Putative protein binding sites
Methods for the Efficient Comparison of Protein Binding Sites and for the Assessment of Protein-Ligand Complexes
... pockets binding to either the cancer drug pemetrexed or ...current binding site comparison ...for putative protein binding sites that use the internal Cavbase format and ...
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Census of halide-binding sites in protein structures
... the putative halide binding sites based on the amino acid sequence ...of binding sites involves conformational changes of interacting side chains, the apo structures are not very likely ...
12
In silico identification and characterization of protein-ligand binding sites
... ligand binding site, showing putative binding site residues, rendered using PyMOL ...the protein is shown as a green ribbon, while the putative ligand binding site residues are ...
31
Mapping of the Tacaribe Arenavirus Z-Protein Binding Sites on the L Protein Identified both Amino Acids within the Putative Polymerase Domain and a Region at the N Terminus of L That Are Critically Involved in Binding
... Our finding that modifications in either domain III or in the N terminus of L impaired or ablated the interaction with Z could be interpreted to mean that both regions are required in concert for binding. Another ...
7
Evolutionary variation of papillomavirus E2 protein and E2 binding sites
... the sites identified from the study were located within the LCR, though in some cases, sequences that were pre- dicted to bind E2 protein were identified within the papillomavirus ...these putative ...
12
Molecular Dynamics of Rab7::REP1::GGTase-II Ternary Complex and Identification of Their Putative Drug Binding Sites
... find putative drug binding sites on the ternary complex of Rab7::REP1::GGTase‑II using Q‑SiteFinder ...as putative drug binding sites on Rab7::REP:: GGTase‑II ternary ...REP ...
8
Characterization of Metal Binding Sites Within the Protein Only RNase P
... metal binding sites with Mg 2+ and Mn 2+ ...a putative active site mutant of the PRORP3-D422N ...mutant protein. The protein was over-expressed and purified one step nickel affinity ...
90
Phosfinder: a web server for the identification of phosphate-binding sites on protein structures
... phosphate binding sites in protein ...query protein and a phos- phate binding motif is detected, the phosphate bound by the known motif is added to the protein structure thus ...
5
EASYMIFS and SITEHOUND: a toolkit for the identification of ligand-binding sites in protein structures
... identify protein structure regions that show a high propensity for interaction with ...of binding site identified depends on the probe atom used in the MIF ...a protein structure; the output MIF ...
6
RNase mediated protein footprint sequencing reveals protein binding sites throughout the human transcriptome
... RNA-binding sites of individual RNA-binding proteins (RBPs), few methods exist that allow assessment of global RBP – RNA ...ribonuclease-mediated protein footprint sequencing approach that ...
16
RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome
... RNA-binding sites of individual RNA-binding proteins (RBPs), few methods exist that allow assessment of global RBP –RNA ...ribonuclease-mediated protein footprint sequencing approach that ...
17
Modeling protein interactions in protein binding sites and oligomeric protein complexes
... Furthermore, incorporating both side-chain and backbone flexibility in docking methods still represents a major problem, because it greatly increases the compu- tational time required both during the sampling space, as ...
277
Phosphate binding sites identification in protein structures
... the protein ligands are bound in one of the top four largest pockets of the interacting protein ...biggest protein clefts using the whole PDB ...
12
Computational Methods for Predicting Protein-protein Interactions and Binding Sites
... for protein-protein interaction site ...with protein-binding residues (PBRs) and sites with strong evolution- ary ...PBR sites closely match known data from ...
138
Structural Perspectives on the Evolutionary Expansion of Unique Protein-Protein Binding Sites
... of protein complexes provide atomistic insights into protein ...the Protein Data Bank; however, available protein complexes cover less than 10% of the human pro- ...homologous protein ...
12
Study of Protein Binding Sites on the GTPase RalA and the Sugar-binding Protein Hen Egg White Lysozyme
... modulating protein-protein contacts through the switch ...of protein-protein ...whether binding occurs by fluctuations between semi-ordered states or by an induced fit process, water ...
289
Carbene footprinting accurately maps binding sites in protein–ligand and protein–protein interactions
... of protein labelling. In investigating other protein systems, we found the labelling efficiency of photoleucine 1 to be highly protein dependent, and that labelled peptides exhibited, in some cases, ...
9
A Genetic Screen Identifies Putative Targets and Binding Partners of CREB-Binding Protein in the Developing Drosophila Eye
... While there is an obvious wealth of opportunities to study the role that CBP plays in both insect and mammalian development, the sheer number of poten- tial means by which CBP influences development can complicate ...
18
The overlap of small molecule and protein binding sites within families of protein structures.
... 2,619 protein structure families observed to bind proteins, 1,028 also bind small molecules (250–1000 Da), and 197 exhibit a statistically significant ...and protein binding ...whose binding ...
11
Crystal structure of the putative peptide-binding protein AppA from Clostridium difficile
... Peptide binding to either protein could not be observed in Thermofluor assays with a set of ten peptides of varying lengths and ...the protein sequences together with structure comparisons prompts ...
9