, Marie-Christine
AU - Charles, Trevor
AU - Chen, Xiaoyulong
AU - Cocolin, Luca
AU - Eversole, Kellye
AU - Herrero Corral, Gema
AU - Kazou, Maria
AU - Kinkel, Linda
AU - Lange, Lene
AU - Lima, Nelson
AU - Loy, Alexander
AU - Macklin, James A
AU - Maguin, Emmanuelle
AU - Mauchline, Tim
AU - McClure, Ryan
AU - Mitter, Birgit
AU - Ryan, Matthew
AU - Sarand, Inga
AU - Smidt, Hauke
AU - Schelkle, Bettina
AU - Roume, Hugo
AU - Seghal Kiran, G
AU - Selvin, Joseph
AU - Soares Correa de Souza, Rafael
AU - van Overbeek, Leo
AU - Singh, Brajesh K
AU - Wagner, Michael
AU - Walsh, Aaron
AU - Sessitsch, Angela
AU - Schloter, Michael
AU - Gasbarrini, Giovanni
AU - Bonvicini, Fiorenza
AU - Gramenzi, Annagiulia
AU - Libertucci, Josie
AU - Young, Vincent B.
AU - Quigley, Eamonn M M
AU - Gajula, Prianka
AU - Van De Wiele Belgium, Tom
AU - Val D'hebron, Hosptial
AU - Scott, K.P.
AU - Grimaldi, R.
AU - Cunningham, M.
AU - Sarbini, S.R. Shahrul Razid S.R. Shahrul Razid
AU - Wijeyesekera, A.
AU - Tang, M.L.K.
AU - Lee, J.C.‐Y.
AU - Yau, Y.F.
AU - Ansell, J.
AU - Theis, S.
AU - Yang, K.
AU - Menon, R.
AU - Arfsten, J.
AU - Manurung, S.
AU - Gourineni, V.
AU - Gibson, G.R. Glenn R.
AU - Nampoothiri, K. M.
AU - Beena, D. J.
AU - Vasanthakumari, D. S.
AU - Ismail, B.
AU - Wendling, Luana Katzuke
AU - Weschenfelder, Simone
AU - Ak, Hakan
AU - To, Nurdan
AU - emadwiandr,
AU - 马树庆,
AU - 王琪,
AU - 罗新兰,
AU - Mothe, Beatriz
AU - Brander, Christian
AU - Costantini, Lara
AU - Molinari, Romina
AU - Farinon, Barbara
AU - Merendino, Nicolò
AU - i gede wisnu paramadita,
AU - Davani-Davari, Dorna
AU - Negahdaripour, Manica
AU - Karimzadeh, Iman
AU - Seifan, Mostafa
AU - Mohkam, Milad
AU - Masoumi, Seyed Jalil
AU - Berenjian, Aydin
AU - Ghasemi, Younes
AU - Dimidi, Eirini
AU - Cox, Selina
AU - Rossi, Megan
AU - Whelan, Kevin
AU - Federal, Universidade
AU - Gerais, D E Minas
AU - Figueiredo, Roberta
AU - Riquette, Resende
AU - emadwiandr,
AU - Enaud, Raphaël
AU - Prevel, Renaud
AU - Ciarlo, Eleonora
AU - Beaufils, Fabien
AU - Wieërs, Gregoire
AU - Guery, Benoit
AU - Delhaes, Laurence
AU - Flemer, Burkhardt
AU - Lynch, Denise B.
AU - Brown, Jillian M.R.
AU - Jeffery, Ian B.
AU - Ryan, Feargal J.
AU - Claesson, Marcus J.
AU - O'Riordain, Micheal
AU - Shanahan, Fergus
AU - O'Toole, Paul W.
AU - Gagnière, Johan
AU - Raisch, Jennifer
AU - Veziant, Julie
AU - Barnich, Nicolas
AU - Bonnet, Richard
AU - Buc, Emmanuel
AU - Bringer, Marie Agnès
AU - Pezet, Denis
AU - Bonnet, Mathilde
AU - Garrett, Wendy S.
AU - Guide, Your
AU - Process, N P D
AU - Heshiki, Yoshitaro
AU - Vazquez-Uribe, Ruben
AU - Li, Jin Jun
AU - Ni, Yueqiong
AU - Quainoo, Scott
AU - Imamovic, Lejla
AU - Li, Jin Jun
AU - Sørensen, Maria
AU - Chow, Billy K.C.
AU - Weiss, Glen J.
AU - Xu, Aimin
AU - Sommer, Morten O.A.
AU - Panagiotou, Gianni
AU - Honda, Kenya
AU - Littman, Dan R.
