日期:
2020 年 — 2026 年
2020
2021
2022
2023
2024
2025
2026
影响因子:

Applying computational protein design to therapeutic antibody discovery - current state and perspectives

将计算蛋白质设计应用于治疗性抗体发现——现状与展望

Bielska, Weronika; Jaszczyszyn, Igor; Dudzic, Pawel; Janusz, Bartosz; Chomicz, Dawid; Wrobel, Sonia; Greiff, Victor; Feehan, Ryan; Adolf-Bryfogle, Jared; Krawczyk, Konrad

Complete combinatorial mutational enumeration of a protein functional site enables sequence-landscape mapping and identifies highly-mutated variants that retain activity.

对蛋白质功能位点进行完整的组合突变枚举,可以绘制序列景观图,并识别保留活性的高度突变变体

Colom Mireia SolÃ, Vučinić Jelena, Adolf-Bryfogle Jared, Bowman James W, Verel Sébastien, Moczygemba Isabelle, Schiex Thomas, Simoncini David, Bahl Christopher D

Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design

在 Rosetta 中构建聚糖:精确的从头聚糖建模、密度拟合和合理的序列设计

Adolf-Bryfogle, Jared; Labonte, Jason W; Kraft, John C; Shapovalov, Maxim; Raemisch, Sebastian; Lütteke, Thomas; DiMaio, Frank; Bahl, Christopher D; Pallesen, Jesper; King, Neil P; Gray, Jeffrey J; Kulp, Daniel W; Schief, William R

Corrigendum to "Computational design of nanomolar-binding antibodies specific to multiple SARS-CoV-2 variants by engineering a specificity switch of antibody 80R using RosettaAntibodyDesign (RAbD) results in potential generalizable therapeutic antibodies for novel SARS-CoV-2 virus" [Heliyon 9(4) (April 2023) e15032]

对“利用 RosettaAntibodyDesign (RAbD) 对抗体 80R 进行特异性转换,计算设计针对多种 SARS-CoV-2 变体的纳摩尔结合抗体,从而获得可用于新型 SARS-CoV-2 病毒的潜在通用治疗性抗体”的更正 [Heliyon 9(4) (2023 年 4 月) e15032]

Hernandez, Nancy E; Jankowski, Wojciech; Frick, Rahel; Kelow, Simon P; Lubin, Joseph H; Simhadri, Vijaya; Adolf-Bryfogle, Jared; Khare, Sagar D; Dunbrack, Roland L Jr; Gray, Jeffrey J; Sauna, Zuben E

Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

通过广泛的自动化基准测试确保生物大分子建模的科学可重复性

Koehler Leman, Julia; Lyskov, Sergey; Lewis, Steven M; Adolf-Bryfogle, Jared; Alford, Rebecca F; Barlow, Kyle; Ben-Aharon, Ziv; Farrell, Daniel; Fell, Jason; Hansen, William A; Harmalkar, Ameya; Jeliazkov, Jeliazko; Kuenze, Georg; Krys, Justyna D; Ljubetič, Ajasja; Loshbaugh, Amanda L; Maguire, Jack; Moretti, Rocco; Mulligan, Vikram Khipple; Nance, Morgan L; Nguyen, Phuong T; Ó Conchúir, Shane; Roy Burman, Shourya S; Samanta, Rituparna; Smith, Shannon T; Teets, Frank; Tiemann, Johanna K S; Watkins, Andrew; Woods, Hope; Yachnin, Brahm J; Bahl, Christopher D; Bailey-Kellogg, Chris; Baker, David; Das, Rhiju; DiMaio, Frank; Khare, Sagar D; Kortemme, Tanja; Labonte, Jason W; Lindorff-Larsen, Kresten; Meiler, Jens; Schief, William; Schueler-Furman, Ora; Siegel, Justin B; Stein, Amelie; Yarov-Yarovoy, Vladimir; Kuhlman, Brian; Leaver-Fay, Andrew; Gront, Dominik; Gray, Jeffrey J; Bonneau, Richard

CoV3D: a database of high resolution coronavirus protein structures

CoV3D:高分辨率冠状病毒蛋白结构数据库

Gowthaman, Ragul; Guest, Johnathan D; Yin, Rui; Adolf-Bryfogle, Jared; Schief, William R; Pierce, Brian G

Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design

利用 Rosetta 进行免疫建模:抗体和抗原设计方法

Schoeder, Clara T; Schmitz, Samuel; Adolf-Bryfogle, Jared; Sevy, Alexander M; Finn, Jessica A; Sauer, Marion F; Bozhanova, Nina G; Mueller, Benjamin K; Sangha, Amandeep K; Bonet, Jaume; Sheehan, Jonathan H; Kuenze, Georg; Marlow, Brennica; Smith, Shannon T; Woods, Hope; Bender, Brian J; Martina, Cristina E; Del Alamo, Diego; Kodali, Pranav; Gulsevin, Alican; Schief, William R; Correia, Bruno E; Crowe, James E Jr; Meiler, Jens; Moretti, Rocco

Development and Evaluation of GlycanDock: A Protein-Glycoligand Docking Refinement Algorithm in Rosetta

GlycanDock 的开发与评估:Rosetta 中的蛋白质-糖配体对接优化算法

Nance, Morgan L; Labonte, Jason W; Adolf-Bryfogle, Jared; Gray, Jeffrey J

PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design

PyRosetta Jupyter Notebooks 教授生物分子结构预测和设计

Le, Kathy H; Adolf-Bryfogle, Jared; Klima, Jason C; Lyskov, Sergey; Labonte, Jason; Bertolani, Steven; Burman, Shourya S Roy; Leaver-Fay, Andrew; Weitzner, Brian; Maguire, Jack; Rangan, Ramya; Adrianowycz, Matt A; Alford, Rebecca F; Adal, Aleexsan; Nance, Morgan L; Wu, Yuanhan; Willis, Jordan; Kulp, Daniel W; Das, Rhiju; Dunbrack, Roland L Jr; Schief, William; Kuhlman, Brian; Siegel, Justin B; Gray, Jeffrey J

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Rosetta中的大分子建模与设计:最新方法和框架

Leman, Julia Koehler; Weitzner, Brian D; Lewis, Steven M; Adolf-Bryfogle, Jared; Alam, Nawsad; Alford, Rebecca F; Aprahamian, Melanie; Baker, David; Barlow, Kyle A; Barth, Patrick; Basanta, Benjamin; Bender, Brian J; Blacklock, Kristin; Bonet, Jaume; Boyken, Scott E; Bradley, Phil; Bystroff, Chris; Conway, Patrick; Cooper, Seth; Correia, Bruno E; Coventry, Brian; Das, Rhiju; De Jong, René M; DiMaio, Frank; Dsilva, Lorna; Dunbrack, Roland; Ford, Alexander S; Frenz, Brandon; Fu, Darwin Y; Geniesse, Caleb; Goldschmidt, Lukasz; Gowthaman, Ragul; Gray, Jeffrey J; Gront, Dominik; Guffy, Sharon; Horowitz, Scott; Huang, Po-Ssu; Huber, Thomas; Jacobs, Tim M; Jeliazkov, Jeliazko R; Johnson, David K; Kappel, Kalli; Karanicolas, John; Khakzad, Hamed; Khar, Karen R; Khare, Sagar D; Khatib, Firas; Khramushin, Alisa; King, Indigo C; Kleffner, Robert; Koepnick, Brian; Kortemme, Tanja; Kuenze, Georg; Kuhlman, Brian; Kuroda, Daisuke; Labonte, Jason W; Lai, Jason K; Lapidoth, Gideon; Leaver-Fay, Andrew; Lindert, Steffen; Linsky, Thomas; London, Nir; Lubin, Joseph H; Lyskov, Sergey; Maguire, Jack; Malmström, Lars; Marcos, Enrique; Marcu, Orly; Marze, Nicholas A; Meiler, Jens; Moretti, Rocco; Mulligan, Vikram Khipple; Nerli, Santrupti; Norn, Christoffer; Ó'Conchúir, Shane; Ollikainen, Noah; Ovchinnikov, Sergey; Pacella, Michael S; Pan, Xingjie; Park, Hahnbeom; Pavlovicz, Ryan E; Pethe, Manasi; Pierce, Brian G; Pilla, Kala Bharath; Raveh, Barak; Renfrew, P Douglas; Burman, Shourya S Roy; Rubenstein, Aliza; Sauer, Marion F; Scheck, Andreas; Schief, William; Schueler-Furman, Ora; Sedan, Yuval; Sevy, Alexander M; Sgourakis, Nikolaos G; Shi, Lei; Siegel, Justin B; Silva, Daniel-Adriano; Smith, Shannon; Song, Yifan; Stein, Amelie; Szegedy, Maria; Teets, Frank D; Thyme, Summer B; Wang, Ray Yu-Ruei; Watkins, Andrew; Zimmerman, Lior; Bonneau, Richard