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 …
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 …
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
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 …
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 …
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
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 …
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
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 …
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 …
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
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 …
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
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 …
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 …
can provide high‐resolution structures, but protein‐DNA complexes are difficult to crystallize …