AU - Irrazábal, Thergiory
AU - Belcheva, Antoaneta
AU - Girardin, Stephen E.
AU - Martin, Alberto
AU - Philpott, Dana J.
AU - Kanjan, Pochanart
AU - Sahasrabudhe, Neha M.
AU - de Haan, Bart J.
AU - de Vos, Paul
AU - Livovsky, Dan M
AU - Pribic, Teorora
AU - Azpiroz, Fernando
AU - Louis, Petra
AU - Hold, Georgina L.
AU - Flint, Harry J.
AU - Long, Shuping
AU - Yang, Yi
AU - Shen, Chengpin
AU - Wang, Yiwen
AU - Deng, Anmei
AU - Qin, Qin
AU - Qiao, Liang
AU - Lordan, Cathy
AU - Thapa, Dinesh
AU - Ross, R. Paul
AU - Cotter, Paul D.
AU - Pinho, Renzo Garcia V O N
AU - Do, Victor
AU - Rodrigues, Nascimento
AU - Rackaityte, E.
AU - Halkias, J.
AU - Fukui, E. M.
AU - Mendoza, V. F.
AU - Hayzelden, C.
AU - Crawford, E. D.
AU - Fujimura, K. E.
AU - Burt, T. D.
AU - Lynch, S. V.
AU - Rawi, Muhamad Hanif
AU - Zaman, Siti Aisyah
AU - Pa’ee, Khairul Faizal
AU - Leong, Sui Sien
AU - Sarbini, S.R. Shahrul Razid S.R. Shahrul Razid
AU - Rooks, Michelle G.
AU - Garrett, Wendy S.
AU - Sears, Cynthia L.
AU - Garrett, Wendy S.
AU - Silva, Ana Carolina Couto
AU - Silva, Nayara Aparecida
AU - Pereira, Mônica Cecília Santana
AU - Vassimon, Helena Siqueira
AU - Prado, Vera Camargo
AU - Biotecnol, Processos
AU - Federal, Universidade
AU - Soccol, Carlos Ricardo
AU - Goytacazes, Campos D O S
AU - Abril, R J
AU - Tomasik, Przemysław
AU - Watson, Henry
AU - Mitra, Suparna
AU - Croden, Fiona C.
AU - Taylor, Morag
AU - Wood, Henry M.
AU - Perry, Sarah L.
AU - Spencer, Jade A.
AU - Quirke, Phil
AU - Toogood, Giles J.
AU - Lawton, Clare L.
AU - Dye, Louise
AU - Loadman, Paul M.
AU - Hull, Mark A.
AU - De Giffoni De Carvalho, José Tarcísio
AU - Da Silva Baldivia, Débora
AU - Leite, Daniel Ferreira
AU - De Araújo, Laura Costa Alves
AU - De Toledo Espindola, Priscilla Pereira
AU - Antunes, Katia Avila
AU - Rocha, Paola Santos
AU - De Picoli Souza, Kely
AU - Dos Santos, Edson Lucas
AU - Zea, De
AU - Santuzza, Adriana
AU - Duarte, De Oliveira
AU - Melo, Alana Rodrigues De
AU - Oliveira, Lenice Freiman De
AU - Ruschid, Valéria
AU - Lagoas, Sete
AU - Hill, Colin
AU - Guarner, Francisco
AU - Reid, Gregor
AU - Gibson, G.R. Glenn R.
AU - Merenstein, Daniel J.
AU - Pot, Bruno
AU - Morelli, Lorenzo
AU - Canani, Roberto Berni
AU - Flint, Harry J.
AU - Salminen, Seppo
AU - Calder, Philip C.
AU - Sanders, Mary Ellen
AU - Korniluk, A.
AU - Koper, O.
AU - Kemona, H.
AU - Dymicka-Piekarska, V.
AU - Lee, Chaelin
AU - Do, Hien Thi Thu
AU - Her, Junhyeok
AU - Kim, Yeonjae
AU - Seo, Dongkyu
AU - Rhee, Inmoo
AU - Li, Yanqun
AU - Kong, Dexin
AU - Fu, Ying
AU - Sussman, Michael R.
AU - Wu, Hong
AU - Rural, Serviço Nacional de Aprendizagem
AU - Su, Grace L.
AU - Ko, Cynthia W.
AU - Bercik, Premysl
AU - Falck-Ytter, Yngve
AU - Sultan, Shahnaz
AU - Weizman, Adam V.
AU - Morgan, Rebecca L.
AU - Pandey, Abhimanu
AU - Shen, Chengpin
AU - Man, Si Ming
AU - Pedrete, Thaís A.
AU - Hauser-Davis, Rachel A.
AU - Moreira, Josino C.
