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PatchDock and SymmDock: servers for rigid and symmetric docking
TLDR
Two freely available web servers for molecular docking that perform structure prediction of protein–protein and protein–small molecule complexes and the SymmDock method predicts the structure of a homomultimer with cyclic symmetry given theructure of the monomeric unit are described.
Shape complementarity at protein–protein interfaces
TLDR
A matching algorithm using surface complementarity between receptor and ligand protein molecules is outlined, and it is shown that out of the 16 protein‐protein complexes tried, 15 were successfully docked, including two immunoglobulins.
Efficient Unbound Docking of Rigid Molecules
TLDR
A new algorithm for unbound (real life) docking of molecules, whether protein-protein or protein-drug, carrying out rigid docking, with surface variability/flexibility implicitly addressed through liberal intermolecular penetration is presented.
Fast algorithm for predicting the secondary structure of single-stranded RNA.
TLDR
A computer method is presented for finding the most stable secondary structures in long single-stranded RNAs and builds an optimal structure in a straightforward inductive procedure based on an exact mathematical algorithm.
Algorithms for Loop Matchings
TLDR
A dynamic programming algorithm is presented which computes the size of the maximum for the given A-B base sequence and which also allows reconstructing a particular folded form of the original string which realizes the maximum matching size.
Factors enhancing protein thermostability.
TLDR
The results indicate that thermostable proteins adapt dual strategies to withstand high temperatures, and thermophilic proteins both have a larger fraction of their residues in the alpha-helical conformation and they avoid Pro in their alpha-helices to a greater extent than the mesophiles.
FireDock: a web server for fast interaction refinement in molecular docking†
TLDR
The FireDock web server, presented here, is the first web server for flexible refinement and scoring of protein–protein docking solutions and includes optimization of side-chain conformations and rigid-body orientation and allows a high-throughput refinement.
FireDock: Fast interaction refinement in molecular docking
TLDR
FireDock's prediction results are comparable to current state‐of‐the‐art refinement methods while its running time is significantly lower, and its refinement procedure significantly improves the ranking of the rigid‐body PatchDock algorithm for these cases.
The role of dynamic conformational ensembles in biomolecular recognition.
TLDR
Experimental evidence supports a new molecular recognition paradigm for processes as diverse as signaling, catalysis, gene regulation and protein aggregation in disease, which has the potential to significantly impact views and strategies in drug design, biomolecular engineering and molecular evolution.
Principles of docking: An overview of search algorithms and a guide to scoring functions
TLDR
The docking field has come of age, and the time is ripe to present the principles of docking, reviewing the current state of the field from both the computational and the biological points of view.
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