Learning protein-ligand binding affinity with atomic environment vectors

Autor: Rocco Meli, Andrew Anighoro, Mike J. Bodkin, Garrett M. Morris, Philip C. Biggin

Publikováno v: Journal of Cheminformatics, Vol 13, Iss 1, Pp 1-19 (2021)

Abstract Scoring functions for the prediction of protein-ligand binding affinity have seen renewed interest in recent years when novel machine learning and deep learning methods started to consistently outperform classical scoring functions. Here we

Externí odkaz: https://doaj.org/article/7f4da096e1a94782b493f06d57758b6e

Scoring Functions for Protein-Ligand Binding Affinity Prediction Using Structure-based Deep Learning: A Review

Autor: Rocco Meli, Garrett M. Morris, Philip C. Biggin

Publikováno v: Frontiers in Bioinformatics, Vol 2 (2022)

The rapid and accurate in silico prediction of protein-ligand binding free energies or binding affinities has the potential to transform drug discovery. In recent years, there has been a rapid growth of interest in deep learning methods for the predi

Externí odkaz: https://doaj.org/article/89fff38ec3314be196ff3d9f42d513ad

Learning protein-ligand binding affinity with atomic environment vectors

Autor: Philip C. Biggin, Garrett M. Morris, Rocco Meli, Andrew Anighoro, Michael J. Bodkin

Publikováno v: Journal of Cheminformatics, Vol 13, Iss 1, Pp 1-19 (2021)
Journal of Cheminformatics

Scoring functions for the prediction of protein-ligand binding affinity have seen renewed interest in recent years when novel machine learning and deep learning methods started to consistently outperform classical scoring functions. Here we explore t

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6db0a40972ad9b62a2ee482c7f8f39fe
https://doaj.org/article/7f4da096e1a94782b493f06d57758b6e

GNINA 1.0: Molecular Docking with Deep Learning

Autor: Paul G. Francoeur, Matthew Ragoza, Tomohide Masuda, Jocelyn Sunseri, Rocco Meli, Rishal Aggarwal, David Ryan Koes, Andrew T. McNutt

Publikováno v: Journal of Cheminformatics
Journal of Cheminformatics, Vol 13, Iss 1, Pp 1-20 (2021)

Molecular docking computationally predicts the conformation of a small molecule when binding to a receptor. Scoring functions are a vital piece of any molecular docking pipeline as they determine the fitness of sampled poses. Here we describe and eva

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::80508e2e3e124bd3d0bf02c4af1b5366
https://doi.org/10.26434/chemrxiv.13578140.v1

Reproducibility of Fluorescent Expression from Engineered Biological Constructs in E. coli

