Ligand binding remodels protein side-chain conformational heterogeneity
Wankowicz, Stephanie A, de Oliveira, Saulo H, Hogan, Daniel W, van den Bedem, Henry, Fraser, James S
Published in eLife (21.03.2022)
Published in eLife (21.03.2022)
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Journal Article
STCRDab: the structural T-cell receptor database
Leem, Jinwoo, de Oliveira, Saulo H P, Krawczyk, Konrad, Deane, Charlotte M
Published in Nucleic acids research (04.01.2018)
Published in Nucleic acids research (04.01.2018)
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Journal Article
qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X‑Ray Electron Density Maps
van Zundert, Gydo C. P, Hudson, Brandi M, de Oliveira, Saulo H. P, Keedy, Daniel A, Fonseca, Rasmus, Heliou, Amelie, Suresh, Pooja, Borrelli, Kenneth, Day, Tyler, Fraser, James S, van den Bedem, Henry
Published in Journal of medicinal chemistry (27.12.2018)
Published in Journal of medicinal chemistry (27.12.2018)
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Journal Article
qFit 3: Protein and ligand multiconformer modeling for X‐ray crystallographic and single‐particle cryo‐EM density maps
Riley, Blake T., Wankowicz, Stephanie A., Oliveira, Saulo H. P., Zundert, Gydo C. P., Hogan, Daniel W., Fraser, James S., Keedy, Daniel A., Bedem, Henry
Published in Protein science (01.01.2021)
Published in Protein science (01.01.2021)
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Journal Article
Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis
Dasgupta, Medhanjali, Budday, Dominik, de Oliveira, Saulo H. P., Madzelan, Peter, Marchany-Rivera, Darya, Seravalli, Javier, Hayes, Brandon, Sierra, Raymond G., Boutet, Sébastien, Hunter, Mark S., Alonso-Mori, Roberto, Batyuk, Alexander, Wierman, Jennifer, Lyubimov, Artem, Brewster, Aaron S., Sauter, Nicholas K., Applegate, Gregory A., Tiwari, Virendra K., Berkowitz, David B., Thompson, Michael C., Cohen, Aina E., Fraser, James S., Wall, Michael E., van den Bedem, Henry, Wilson, Mark A.
Published in Proceedings of the National Academy of Sciences - PNAS (17.12.2019)
Published in Proceedings of the National Academy of Sciences - PNAS (17.12.2019)
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Journal Article
Insights into the organization of dorsal spinal cord pathways from an evolutionarily conserved raldh2 intronic enhancer
Castillo, Hozana A, Cravo, Roberta M, Azambuja, Ana P, Simões-Costa, Marcos S, Sura-Trueba, Sylvia, Gonzalez, Jose, Slonimsky, Esfir, Almeida, Karla, Abreu, José G, de Almeida, Marcio A Afonso, Sobreira, Tiago P, de Oliveira, Saulo H Pires, de Oliveira, Paulo S Lopes, Signore, Iskra A, Colombo, Alicia, Concha, Miguel L, Spengler, Tatjana S, Bronner-Fraser, Marianne, Nobrega, Marcelo, Rosenthal, Nadia, Xavier-Neto, José
Published in Development (Cambridge) (01.02.2010)
Published in Development (Cambridge) (01.02.2010)
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Journal Article
Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction
de Oliveira, Saulo H P, Law, Eleanor C, Shi, Jiye, Deane, Charlotte M
Published in Bioinformatics (01.04.2018)
Published in Bioinformatics (01.04.2018)
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Journal Article
Sequence-guided protein structure determination using graph convolutional and recurrent networks
Li, Po-Nan, de Oliveira, Saulo H. P., Wakatsuki, Soichi, van den Bedem, Henry
Published in 2020 IEEE 20th International Conference on Bioinformatics and Bioengineering (BIBE) (01.10.2020)
Published in 2020 IEEE 20th International Conference on Bioinformatics and Bioengineering (BIBE) (01.10.2020)
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Conference Proceeding
Sequence-guided protein structure determination using graph convolutional and recurrent networks
Li, Po-Nan, de Oliveira, Saulo H. P, Wakatsuki, Soichi, Bedem, Henry van den
Year of Publication 14.07.2020
Year of Publication 14.07.2020
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Journal Article
qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps
Riley, Blake T, Wankowicz, Stephanie A, Saulo H P De Oliveira, Gydo C P Van Zundert, Hogan, Daniel, Fraser, James S, Keedy, Daniel A, Van Den Bedem, Henry
Published in bioRxiv (03.09.2020)
Published in bioRxiv (03.09.2020)
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Paper
Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis
Dasgupta, Medhanjali, Budday, Dominik, Saulo H P De Oliveira, Madzelan, Peter, Marchany-Rivera, Darya, Seravalli, Javier, Hayes, Brandon, Sierra, Raymond G, Boutet, Sebastian, Hunter, Mark, Alonso-Mori, Roberto, Batyuk, Alexander, Wierman, Jennifer, Lyubimov, Artem, Brewster, Aaron S, Sauter, Nicholas K, Applegate, Gregory A, Tiwari, Virendra K, Berkowitz, David B, Thompson, Michael C, Cohen, Aina E, Fraser, James S, Wall, Michael E, Van Den Bedem, Henry, Wilson, Mark A
Published in bioRxiv (24.08.2019)
Published in bioRxiv (24.08.2019)
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Paper