Published in Nucleic Acids Res on July 01, 2006
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Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms. Mol Biosyst (2009) 2.18
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PRISM: protein interactions by structural matching. Nucleic Acids Res (2005) 2.11
Protein-protein interactions; coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking. Structure (2004) 2.06
Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Mol Syst Biol (2006) 1.98
Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking. Proteins (2003) 1.95
Geometry-based flexible and symmetric protein docking. Proteins (2005) 1.95
Flexible protein alignment and hinge detection. Proteins (2002) 1.93
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Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima. J Mol Biol (2008) 1.80
Principles of flexible protein-protein docking. Proteins (2008) 1.71
Simulations as analytical tools to understand protein aggregation and predict amyloid conformation. Curr Opin Chem Biol (2006) 1.70
ARTS: alignment of RNA tertiary structures. Bioinformatics (2005) 1.67
Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking. J Mol Biol (2004) 1.64
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Enzyme dynamics point to stepwise conformational selection in catalysis. Curr Opin Chem Biol (2010) 1.61
Similar binding sites and different partners: implications to shared proteins in cellular pathways. Structure (2007) 1.60
Molecular dynamics simulations of alanine rich beta-sheet oligomers: Insight into amyloid formation. Protein Sci (2002) 1.59
Dynamic allostery: linkers are not merely flexible. Structure (2011) 1.58
Correlated mutations: advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families. Proteins (2006) 1.58
Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomers. J Mol Biol (2004) 1.54
MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions. Nucleic Acids Res (2008) 1.52
Architectures and functional coverage of protein-protein interfaces. J Mol Biol (2008) 1.51
Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly. J Mol Biol (2009) 1.48
Truncated beta-amyloid peptide channels provide an alternative mechanism for Alzheimer's Disease and Down syndrome. Proc Natl Acad Sci U S A (2010) 1.48
A survey of available tools and web servers for analysis of protein-protein interactions and interfaces. Brief Bioinform (2009) 1.47
FiberDock: Flexible induced-fit backbone refinement in molecular docking. Proteins (2010) 1.47
Models of beta-amyloid ion channels in the membrane suggest that channel formation in the bilayer is a dynamic process. Biophys J (2007) 1.44
Modeling the Alzheimer Abeta17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities. Biophys J (2007) 1.44
New structures help the modeling of toxic amyloidbeta ion channels. Trends Biochem Sci (2008) 1.43
Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: significant role of Asn ladder. Proc Natl Acad Sci U S A (2005) 1.43
Atomic-level description of amyloid beta-dimer formation. J Am Chem Soc (2006) 1.41
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Short peptide amyloid organization: stabilities and conformations of the islet amyloid peptide NFGAIL. Biophys J (2003) 1.33
Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35. Biophys J (2006) 1.33
Multiple structural alignment by secondary structures: algorithm and applications. Protein Sci (2003) 1.32
Zinc ions promote Alzheimer Abeta aggregation via population shift of polymorphic states. Proc Natl Acad Sci U S A (2010) 1.32
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Models of toxic beta-sheet channels of protegrin-1 suggest a common subunit organization motif shared with toxic alzheimer beta-amyloid ion channels. Biophys J (2008) 1.30
MolAxis: efficient and accurate identification of channels in macromolecules. Proteins (2008) 1.30
Nanoparticle-induced vascular blockade in human prostate cancer. Blood (2010) 1.30
The multiple common point set problem and its application to molecule binding pattern detection. J Comput Biol (2006) 1.28
Topological properties of protein interaction networks from a structural perspective. Biochem Soc Trans (2008) 1.28
Molecular-level examination of Cu2+ binding structure for amyloid fibrils of 40-residue Alzheimer's β by solid-state NMR spectroscopy. J Am Chem Soc (2011) 1.27
Protein-protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach. Phys Biol (2005) 1.26
Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families. Protein Sci (2006) 1.26
How different are structurally flexible and rigid binding sites? Sequence and structural features discriminating proteins that do and do not undergo conformational change upon ligand binding. J Mol Biol (2006) 1.26
A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method. BMC Bioinformatics (2011) 1.25
FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking. Nucleic Acids Res (2010) 1.25
Predicting molecular interactions in silico: II. Protein-protein and protein-drug docking. Curr Med Chem (2004) 1.25
PRISM: protein-protein interaction prediction by structural matching. Methods Mol Biol (2008) 1.24
Protein-protein interaction networks: how can a hub protein bind so many different partners? Trends Biochem Sci (2009) 1.24
Theoretical characterization of substrate access/exit channels in the human cytochrome P450 3A4 enzyme: involvement of phenylalanine residues in the gating mechanism. J Phys Chem B (2009) 1.23
Spatial chemical conservation of hot spot interactions in protein-protein complexes. BMC Biol (2007) 1.22
Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets. Nucleic Acids Res (2007) 1.22
β-Barrel topology of Alzheimer's β-amyloid ion channels. J Mol Biol (2010) 1.21
How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues. Biophys J (2004) 1.21