Autor: Jacob, Beal, Trac Haddock Angellii, Markus, Gershater, Kim de Mora, Meagan, Lizarazo, Jim, Hollenhorst, Randy, Rettberg, Philipp, Demling, Rene, Hanke, Michae, Osthegel, Anna, Schechtel, Suresh, Sudarsan, Arne, Zimmermann, Bartosz, Gabryelczyk, Martina, Ikonen, Minnamari, Salmela, Muradıye, Acar, Muhammed Fatih Aktas, Furkan, Bestepe, Furkan Sacit Ceylan, Sadık, Cigdem, Mikail, Dohan, Mustafa, Elitok, Mehmet, Gunduz, Esra, Gunduz, Omer Faruk Hatipoglu, Turan, Kaya, Orhan, Sayin, Safa, Tapan, Osman Faruk Tereci, Abdullah, Uçar, Mustafa, Yilmaz, Jeffrey, Barrick, Alex, Gutierrez, Dennis, Mishler, Jordan, Monk, Kate, Mortensen, Nathan, Shin, Ella, Watkins, Yintong, Chen, Yuji, Jin, Yuanjie, Shi, Haoqian Myelin Zhang, Bruno, Ono, Ieda Maria Martinez Paino, Lais, Ribovski, Ivan, Silva, Danilo Keiji Zampronio, Nils, Birkholz, Rudiger Frederik Busche, Oliver, Konzock, Steffen, Lippold, Carsten, Ludwig, Melanie, Philippi, Lukas, Platz, Christian, Sigismund, Susanne, Weber, Maren, Wehrs, Niels, Werchau, Anna, Wronska, Zen Zen Yen, Yash, Agarwal, Evan, Appleton, Douglas, Densmore, Ariela, Esmurria, Kathleen, Lewis, Alan, Pacheco, Marcel, Bruchez, Danielle, Peters, Cheryl, Telmer, Lena, Wang, Silvia Canas Duarte, Daniel Giraldo Perez, Camilo Gomez Garzon, Jorge Madrid Wolff, Nathaly Marin Medina, Valentina, Mazzanti, Laura Rodriguez Forero, Eitan, Scher, Robin, Dowell, Samantha, O’Hara, Cloe Simone Pogoda, Kendra, Shattuck, Ali, Altintas, Anne Pihl Bali, Rasmus, Bech, Anne, Egholm, Anne Sofie Laerke Hansen, Kristian, Jensen, Kristian Barreth Karlsen, Caroline, Mosbech, Sophia, Belkhelfa, Noemie, Berenger, Romain, Bodinier, Cecile, Jacry, Laura Matabishi Bibi, Pierre, Parutto, Julie, Zaworski, Andries de Vries, Freek de Wijs, Rick, Elbert, Lisa, Hielkema, Chandhuru, Jagadeesan, Bayu, Jayawardhana, Oscar, Kuipers, Anna, Lauxen, Thomas, Meijer, Sandra, Mous, Renske van Raaphorst, Aakanksha, Saraf, Otto, Schepers, Oscar, Smits, Jan Willem Veening, Ruud Detert Oude Weme, Lianne, Wieske, Catherine, Ainsworth, Xenia Spencer Milnes, Alejandro, Gómezávila, Eddie Cano Gamez, Ana Laura Torres Huerta, Carlos Alejandro Meza Ramirez, Philipp, Popp, Jara, Radeck, Anna, Sommer, Xiangkai, Li, Qi, Wu, Hongxia, Zhao, Ruixue, Zhao, Irem, Bastuzel, Yasemin, Ceyhan, Mayda, Gursel, Burak, Kizil, Ilkem, Kumru, Yasemin, Kuvvet, Helin, Tercan, Seniz, Yuksel, Luiza, Niyazmetova, Timothy, Ang, Lucas, Black, Ciaran, Kelly, George, Wadhams, Clovis, Basier, Urszula, Czerwinska, Cindy Suci Ananda, Muhammad Al Azhar, Adelia, Elviantari, Maya, Fitriana, Arief Budi Witarto, Yuliant, Jia Fangxing, Qingfeng, Hou, Wan, Pei, Chen, Rifei, Wang, Rong, Huang, Wei, Zhang, Yushan, Jianguo, He, Dengwen, Lai, Pai, Li, Jianheng, Liu, Chunyang, Ni, Qianbin, Zhang, Cinthya, Cadenas, Zardain Canabal, Eduardo J., Claudia Nallely Alonso Cantu, Mercedes Alejandra Vazquez