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Hamed Khakzad
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Macromolecular modeling and design in Rosetta: recent methods and frameworks
JK Leman, BD Weitzner, SM Lewis, J Adolf-Bryfogle, N Alam, RF Alford, ...
Nature methods 17 (7), 665-680, 2020
2062020
Rapid determination of quaternary protein structures in complex biological samples
S Hauri*, H Khakzad*, L Happonen, J Teleman, J Malmström, ...
Nature communications 10 (1), 1-10, 2019
382019
A quantitative Streptococcus pyogenes–human protein–protein interaction map reveals localization of opsonizing antibodies
L Happonen, S Hauri, G Svensson Birkedal, C Karlsson, T de Neergaard, ...
Nature communications 10 (1), 1-15, 2019
202019
Better together: Elements of successful scientific software development in a distributed collaborative community
J Koehler Leman, BD Weitzner, PD Renfrew, SM Lewis, R Moretti, ...
PLoS computational biology 16 (5), e1007507, 2020
162020
Structural proteomics, electron cryo-microscopy and structural modeling approaches in bacteria–human protein interactions
S Chowdhury, L Happonen, H Khakzad, L Malmström, J Malmström
Medical microbiology and immunology 209 (3), 265-275, 2020
102020
Protein structure prediction using bio-inspired algorithm: a review
Y Karami, H Khakzad, H Shirazi, S Arab
The 16th CSI international symposium on artificial intelligence and signal …, 2012
102012
Accelerating protein structure prediction using particle swarm optimization on GPU
H Khakzad, Y Karami, SS Arab
Biorxiv, 022434, 2015
62015
In vivo Cross-Linking MS of the Complement System MAC Assembled on Live Gram-Positive Bacteria
H Khakzad, L Happonen, G Tran Van Nhieu, J Malmström, L Malmström
Frontiers in Genetics 11, 612475, 2021
52021
Structural determination of Streptococcus pyogenes M1 protein interactions with human immunoglobulin G using integrative structural biology
H Khakzad, L Happonen, Y Karami, S Chowdhury, GE Bergdahl, M Nilges, ...
PLoS computational biology 17 (1), e1008169, 2021
52021
PDB2Graph: a toolbox for identifying critical amino acids map in proteins based on graph theory
N Niknam, H Khakzad, SS Arab, H Naderi-Manesh
Computers in biology and medicine 72, 151-159, 2016
52016
Streptococcus pyogenes Forms Serotype-and Local Environment-Dependent Interspecies Protein Complexes
S Chowdhury, H Khakzad, GE Bergdahl, R Lood, S Ekstrom, D Linke, ...
Msystems 6 (5), e00271-21, 2021
42021
Spike-dependent opsonization indicates both dose-dependent inhibition of phagocytosis and that non-neutralizing antibodies can confer protection to SARS-CoV-2
W Bahnan, S Wrighton, M Sundwall, A Bläckberg, O Larsson, U Höglund, ...
Frontiers in immunology 12, 2021
42021
Opsonization by non-neutralizing antibodies can confer protection to SARS-CoV-2 despite Spike-dependent modulation of phagocytosis
W Bahnan, S Wrighton, M Sundwall, A Bläckberg, O Larsson, U Höglund, ...
bioRxiv, 2021
42021
Protection induced by a human monoclonal antibody recognizing two different epitopes in a conserved region of streptococcal M proteins
W Bahnan, L Happonen, H Khakzad, VK Ahnlide, T de Neergaard, ...
BioRxiv, 2021
42021
Macromolecular modeling and design in Rosetta: new methods and frameworks
JK Leman, BD Weitzner, SM Lewis, R Bonneau, ...
Preprints, 2019
42019
The structure of human dermatan sulfate epimerase 1 emphasizes the importance of C5-epimerization of glucuronic acid in higher organisms
M Hasan*, H Khakzad*, L Happonen, A Sundin, J Unge, U Mueller, ...
Chemical science 12 (5), 1869-1885, 2021
32021
Greedy de novo motif discovery to construct motif repositories for bacterial proteomes
H Khakzad, J Malmström, L Malmström
BMC bioinformatics 20 (4), 1-10, 2019
32019
Cheetah-MS: a web server to model protein complexes using tandem cross-linking mass spectrometry data
H Khakzad, L Happonen, J Malmström, L Malmström
Bioinformatics 37 (24), 4871-4872, 2021
2021
Quaternary structure modeling through chemical cross-linking mass spectrometry: Extending tx-ms jupyter reports
H Khakzad, S Vermeul, L Malmström
Journal of Visualized Experiments, e60311, 2021
2021
ipaA triggers vinculin oligomerization to strengthen cell adhesion during Shigella invasion
C Valencia-Gallardo, DI Aguilar-Salvador, H Khakzad, C Bou-Nader, ...
bioRxiv, 773283, 2020
2020
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Articles 1–20