User profiles for T. Hrabe

Thomas Hrabe

BASF Enzymes
Verified email at sbpdiscovery.org
Cited by 905

[HTML][HTML] Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework

…, JJ Gao, A Godzik, M Heuer, M Hicks, T Hrabe… - Genome medicine, 2017 - Springer
The translation of personal genomics to precision medicine depends on the accurate
interpretation of the multitude of genetic variants observed for each individual. However, even …

PyTom: a python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis

T Hrabe, Y Chen, S Pfeffer, LK Cuellar… - Journal of structural …, 2012 - Elsevier
… The annealing ‘temperature’ T controls the acceptance of sub-optimal class assignments.
T is decreased linearly over the annealing iterations. Here, T depends on the standard …

[HTML][HTML] A pan-cancer catalogue of cancer driver protein interaction interfaces

E Porta-Pardo, L Garcia-Alonso, T Hrabe… - PLoS computational …, 2015 - journals.plos.org
… , p t is a vector in which the i-th element holds the probability of being at node i at time t and
… The algorithm iterates the equation until the L 1 norm between p t and p t+1 is less than 10 −…

[PDF][PDF] Structure and 3D arrangement of endoplasmic reticulum membrane-associated ribosomes

S Pfeffer, F Brandt, T Hrabe, S Lang, M Eibauer… - Structure, 2012 - cell.com
In eukaryotic cells, cotranslational protein translocation across the endoplasmic reticulum (ER)
membrane requires an elaborate macromolecular machinery. While structural details of …

PDBFlex: exploring flexibility in protein structures

T Hrabe, Z Li, M Sedova, P Rotkiewicz… - Nucleic acids …, 2016 - academic.oup.com
The PDBFlex database, available freely and with no login requirements at http://pdbflex.org
, provides information on flexibility of protein structures as revealed by the analysis of …

Fast and accurate reference-free alignment of subtomograms

Y Chen, S Pfeffer, T Hrabe, JM Schuller… - Journal of structural …, 2013 - Elsevier
… Use Algorithm 1 to align all the subtomograms against T i . Average all the aligned
subtomograms will result in a new reference T i + 1 , which can be used for the next iteration. …

POSA: a user-driven, interactive multiple protein structure alignment server

Z Li, P Natarajan, Y Ye, T Hrabe… - Nucleic acids …, 2014 - academic.oup.com
… Thomas Hrabe , Thomas Hrabe … Zhanwen Li, Padmaja Natarajan, Yuzhen Ye, Thomas
Hrabe, Adam Godzik, POSA: a user-driven, interactive multiple protein structure alignment server, …

Cancer3D: understanding cancer mutations through protein structures

E Porta-Pardo, T Hrabe, A Godzik - Nucleic acids research, 2015 - academic.oup.com
The new era of cancer genomics is providing us with extensive knowledge of mutations and
other alterations in cancer. The Cancer3D database at http://www.cancer3d.org gives an …

[HTML][HTML] ConSole: using modularity of Contact maps to locate Solenoid domains in protein structures

T Hrabe, A Godzik - BMC bioinformatics, 2014 - Springer
… We use the distance threshold of t = 4.5 Å, following our earlier applications of contact maps
[23], and assign a value of 1 (True) or 0 (False) to each of the N × N positions on the map. As …

Detection and identification of macromolecular complexes in cryo-electron tomograms using support vector machines

Y Chen, T Hrabe, S Pfeffer, O Pauly… - 2012 9th IEEE …, 2012 - ieeexplore.ieee.org
… Given a tomogram V and the structural template T of the target macromolecular complex,
we … If the candidate is closer than a threshold T, it is labeled as positive, otherwise negative. …