… Another important feature in which multiple alignment is superior to more conventional
pairwise alignment is its reliability, because simultaneous comparison of many sequences can …

… One idea to overcome this conundrum may be the simultaneous use of multiple restraints148,
192 and/or adaptive restraints15, 89, 90 to limit sampling while still being able to reach the …

… 13, 14, but here we focus on near native structural refinement and the metric training allows
us to work on many (here 924 nonhomologous) proteins and all their decoys simultaneously. …

… of four proteins were selected from a total of 50 refined structures by choosing the structure
with … Five separate ensemble refinements were carried out for each protein by using different …

… In this work, we presented a method for refining protein-protein complex structures generated
by other docking programs. This method, called GalaxyRefineComplex, was compared …

… Refinement is the last step in protein structure prediction pipelines to convert approximate …
refinement. To explore the energy landscape between homology models and native structures …

… The amino acid sequence and a 3D model (in Protein Data Bank (PDB) format) of the target
are the only required inputs to refine protein structures and the method has recently been …

… dard refinement technique in this laboratory is now, however, that of Jack and Levitt, 7.8
a procedure which minimizes simultaneously the X-ray residual and potential energy. This …

… for the refinement of reduced-model structures of proteins. A … of molecules can be
simultaneously simulated. The calculation … The results of the refinement are shown for the test …

… refined structures can be calculated using simultaneously X-ray … of the protein matrix
metalloproteinase 1, for the protein … of protein G, thus indicating that no appreciable structural …