Cantu, Eduardo Cepeda Canedo, Cesar Miguel Valdez Cordova, Jose Alberto de la Paz Espinosa, Carlos Enrique Alavez Garcia, Ana Laura Navarro Heredia, Adriana, Hernandez, Sebastian Valdivieso Jauregui, Eduardo Ramirez Montiel, Eduardo Serna Morales, Yamile Minerva Castellanos Morales, Omar Alonso Cantu Pena, Ramirez Rodríguez, Eduardo A., Elizabeth Vallejo Trejo, Jesus Gilberto Rodriguez Ceja, Jesus Eduardo Martinez Hernandez, Mario Alberto Pena Hernandez, Enrique Amaya Perez, Rebeca Paola Torres Ramirez, Cla, J., Martin, Hanzel, Sarah Mohand Said, Shihab, Sawar, Dylan, Siriwardena, Alex, Tzahristos, Nils, Anlind, Martin, Friberg, Erik, Gullberg, Stephanie, Herman, Dallin, Christensen, Sara, Gertsch, Cody, Maxfield, Charles, Miller, Ryan, Putman, Christine, Bauerl, Estelles Lopez, Lucia T., Estefania Huet Trujillo, Marta Vazquez Vilar, Marlène Sophie Birk, Nico, Claassens, Walter de Koster, Rik van Rosmalen, Wen Ying Wu, Sian, Davies, Dan, Goss, William, Rostain, Chelsey, Tye, Waqar, Yousaf, Natalie, Farny, Chloe, Lajeunesse, Alex, Turland, Chen, An, Jielin, Chen, Yahong, Chen, Zehua, Che, Baishan, Fang, Xiaotong, Fu, Xifeng, Guo, Yue, Jiang, Yiying, Lei, Jianqiao, Li, Zhe, Li, Chang, Liu, Weibing, Liu, Yang, Li, Yizhu, Lv, Qingyu, Ruan, Yue, Su, Chun, Tang, Yushen, Wang, Fan, Wu, Xiaoshan, Yan, Ruihua, Zhang, Tangduo, Zhang, Farren, Isaacs, Ariel Leyva Hernandez, Natalie, Ma, Stephanie, Mao, Yamini, Naidu, Tuukka, Miinalainen, Marion Aruann, Daniel Calendini, Yoann Chabert, Gael Chambonnier, Myriam, Choukour, Ella de Gaulejac, Camille, Houy, Axel, Levier, Loreen, Logger, Sebastien, Nin, Valerie, Prima, Sturgis, James N., Beibei, Fang, Sadik, Cigdem, Abdullah, Ucar, Alejandro, Gutierrez, Revanth, Poondla, Sanjana, Reddy, Tyler, Rocha, Natalie, Schulte, Devin, Wehle, Marta Eva Jackowski, Sean Ross Craig, Ariana Mirzarafie Ahi, Elliott, Parris, Luba, Prout, Barbara, Steijl, Rachel, Wellman, Zhao, Fan, Zhang, Jing, Yang, Wei, Yang, Yuanzhan, Wen, Zhaosen, Evan, Appletion, Jeffrey, Chen, Abha, Patil, Shaheer, Priracha, Kate, Ryan, Nick, Salvador, John, Viola, Boralli, Camila Maria S., Camila Barbosa Bramorski, Juliana Cancino Bernardi, Ana Laura de Lima, Paula Maria Pincela Lins, Cristiane Casonato Melo, Deborah Cezar Mendonca, Thiago, Mosqueiro, Everton, Silva, Graziele, Vasconcelos, Ruchi, Asthana, Donna, Lee, Michelle, Yu, Peter, Choi, Effie, Lau, Kenneth, Lau, Oscar, Ying, Brandon, Malone, Paul, Young, Aidan, Ceney, Dakota, Hawthorne, Sharon, Lian, Sam, Mellentine, Dylan, Miller, Barbara Castro Moreira, Christie, Peebles, Olivia, Smith, Kevin, Walsh, Allison, Zimont, Michael, Brasino, Michael, Donovan, Hannah, Young, Jan, Bejvl, Daniel, Georgiev, Hynek, Kasl, Katerina Pechotova, Vaclav Pelisek, Anna, Sosnova, Pavel, Zach, Anthony, Ciesla, Benjamin, Hoover, Elliott, Chapman, Jon Marles Wright, Vicky, Moynihan, Liusaidh, Owen, Brooke