AU - Em, Saúde
AU - Lácteos, Produtos
AU - Scapim, Carlos Alberto
AU - Carvalho, Claudio Guilherme Portela de
AU - Cruz, Cosme Damião
AU - Medeiros, Alessandra Cardozo
AU - De, Lves
AU - Da Rosa, Rosângela Aquino
AU - Miranda, Diego Oliveira
AU - Miranda, Diego Oliveira
AU - Da, Estágios
AU - Antitumoral, Terapia
PY - 2020
Y1 - 2020
N2 - 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.
AB - 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.
KW - 08
KW - 12
KW - 18
KW - 20
KW - 2015
KW - 3 e cândido a
KW - Acute inflammation
KW - Adhesion molecules
KW - Anakinra (PubChem CID: 90470007)
KW - BAY-11-7082 (PubChem CID: 5353431)
KW - Behavioral disorders
KW - Cancer
KW - Chronic inflammation
KW - Colitis
KW - Colonic fermentation
KW - Colorectal cancer
KW - Cyclomodulin
KW - DHA
KW - Dectin-1
KW - Diabetes
KW - Dietary fiber
KW - Dysbiosis
KW - EPA
KW - Environmental factors
KW - Fructo-oligosaccharides
KW - Galacto-oligosaccharides
KW - Glyburide (PubChem CID: 3488)
KW - Growth and development
KW - Gut microbiota
KW - Gut-Lung Axis
KW - Hydroxybutyrate (PubChem CID: 441)
KW - ISAPP
KW - Inflammasome
KW - Inflammasomes
KW - Inflammation
KW - Inhibitors
KW - Innate immunity
KW - MCC950 (PubChem CID: 9910393)
KW - Machine learning
KW - Medicinal plant
KW - Medicinal plants
KW - Microbiome
KW - Microbiota
KW - Mycobiota
KW - N-acetyl Cysteine (PubChem CID: 12035)
KW - NLRP
KW - Oligosaccharide
KW - Omega-3 PUFAs
KW - Organelle
KW - Oxidative stress
KW - Prebiotic
KW - Prebiotics
KW - Probiotic
KW - Proteomics
KW - Respiratory disease
KW - Ritonavir (PubChem CID: 392622)
KW - Secondary metabolites
KW - Short chain fatty acids
KW - Short-chain fatty acids
KW - THP-1 macrophage
KW - TLRs
KW - Thalidomide (PubChem CID: 5426)
KW - Therapeutics
KW - Therapy
KW - Treatment outcome
KW - VX-740 (PubChem CID: 153270)
KW - VX-765 (PubChem CID: 11398092)
KW - Zea mays
KW - altura da inserção da espiga
KW - altura da planta
KW - anna christina de almeida
KW - antibiotic
KW - aprovado para publicação em
KW - autor para correspondência
KW - bacteria
KW - beneficial microbes
KW - colorectal cancer
KW - consumer preferences
KW - convencional
KW - da costa 4
KW - de cultivo orgânico e
KW - diet
KW - digestion
KW - digestive well-being
KW - dysbiosis
KW - fatty acid
KW - fecal microbiota transplantation
KW - fermented food
KW - fermented milk
KW - food ingestion
KW - functional food
KW - grãos
KW - gut fermentation
KW - health benefits
KW - health-promoting gut bacteria
KW - icle
KW - kefir
KW - kimchi
KW - kombucha
KW - lucinéia de pinho 1
KW - maria cristina d
KW - melhoramento genético
KW - microbiome
KW - microbiota
KW - microorganisms
KW - miso
KW - natto
KW - nutraceuticals
KW - nutritional supplement
KW - omega-3
KW - organic production
KW - paes 2
KW - pharmabiotic
KW - prebiotic
KW - prebiotics
KW - probiosis
KW - probiotic
KW - prolificidade
KW - recebido para publicação em
KW - satiety
KW - sauerkraut
KW - sourdough
KW - soy
KW - spikelets
KW - study
KW - taste
KW - tempeh
KW - β-glucan
KW - Киари
UR - https://doi.org/10.1016/j.ijbiomac.2019.08.035%0Ahttps://doi.org/10.1053/j.gastro.2020.05.059%0Ahttps://doi.org/10.1016/j.plaphy.2020.01.006%0Ahttp://dx.doi.org/10.1016/j.chom.2014.02.007%0Ahttps://doi.org/10.1007/s13197-020-04244-5%0Ahttp://dx.doi.org/10
UR - https://www.mendeley.com/catalogue/e613e7e4-3174-3138-ba2b-32f8fe3732a7/
M3 - Chapter
C2 - 25246403
SN - 9788578110796
T3 - Gut
SP - 2020
BT - Gut
ER -