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

Modeling Protein-Protein and Protein-Ligand Interactions by the ClusPro Team in CASP16

ClusPro团队在CASP16中对蛋白质-蛋白质和蛋白质-配体相互作用进行了建模

Ashizawa, Ryota; Kotelnikov, Sergei; Khan, Omeir; Li, Stan Xiaogang; Glukhov, Ernest; Cao, Xin; Lazou, Maria; Bekar-Cesaretli, Ayse; Hailegeorgis, Derara; Averkava, Veranika; Zhu, Yimin; Jones, George; Yu, Hao; Kalitin, Dmytro; Stepanenko, Darya; Koirala, Kushal; Patsahan, Taras; Beglov, Dmitri; Lukin, Mark; Joseph-McCarthy, Diane; Simmerling, Carlos; Tropsha, Alexander; Coutsias, Evangelos; Dill, Ken A; Padhorny, Dzmitry; Vajda, Sandor; Kozakov, Dima

Conventional and non-conventional antigen-binding sites promote the development and function of chronic lymphocytic leukemia stereotyped subset #4 clones

常规和非常规抗原结合位点促进慢性淋巴细胞白血病刻板亚群#4克隆的发育和功能

Liu, Yun; Padhorny, Dzmitry; Catera, Rosa; Nicolo, Antonella; Yan, Xiao-Jie; Li, Stan Xiaogang; Iatrou, Anastasia; Mazzarello, Andrea N; Destefani, Noemi; Allen, Steven L; Kolitz, Jonathan E; Rai, Kanti R; Degano, Massimo; Ghia, Paolo P; Chu, Charles C; Krammer, Florian; Jumaa, Hassan; Stamatopoulos, Kostas; Kozakov, Dima; Chiorazzi, Nicholas

Predicting multiple conformations of ligand binding sites in proteins suggests that AlphaFold2 may remember too much

预测蛋白质中配体结合位点的多种构象表明,AlphaFold2 可能记忆过多。

Lazou, Maria; Khan, Omeir; Nguyen, Thu; Padhorny, Dzmitry; Kozakov, Dima; Joseph-McCarthy, Diane; Vajda, Sandor

Multiomic profiling of chronically activated CD4+ T cells identifies drivers of exhaustion and metabolic reprogramming

慢性活化 CD4+ T 细胞的多组学分析可识别衰竭和代谢重编程的驱动因素

Matthew L Lawton, Melissa M Inge, Benjamin C Blum, Erika L Smith-Mahoney, Dante Bolzan, Weiwei Lin, Christina McConney, Jacob Porter, Jarrod Moore, Ahmed Youssef, Yashasvi Tharani, Xaralabos Varelas, Gerald V Denis, Wilson W Wong, Dzmitry Padhorny, Dima Kozakov, Trevor Siggers, Stefan Wuchty, Jennif

MHC-Fine: Fine-tuned AlphaFold for precise MHC-peptide complex prediction

MHC-Fine:用于精确预测 MHC-肽复合物的精细化 AlphaFold

Glukhov, Ernest; Kalitin, Dmytro; Stepanenko, Darya; Zhu, Yimin; Nguyen, Thu; Jones, George; Patsahan, Taras; Simmerling, Carlos; Mitchell, Julie C; Vajda, Sandor; Dill, Ken A; Padhorny, Dzmitry; Kozakov, Dima

Parallelized multidimensional analytic framework applied to mammary epithelial cells uncovers regulatory principles in EMT

并行多维分析框架应用于乳腺上皮细胞揭示 EMT 的调控原理

Indranil Paul, Dante Bolzan, Ahmed Youssef, Keith A Gagnon, Heather Hook, Gopal Karemore, Michael U J Oliphant, Weiwei Lin, Qian Liu, Sadhna Phanse, Carl White, Dzmitry Padhorny, Sergei Kotelnikov, Christopher S Chen, Pingzhao Hu, Gerald V Denis, Dima Kozakov, Brian Raught, Trevor Siggers, Stefan Wu

Opinion: Protein folds vs. protein folding: Differing questions, different challenges

观点:蛋白质折叠与蛋白质折叠:不同的问题,不同的挑战

Chen, Shi-Jie; Hassan, Mubashir; Jernigan, Robert L; Jia, Kejue; Kihara, Daisuke; Kloczkowski, Andrzej; Kotelnikov, Sergei; Kozakov, Dima; Liang, Jie; Liwo, Adam; Matysiak, Silvina; Meller, Jarek; Micheletti, Cristian; Mitchell, Julie C; Mondal, Sayantan; Nussinov, Ruth; Okazaki, Kei-Ichi; Padhorny, Dzmitry; Skolnick, Jeffrey; Sosnick, Tobin S; Stan, George; Vakser, Ilya; Zou, Xiaoqin; Rose, George D

Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment

AlphaFold对蛋白质复合物结构预测的影响:CASP15-CAPRI实验

Lensink, Marc F; Brysbaert, Guillaume; Raouraoua, Nessim; Bates, Paul A; Giulini, Marco; Honorato, Rodrigo V; van Noort, Charlotte; Teixeira, Joao M C; Bonvin, Alexandre M J J; Kong, Ren; Shi, Hang; Lu, Xufeng; Chang, Shan; Liu, Jian; Guo, Zhiye; Chen, Xiao; Morehead, Alex; Roy, Raj S; Wu, Tianqi; Giri, Nabin; Quadir, Farhan; Chen, Chen; Cheng, Jianlin; Del Carpio, Carlos A; Ichiishi, Eichiro; Rodriguez-Lumbreras, Luis A; Fernandez-Recio, Juan; Harmalkar, Ameya; Chu, Lee-Shin; Canner, Sam; Smanta, Rituparna; Gray, Jeffrey J; Li, Hao; Lin, Peicong; He, Jiahua; Tao, Huanyu; Huang, Sheng-You; Roel-Touris, Jorge; Jimenez-Garcia, Brian; Christoffer, Charles W; Jain, Anika J; Kagaya, Yuki; Kannan, Harini; Nakamura, Tsukasa; Terashi, Genki; Verburgt, Jacob C; Zhang, Yuanyuan; Zhang, Zicong; Fujuta, Hayato; Sekijima, Masakazu; Kihara, Daisuke; Khan, Omeir; Kotelnikov, Sergei; Ghani, Usman; Padhorny, Dzmitry; Beglov, Dmitri; Vajda, Sandor; Kozakov, Dima; Negi, Surendra S; Ricciardelli, Tiziana; Barradas-Bautista, Didier; Cao, Zhen; Chawla, Mohit; Cavallo, Luigi; Oliva, Romina; Yin, Rui; Cheung, Melyssa; Guest, Johnathan D; Lee, Jessica; Pierce, Brian G; Shor, Ben; Cohen, Tomer; Halfon, Matan; Schneidman-Duhovny, Dina; Zhu, Shaowen; Yin, Rujie; Sun, Yuanfei; Shen, Yang; Maszota-Zieleniak, Martyna; Bojarski, Krzysztof K; Lubecka, Emilia A; Marcisz, Mateusz; Danielsson, Annemarie; Dziadek, Lukasz; Gaardlos, Margrethe; Gieldon, Artur; Liwo, Adam; Samsonov, Sergey A; Slusarz, Rafal; Zieba, Karolina; Sieradzan, Adam K; Czaplewski, Cezary; Kobayashi, Shinpei; Miyakawa, Yuta; Kiyota, Yasuomi; Takeda-Shitaka, Mayuko; Olechnovic, Kliment; Valancauskas, Lukas; Dapkunas, Justas; Venclovas, Ceslovas; Wallner, Bjorn; Yang, Lin; Hou, Chengyu; He, Xiaodong; Guo, Shuai; Jiang, Shenda; Ma, Xiaoliang; Duan, Rui; Qui, Liming; Xu, Xianjin; Zou, Xiaoqin; Velankar, Sameer; Wodak, Shoshana J

Accurate ligand-protein docking in CASP15 using the ClusPro LigTBM server

使用 ClusPro LigTBM 服务器在 CASP15 中进行精确的配体-蛋白对接

Kotelnikov, Sergei; Ashizawa, Ryota; Popov, Konstantin I; Khan, Omeir; Ignatov, Mikhail; Li, Stan Xiaogang; Hassan, Mosavverul; Coutsias, Evangelos A; Poda, Gennady; Padhorny, Dzmitry; Tropsha, Alexander; Vajda, Sandor; Kozakov, Dima

MHC-Fine: Fine-tuned AlphaFold for Precise MHC-Peptide Complex Prediction

MHC-Fine:用于精确预测 MHC-肽复合物的精细化 AlphaFold

Glukhov, Ernest; Kalitin, Dmytro; Stepanenko, Darya; Zhu, Yimin; Nguyen, Thu; Jones, George; Simmerling, Carlos; Mitchell, Julie C; Vajda, Sandor; Dill, Ken A; Padhorny, Dzmitry; Kozakov, Dima