Rothschild Mancinelli, Emilie, Cuillery, Joseph, Heng, Vincent, Jacquot, Paola, Malsot, Rocco, Meli, Cyril, Pulver, Ari, Sarfatis, Loic, Steiner, Victor, Steininger, Nina van Tiel, Gregoire, Thouvenin, Axel, Uran, Lisa, Baumgartner, Anna, Fomitcheva, Daniel, Gerngross, Verena, Jagger, Michael, Meier, Anja, Michel, Jasmine, Bird, Bradley, Brown, Todd, Burlington, Daniel, Herring, Joseph, Slack, Georgina, Westwood, Emilia, Wojcik, Julian, Bender, Julia, Donauer, Ramona, Emig, Rabea, Jesser, Julika, Neumann, Lara, Stuhn, Takema, Hasegawa, Tomoya, Kozakai, Haruka, Maruyama, Sean, Colloms, Charlotte, Flynn, Vilija, Lomeikaite, James, Provan, Kang, Ning, Shuyan, Tang, Guozhao, Wu, Yunjun, Yang, Zhi, Zeng, Zhan, Yi, Pan, Chu, Jun, Li, Keji, Yan, Athale, Chaitanya A., Swapnil, Bodkhe, Manasi, Gangan, Harsh, Gakhare, Yash, Jawale, Snehal, Kadam, Prachiti, Moghe, Gayatri, Mundhe, Neha, Khetan, Ira, Phadke, Prashant, Uniyal, Siddhesh, Zadey, Ines, Cottignie, Eline, Deprez, Astrid, Deryckere, Jasper, Janssens, Frederik, Jonnaert, Katarzyna, Malczewska, Thomas, Pak, Johan, Robben, Ovia Margaret Thirukkumaran, Vincent Van Deuren, Laurens, Vandebroek, Laura Van Hese, Laetitia Van Wonterghem, Leen, Verschooten, Moritz, Wolter, Joss, Auty, Richard, Badge, Liam, Crawford, Raymond, Dalgleish, Amy, Evans, Cameron, Grundy, Charlie, Kruczko, Payal, Karia, Graeme, Glaister, Rhys, Hakstol, Seme, Mate, Karin, Otero, Dustin, Smith, Jeff, Tingley, Hans Joachim Wieden, Haotian, Wang, Ningning, Yao, Matthias, Franz, Anna, Knoerlein, Nicolas, Koutsoubelis, Loechner, Anne C., Max, Mundt, Alexandra, Richter, Oliver, Schauer, Marjorie, Buss, Sivateja, Tangirala, Brian, Teague, Tianyi, Huang, Xinhao, Song, Yibing, Wei, Zhaoran, Zhang, Longzhi, Cao, Cheng Li, Kang Yang, Zhiqin, Chen, Yuxing, Fang, Libo, Sun, Weiyi, Wang, Yang, Yang, David, Adams, Joshua, Colls, Joshua, Timmons, David, Urick, Julia Anna Adrian, Madina, Akan, Youssef, Chahibi, Rahmi, Lale, Typhaine Le Doujet, Marit Vaagen Roee, Altynay, Abdirakhmanova, Askarbek, Orakov, Azhar, Zhailauova, Jinyang, Liang, Yu, Ma, Qikai, Qin, Yetian, Su, Ju Yeon Han, Raphaella, Hull, Wei Chung Kong, Li Chieh Lu, Duke, Quinton, Pauline, Aubert, Johan, Bourdarias, Olivier, Bugaud, Coralie Demon Chaine, Isabelle, Hatin, Ibtissam Kaid Slimane, Seong Koo Kang, Audrey, Moatti, Cheikh Fall Ndiaye, Mathilde, Ananos, Alexander, Arkhipenko, Valentin, Bailly, Jules, Caput, Javier, Castillo, Alma Chapet Batlle, Floriane, Cherrier, Claudia Demarta Gatsi, Deshmukh, Gopaul, Muriel, Gugger, Caroline, Lambert, Lucas, Krauss, Amelie, Vandendaele, Xiaojing, Li, Lin, Xiaomei, Luo Xunxun, Anders C. h. r. Hansen, Tina, Kronborg, Pettersen, Jens S., Charles, Calvet, Tyler Dae Devlin, Kosuke, Fujishima, Danny, Greenberg, Tina, Ju, Ryan, Kent, Daniel, Kunin, Erica, Lieberman, Griffin, Mccutcheon, Thai, Nguyen, Lynn, Rothschild, Shih, Joseph