| KVFinder: steered identification of protein cavities as a PyMOL plugin SHP Oliveira, FAN Ferraz, RV Honorato, J Xavier-Neto, TJP Sobreira, ... BMC bioinformatics 15, 1-8, 2014 | 117 | 2014 |
| STCRDab: the structural T-cell receptor database J Leem, SHP de Oliveira, K Krawczyk, CM Deane Nucleic Acids Research, 2017 | 99 | 2017 |
| Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis M Dasgupta, D Budday, SHP De Oliveira, P Madzelan, ... Proceedings of the National Academy of Sciences 116 (51), 25634-25640, 2019 | 81 | 2019 |
| Ligand binding remodels protein side-chain conformational heterogeneity SA Wankowicz, SH de Oliveira, DW Hogan, H van den Bedem, JS Fraser Elife 11, e74114, 2022 | 62 | 2022 |
| qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps GCP van Zundert, BM Hudson, SHP de Oliveira, DA Keedy, R Fonseca, ... Journal of Medicinal Chemistry 61 (24), 11183-11198, 2018 | 55 | 2018 |
| qFit 3: Protein and ligand multiconformer modeling for X‐ray crystallographic and single‐particle cryo‐EM density maps BT Riley, SA Wankowicz, SHP de Oliveira, GCP van Zundert, DW Hogan, ... Protein Science 30 (1), 270-285, 2021 | 45 | 2021 |
| Building a better fragment library for de novo protein structure prediction SHP de Oliveira, J Shi, CM Deane PloS one 10 (4), e0123998, 2015 | 41 | 2015 |
| Comparing co-evolution methods and their application to template-free protein structure prediction SHP de Oliveira, J Shi, CM Deane Bioinformatics 33 (3), 373-381, 2017 | 40 | 2017 |
| Co-evolution techniques are reshaping the way we do structural bioinformatics SHP de Oliveira, CM Deane | 39 | 2017 |
| AI is a viable alternative to high throughput screening: a 318-target study Scientific reports 14 (1), 7526, 2024 | 34 | 2024 |
| Insights into the organization of dorsal spinal cord pathways from an evolutionarily conserved raldh2 intronic enhancer HA Castillo, RM Cravo, AP Azambuja, MS Simões-Costa, S Sura-Trueba, ... Development 137 (3), 507-518, 2010 | 32 | 2010 |
| Antimalarials and the fight against malaria in Brazil LMA Carmargo, S de Oliveira, S Basano, CRS Garcia Therapeutics and Clinical Risk Management, 311-317, 2009 | 30 | 2009 |
| FERM domain interaction with myosin negatively regulates FAK in cardiomyocyte hypertrophy AM Santos, D Schechtman, AC Cardoso, CFMZ Clemente, JC Silva, ... Nature chemical biology 8 (1), 102-110, 2012 | 25 | 2012 |
| Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction SHP de Oliveira, EC Law, J Shi, CM Deane Bioinformatics 34 (7), 1132-1140, 2018 | 21 | 2018 |
| Sequence-guided protein structure determination using graph convolutional and recurrent networks PN Li, SHP de Oliveira, S Wakatsuki, H van den Bedem 2020 IEEE 20th international conference on bioinformatics and bioengineering …, 2020 | 12 | 2020 |
| Discovery of a cryptic pocket in the AI-predicted structure of PPM1D phosphatase explains the binding site and potency of its allosteric inhibitors A Meller, S De Oliveira, A Davtyan, T Abramyan, GR Bowman, ... Frontiers in molecular biosciences 10, 1171143, 2023 | 9 | 2023 |
| Combining co-evolution and secondary structure prediction to improve fragment library generation. SHP de Oliveira, CM Deane Bioinformatics 1, 9, 2018 | 9 | 2018 |
| The evolution of contact prediction: Evidence that contact selection in statistical contact prediction is changing M Chonofsky, SHP de Oliveira, K Krawczyk, CM Deane Bioinformatics 36 (6), 1750-1756, 2020 | 8 | 2020 |
| RFQAmodel: Random Forest Quality Assessment to identify a predicted protein structure in the correct fold CE West, SHP de Oliveira, CM Deane PLoS One 14 (10), e0218149, 2019 | 5 | 2019 |
| Processing biophysical screening data and identifying and characterizing protein sites for drug discovery S De Oliveira, J Hermann, C Varma US Patent App. 17/444,019, 2022 | 4 | 2022 |
