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Pranav M Khade
Pranav M Khade
Postdoctoral Fellow at Genentech
Verified email at gene.com - Homepage
Title
Cited by
Cited by
Year
Characterizing and predicting protein hinges for mechanistic insight
PM Khade, A Kumar, RL Jernigan
Journal of molecular biology 432 (2), 508-522, 2020
212020
Structural compliance: A new metric for protein flexibility
D Scaramozzino, PM Khade, RL Jernigan, G Lacidogna, A Carpinteri
Proteins: Structure, Function, and Bioinformatics 88 (11), 1482-1492, 2020
112020
hdANM: a new comprehensive dynamics model for protein hinges
PM Khade, D Scaramozzino, A Kumar, G Lacidogna, A Carpinteri, ...
Biophysical Journal 120 (22), 4955-4965, 2021
82021
Entropies Derived from the Packing Geometries within a Single Protein Structure
PM Khade, RL Jernigan
ACS omega 7 (24), 20719-20730, 2022
42022
Coarse-graining protein structures into their dynamic communities with DCI, a dynamic community identifier
A Kumar, PM Khade, KS Dorman, RL Jernigan
Bioinformatics 38 (10), 2727-2733, 2022
22022
Protein Fluctuations in Response to Random External Forces
D Scaramozzino, PM Khade, RL Jernigan
Applied Sciences 12 (5), 2344, 2022
22022
PACKMAN-Molecule: Python toolbox for structural bioinformatics
PM Khade, RL Jernigan
Bioinformatics Advances 2 (1), vbac007, 2022
22022
Mixed structure-and sequence-based approach for protein graph neural networks with application to antibody developability prediction
PM Khade, M Maser, V Gligorijevic, AM Watkins
bioRxiv, 2023.06. 26.546331, 2023
12023
Computationally efficient graph neural/convolutional network captures protein geometry to predict affinity and developability
PM Khade, V Gligorijevic, A Watkins
Biophysical Journal 122 (3), 180a, 2023
2023
GOThresher: a program to remove annotation biases from protein function annotation datasets
P Joshi, S Banerjee, X Hu, PM Khade, I Friedberg
Bioinformatics 39 (1), btad048, 2023
2023
Using Surface Hydrophobicity Together with Empirical Potentials to Identify Protein–Protein Binding Sites: Application to the Interactions of E-cadherins
RL Jernigan, P Khade, A Kumar, A Kloczkowski
Computer Simulations of Aggregation of Proteins and Peptides, 41-50, 2022
2022
Aggregation sickle hemoglobin
V Anderson, PM Khade, A Kumar, K Jia, RL Jernigan
Biophysical Journal 121 (3), 323a, 2022
2022
Fast, simple molecular entropy calculations from Voronoi diagrams of a single structure
PM Khade, RL Jernigan
Biophysical Journal 121 (3), 17a-18a, 2022
2022
Role of protein packing in protein dynamics
PM Khade
Iowa State University, 2022
2022
Hd-ANM a Computationally Efficient, Highly Customizable and Comprehensive Elastic Network Model
PM Khade, D Scaramozzino, A Kumar, RL Jernigan
Biophysical Journal 120 (3), 115a, 2021
2021
Generating Protein Ensembles by Applying Forces to an Improved Elastic Network Model
A Kumar, PM Khade, D Scaramozzino, K Dorman, RL Jernigan
Biophysical Journal 120 (3), 115a, 2021
2021
Using Alpha Shapes to Characterize Protein Packing and Capture the Multiscale Aspects of Allostery
PM Khade, A Kumar, RL Jernigan
Biophysical Journal 118 (3), 40a, 2020
2020
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