D., Jack, Takahashi, Kirsten, Thompson, Forrest, Tran, Daniel, Xiang, Felix, Richter, Yang, Xiaoran, Xiangyue, Hu, Changyuan, Deng, Shuyu, Hua, Yumeng, Li, Xinyu, Meng, Boxiang, Wang, Yingqi, Wang, Xuan, Wang, Zixuan, Xu, Jieyu, Yan, Ming, Yan, Yineng, Zhou, Edgar Alberto Alcalá Orozco, José Alberto Cristerna Bermúdez, Daniela Flores Gómez, José Ernesto Hernández Castañeda, Diana Clarisse Montaño Navarro, Juana Yessica PérezÁvila, María Fernanda Salazar Figueroa, María Fernanda Sánchez Arroyo, Oliva Angélica Sánchez Montesinos, Ángel Farid Rojas Cruz, Carlos Ramos Gutiérrez, Alonso Pérez Lona, Carlos Alejandro Meza Ramírez, Fernanda Sotomayor Olivares, Jorge Sebastián Rodríguez Iniesta, Juan Carlos Rueda Silva, Shotaro, Ayukawa, Takahiro, Kashiwagi, Daisuke, Kiga, Misa, Minegishi, Riku, Shinohara, Hiraku, Tokuma, Yuta, Yamazaki, Shuhei, Yasunishi, Erinn Sim Zixuan, Remsha, Afzal, Matthew, Carrigan, Barry, Moran, Marlena, Mucha, Arnas, Petrauskas, Stefan, Marsden, Michelle, Post, Anne, Rodenburg, Hector, Sanguesa, Marit van der Does, Erwin van Rijn, Max van’t Hof, Yeshi de Bruin, Hans de Ferrante, Elles, Elschot, Laura, Jacobs, Jan Willem Muller, Sjoerd, Nooijens, Femke, Vaassen, Cas van der Putten, Esther van Leeuwen, Laura van Smeden, Kwan Kwan Zhu, Kevin, Sabath, Katharina, Sporbeck, Nicolai von Kügelgen, Lisa, Wellinger, Stefanie, Braun, Jack, Ho, Yash, Mishra, Mariola, Sebastian, Lucas von Chamier, Ahsan, Fasih M., Satyadi, Megan A., Vivienne, Gunadhi, Phillip, Kyriakakis, Jenny, Lee, Walter, Thavarajah, Kimia, Abtahi, Robert, Hand, Chun Mun Loke, Adam, Wahab, Iowis, Zhu, Del Bianco, Cristina, Chizzolini, Fabio, Elisa, Godino, Lentini, Roberta, Mansy, Sheref Samir, Yeh Martin, Noel, Claudio Oss Pegorar, Alexander, Cook, Timothy, Kerns, Chad, Nielsen, Michael, Paskett, Alexander, Torgesen, Stephen, Lee, Ophir, Ospovat, Sikandar, Raza, Daniel, Shaykevich, Jarrod, Shilts, Barbora, Bajorinaite, Mykolas, Bendorius, Ieva, Rauluseviciute, Ieva, Savickyte, Sarunas, Tumas, William, Buchser, Elli, Cryan, Caroline, Golino, Andrew, Halleran, Taylor, Jacobs, Michael, Lefew, Joe, Maniaci, John, Marken, Margaret, Saha, Panya, Vij, Kayla, Desanty, Julie, Mazza

Publikováno v: PLoS ONE
PLoS ONE, Public Library of Science, 2016, 11 (3), pp.e0150182. ⟨10.1371/journal.pone.0150182⟩
PloS one, vol 11, iss 3
BASE-Bielefeld Academic Search Engine
PLoS ONE, Vol 11, Iss 3, p e0150182 (2016)
PLOS ONE
PLoS ONE, 11(3):e0150182. PUBLIC LIBRARY SCIENCE
PLoS ONE, 11 (3)

We present results of the first large-scale interlaboratory study carried out in synthetic biology, as part of the 2014 and 2015 International Genetically Engineered Machine (iGEM) competitions. Participants at 88 institutions around the world measur

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::243ad737ce1604fc761ea2d853c79295
http://europepmc.org/articles/PMC4777433