Docking and scoring in drug discovery

F Spyrakis, P Cozzini… - … Medicinal Chemistry and …, 2003 - Wiley Online Library
The rational development of new lead compounds requires good understanding of the
relationship between all the actors involved in a binding event (protein, ligand, water, metal …

NMR structure validation in relation to dynamics and structure determination

WF Vranken - Progress in nuclear magnetic resonance spectroscopy, 2014 - Elsevier
NMR spectroscopy is a key technique for understanding the behaviour of proteins,
especially highly dynamic proteins that adopt multiple conformations in solution. Overall …

[HTML][HTML] A structural analysis of DNA binding by myelin transcription factor 1 double zinc fingers

R Gamsjaeger, MR O'Connell, L Cubeddu… - Journal of Biological …, 2013 - ASBMB
Myelin transcription factor 1 (MyT1/NZF2), a member of the neural zinc-finger (NZF) protein
family, is a transcription factor that plays a central role in the developing central nervous …

[HTML][HTML] Structural and biophysical analysis of the DNA binding properties of myelin transcription factor 1

R Gamsjaeger, MK Swanton, FJ Kobus… - Journal of biological …, 2008 - ASBMB
Zinc binding domains, or zinc fingers (ZnFs), form one of the most numerous and most
diverse superclasses of protein structural motifs in eukaryotes. Although our understanding …

Molecular basis of the recognition of the ap65-1 gene transcription promoter elements by a Myb protein from the protozoan parasite Trichomonas vaginalis

I Jiang, CK Tsai, SC Chen, S Wang… - Nucleic acids …, 2011 - academic.oup.com
Iron-inducible transcription of the ap65-1 gene in Trichomonas vaginalis involves at least
three Myb-like transcriptional factors (tv Myb1, tv Myb2 and tv Myb3) that differentially bind to …

RNA–LIM: A novel procedure for analyzing protein/single-stranded RNA propensity data with concomitant estimation of interface structure

D Hall, S Li, K Yamashita, R Azuma, JA Carver… - Analytical …, 2015 - Elsevier
RNA–LIM is a procedure that can analyze various pseudo-potentials describing the affinity
between single-stranded RNA (ssRNA) ribonucleotides and surface amino acids to produce …

NMR structural analysis of DNA recognition by a novel Myb1 DNA-binding domain in the protozoan parasite Trichomonas vaginalis

YC Lou, SY Wei, M Rajasekaran, CC Chou… - Nucleic acids …, 2009 - academic.oup.com
The transcription regulator, tv Myb1, is the first Myb family protein identified in Trichomonas
vaginalis. Using an electrophoretic mobility shift assay, we defined the amino-acid sequence …

[HTML][HTML] Predicting target DNA sequences of DNA-binding proteins based on unbound structures

CY Chen, TY Chien, CK Lin, CW Lin, YZ Weng… - PloS one, 2012 - journals.plos.org
DNA-binding proteins such as transcription factors use DNA-binding domains (DBDs) to
bind to specific sequences in the genome to initiate many important biological functions …

[HTML][HTML] PDA: an automatic and comprehensive analysis program for protein-DNA complex structures

RG Kim, J Guo - BMC genomics, 2009 - Springer
Background Knowledge of protein-DNA interactions at the structural-level can provide
insights into the mechanisms of protein-DNA recognition and gene regulation. Although over …

Predicting protein–DNA interactions by full search computational docking

VA Roberts, ME Pique, LF Ten Eyck… - … : Structure, Function, and …, 2013 - Wiley Online Library
Protein–DNA interactions are essential for many biological processes. X‐ray crystallography
can provide high‐resolution structures, but protein‐DNA complexes are difficult to crystallize …