K
Krishna Praneeth Kilambi
Researcher at Johns Hopkins University
Publications - 18
Citations - 858
Krishna Praneeth Kilambi is an academic researcher from Johns Hopkins University. The author has contributed to research in topics: Searching the conformational space for docking & Macromolecular docking. The author has an hindex of 12, co-authored 16 publications receiving 701 citations. Previous affiliations of Krishna Praneeth Kilambi include Biogen Idec.
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Journal ArticleDOI
Structural and kinetic basis for the selectivity of aducanumab for aggregated forms of amyloid-β
Joseph Arndt,Fang Qian,Benjamin A. Smith,Chao Quan,Krishna Praneeth Kilambi,Martin Bush,Thomas Walz,Thomas Walz,R. B. Pepinsky,Thierry Bussiere,S. Hamann,Thomas Cameron,Paul H. Weinreb +12 more
TL;DR: A structural rationale for the low affinity of aducanumab for non-pathogenic monomers and its greater selectivity for aggregated forms than is seen for other Aβ-targeting antibodies is provided.
Journal ArticleDOI
Community-wide assessment of protein-interface modeling suggests improvements to design methodology
Sarel J. Fleishman,Sarel J. Fleishman,Timothy A. Whitehead,Eva-Maria Strauch,Jacob E. Corn,Jacob E. Corn,Sanbo Qin,Huan-Xiang Zhou,Julie C. Mitchell,Omar N. A. Demerdash,Mayuko Takeda-Shitaka,Genki Terashi,Iain H. Moal,Xiaofan Li,Paul A. Bates,Martin Zacharias,Hahnbeom Park,Junsu Ko,Hasup Lee,Chaok Seok,Thomas Bourquard,Julie Bernauer,Anne Poupon,Jérôme Azé,Seren Soner,Şefik Kerem Ovali,Pemra Ozbek,Nir Ben Tal,Turkan Haliloglu,Howook Hwang,Thom Vreven,Brian G. Pierce,Zhiping Weng,Laura Pérez-Cano,Carles Pons,Juan Fernández-Recio,Fan Jiang,Feng Yang,Xinqi Gong,Libin Cao,Xianjin Xu,Bin Liu,Panwen Wang,Chunhua Li,Cunxin Wang,Charles H. Robert,Mainak Guharoy,Shiyong Liu,Yangyu Huang,Lin Li,Dachuan Guo,Ying Chen,Yi Xiao,Nir London,Zohar Itzhaki,Ora Schueler-Furman,Yuval Inbar,Vladimir Potapov,Mati Cohen,Gideon Schreiber,Yuko Tsuchiya,Eiji Kanamori,Daron M. Standley,Haruki Nakamura,Kengo Kinoshita,C.M. Driggers,Robert G. Hall,Jessica L. Morgan,Victor L. Hsu,Jian Zhan,Yuedong Yang,Yaoqi Zhou,Panagiotis L. Kastritis,Alexandre M. J. J. Bonvin,Weiyi Zhang,Carlos J. Camacho,Krishna Praneeth Kilambi,Aroop Sircar,Jeffrey J. Gray,Masahito Ohue,Nobuyuki Uchikoga,Yuri Matsuzaki,Takashi Ishida,Yutaka Akiyama,Raed Khashan,Stephen Bush,Denis Fouches,Alexander Tropsha,Juan Esquivel-Rodríguez,Daisuke Kihara,P. Benjamin Stranges,Ron Jacak,Brian Kuhlman,Sheng-You Huang,Xiaoqin Zou,Shoshana J. Wodak,Joël Janin,David Baker +97 more
TL;DR: A number of designed protein-protein interfaces with very favorable computed binding energies but which do not appear to be formed in experiments are generated, suggesting that there may be important physical chemistry missing in the energy calculations.
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Functional loss of semaphorin 3C and/or semaphorin 3D and their epistatic interaction with ret are critical to hirschsprung disease liability
Qian Jiang,Stacey Arnold,Tiffany A. Heanue,Krishna Praneeth Kilambi,Betty Q. Doan,Ashish Kapoor,Albee Y. Ling,Maria X. Sosa,Moltu Guy,Qingguang Jiang,Grzegorz M. Burzynski,Kristen West,Seneca L. Bessling,Paola Griseri,Jeanne Amiel,Jeanne Amiel,Raquel M. Fernández,Joke B. G. M. Verheij,Robert M.W. Hofstra,Robert M.W. Hofstra,Salud Borrego,Stanislas Lyonnet,Stanislas Lyonnet,Isabella Ceccherini,Jeffrey J. Gray,Vassilis Pachnis,Andrew S. McCallion,Aravinda Chakravarti +27 more
TL;DR: Semaphorin 3C/3D signaling is an evolutionarily conserved regulator of ENS development whose dys-regulation is a cause of enteric aganglionosis.
Journal ArticleDOI
Community-wide Evaluation of Methods for Predicting the Effect of Mutations on Protein-Protein Interactions
Rocco Moretti,Sarel J. Fleishman,Rudi Agius,Mieczyslaw Torchala,Paul A. Bates,Panagiotis L. Kastritis,João P. G. L. M. Rodrigues,Mikael Trellet,Alexandre M. J. J. Bonvin,Meng Cui,Marianne Rooman,Dimitri Gillis,Yves Dehouck,Iain H. Moal,Miguel Romero-Durana,Laura Pérez-Cano,Chiara Pallara,Brian Jimenez,Juan Fernández-Recio,Samuel C. Flores,Michael S. Pacella,Krishna Praneeth Kilambi,Jeffrey J. Gray,Petr Popov,Petr Popov,Sergei Grudinin,Sergei Grudinin,Juan Esquivel-Rodríguez,Daisuke Kihara,Nan Zhao,Dmitry Korkin,Xiaolei Zhu,Omar N. A. Demerdash,Julie C. Mitchell,Eiji Kanamori,Yuko Tsuchiya,Haruki Nakamura,Hasup Lee,Hahnbeom Park,Chaok Seok,Jamica Sarmiento,Shide Liang,Shusuke Teraguchi,Daron M. Standley,Hiromitsu Shimoyama,Genki Terashi,Mayuko Takeda-Shitaka,Mitsuo Iwadate,Hideaki Umeyama,Dmitri Beglov,David R. Hall,Dima Kozakov,Sandor Vajda,Brian G. Pierce,Howook Hwang,Thom Vreven,Zhiping Weng,Yangyu Huang,Haotian Li,Xiufeng Yang,Xiaofeng Ji,Shiyong Liu,Yi Xiao,Martin Zacharias,Sanbo Qin,Huan-Xiang Zhou,Sheng-You Huang,Xiaoqin Zou,Sameer Velankar,Joël Janin,Shoshana J. Wodak,David Baker +71 more
TL;DR: A community‐wide assessment of methods to predict the effects of mutations on protein–protein interactions found that large‐scale fitness landscapes should continue to provide an excellent test bed for continued evaluation of both existing and new prediction methodologies.
Journal ArticleDOI
Rapid Calculation of Protein pKa Values Using Rosetta
TL;DR: A simple and fast method based on the Rosetta score function and limited conformational sampling produces pK(a) values that will be useful when rapid estimation is essential, such as in docking, design, and folding.