[HTML][HTML] A Bayesian machine learning approach for drug target identification using diverse data types

NS Madhukar, PK Khade, L Huang, K Gayvert… - Nature …, 2019 - nature.com
Drug target identification is a crucial step in development, yet is also among the most
complex. To address this, we develop BANDIT, a Bayesian machine-learning approach that …

[HTML][HTML] Functional role of the sarcin–ricin loop of the 23S rRNA in the elongation cycle of protein synthesis

X Shi, PK Khade, KY Sanbonmatsu… - Journal of molecular …, 2012 - Elsevier
The sarcin–ricin loop (SRL) is one of the longest conserved sequences in the 23S ribosomal
RNA. The SRL has been accepted as crucial for the activity of the ribosome because it is …

Messenger RNA interactions in the decoding center control the rate of translocation

PK Khade, S Joseph - Nature structural & molecular biology, 2011 - nature.com
During protein synthesis, mRNA and tRNAs are iteratively translocated by the ribosome.
Precisely what molecular event is rate limiting for translocation is not known. Here we show that …

Anthracene-9-methanol—a novel fluorescent phototrigger for biomolecular caging

AK Singh, PK Khade - Tetrahedron letters, 2005 - Elsevier
Photoexcitation of a solution of anthracene-9-methanol derived esters at ∼386nm in CH 3
CN/H 2 O (3:2 v/v) results in fluorescence emission in the 380–480nm range, with quantum …

[HTML][HTML] Steric complementarity in the decoding center is important for tRNA selection by the ribosome

PK Khade, X Shi, S Joseph - Journal of molecular biology, 2013 - Elsevier
Accurate tRNA selection by the ribosome is essential for the synthesis of functional proteins.
Previous structural studies indicated that the ribosome distinguishes between cognate and …

3-Nitro-2-naphthalenemethanol: a photocleavable protecting group for carboxylic acids

AK Singh, PK Khade - Tetrahedron, 2005 - Elsevier
Photocleavable protecting groups are important in synthesis and caging. Among many such
groups, 2-nitrobenzyl and related groups have been found useful in many applications. …

Polyamines accelerate codon recognition by transfer RNAs on the ribosome

B Hetrick, PK Khade, K Lee, J Stephen, A Thomas… - Biochemistry, 2010 - ACS Publications
The selection of aminoacyl-tRNAs by the ribosome is a fundamental step in the elongation
cycle of protein synthesis. tRNA selection is a multistep process that ensures only correct …

A new big-data paradigm for target identification and drug discovery

NS Madhukar, PK Khade, L Huang, K Gayvert… - Biorxiv, 2017 - biorxiv.org
Drug target identification is one of the most important aspects of pre-clinical development yet
it is also among the most complex, labor-intensive, and costly. This represents a major issue…

Synthesis and photochemical properties of nitro-naphthyl chromophore and the corresponding immunoglobulin bioconjugate

AK Singh, PK Khade - Bioconjugate chemistry, 2002 - ACS Publications
Synthesis, photochemistry, and biomolecular caging properties of a new chromophore namely
3-nitro-2-naphthalenemethanol are described. This chromophore is photoexcitable with …

7-Methoxy-3-nitro-2-naphthalenemethanol—a new phototrigger for caging applications

AK Singh, PK Khade - Tetrahedron letters, 2011 - Elsevier
Synthesis, photochemistry and photorelease properties of 7-methoxy-3-nitro-2-
naphthalenemethanol (MNNM) are described. Photoirradiation (⩾ 370 nm) of MNNM …