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PatchDock and SymmDock: servers for rigid and symmetric docking
TLDR
We describe two freely available web servers for molecular docking using the PatchDock and SymmDock algorithms. Expand
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Shape complementarity at protein–protein interfaces
A matching algorithm using surface complementarity between receptor and ligand protein molecules is outlined. The molecular surfaces are represented by “critical points,” describing holes and knobs.Expand
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Efficient Unbound Docking of Rigid Molecules
TLDR
We present a new algorithm for unbound (real life) docking of molecules, whether protein-protein or protein-drug. Expand
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Fast algorithm for predicting the secondary structure of single-stranded RNA.
A computer method is presented for finding the most stable secondary structures in long single-stranded RNAs. It is 1-2 orders of magnitude faster than existing codes. The time required for itsExpand
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Factors enhancing protein thermostability.
Several sequence and structural factors have been proposed to contribute toward greater stability of thermophilic proteins. Here we present a statistical examination of structural and sequenceExpand
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Algorithms for Loop Matchings
A simplified (two-base) version of the problem of planar folding of long chains (e.g., RNA and DNA biomolecules) is formulated as a matching problem. The chain is prescribed as a loop or circularExpand
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FireDock: a web server for fast interaction refinement in molecular docking†
TLDR
The FireDock web server is the first web server for flexible refinement and scoring of protein–protein docking solutions. Expand
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FireDock: Fast interaction refinement in molecular docking
TLDR
We present FireDock, an efficient method for the refinement and rescoring of rigid‐body docking solutions. Expand
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Principles of docking: An overview of search algorithms and a guide to scoring functions
TLDR
We present the principles of docking, reviewing the current state of the field. Expand
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The role of dynamic conformational ensembles in biomolecular recognition.
Molecular recognition is central to all biological processes. For the past 50 years, Koshland's 'induced fit' hypothesis has been the textbook explanation for molecular recognition events. However,Expand
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