Published in Curr Top Med Chem on January 01, 2007
Polymorphism in Alzheimer Abeta amyloid organization reflects conformational selection in a rugged energy landscape. Chem Rev (2010) 1.62
Enabling large-scale design, synthesis and validation of small molecule protein-protein antagonists. PLoS One (2012) 1.60
Dimerization-Induced Allosteric Changes of the Oxyanion-Hole Loop Activate the Pseudorabies Virus Assemblin pUL26N, a Herpesvirus Serine Protease. PLoS Pathog (2015) 1.41
Structure-based design of a T-cell receptor leads to nearly 100-fold improvement in binding affinity for pepMHC. Proteins (2009) 1.16
PCRPi: Presaging Critical Residues in Protein interfaces, a new computational tool to chart hot spots in protein interfaces. Nucleic Acids Res (2009) 1.08
Ivermectin antagonizes ethanol inhibition in purinergic P2X4 receptors. J Pharmacol Exp Ther (2010) 1.01
GM1 gangliosidosis and Morquio B disease: an update on genetic alterations and clinical findings. Biochim Biophys Acta (2011) 0.97
Amyloidogenic regions and interaction surfaces overlap in globular proteins related to conformational diseases. PLoS Comput Biol (2009) 0.94
Ile-phe dipeptide self-assembly: clues to amyloid formation. Biophys J (2006) 0.93
Mutations that replace aromatic side chains promote aggregation of the Alzheimer's Aβ peptide. Biochemistry (2011) 0.92
Comprehensive experimental and computational analysis of binding energy hot spots at the NF-κB essential modulator/IKKβ protein-protein interface. J Am Chem Soc (2013) 0.91
Erythrocyte Binding Activity Displayed by a Selective Group of Plasmodium vivax Tryptophan Rich Antigens Is Inhibited by Patients' Antibodies. PLoS One (2012) 0.88
Targeting protein-protein interactions in hematologic malignancies: still a challenge or a great opportunity for future therapies? Immunol Rev (2015) 0.88
A leap into the chemical space of protein-protein interaction inhibitors. Curr Pharm Des (2012) 0.86
Tryptophan 46 is a site for ethanol and ivermectin action in P2X4 receptors. Purinergic Signal (2013) 0.84
Enzyme inhibition by allosteric capture of an inactive conformation. J Mol Biol (2011) 0.83
Mutations in protein-binding hot-spots on the hub protein Smad3 differentially affect its protein interactions and Smad3-regulated gene expression. PLoS One (2011) 0.82
P2X4 receptors (P2X4Rs) represent a novel target for the development of drugs to prevent and/or treat alcohol use disorders. Front Neurosci (2014) 0.81
Hot spots in a network of functional sites. PLoS One (2013) 0.80
Prediction and redesign of protein-protein interactions. Prog Biophys Mol Biol (2014) 0.80
Characterizing changes in the rate of protein-protein dissociation upon interface mutation using hotspot energy and organization. PLoS Comput Biol (2013) 0.80
Cooperativity among short amyloid stretches in long amyloidogenic sequences. PLoS One (2012) 0.80
Computational analysis of protein-protein interfaces involving an alpha helix: insights for terphenyl-like molecules binding. BMC Pharmacol Toxicol (2013) 0.78
Characterization of EPPIN's semenogelin I binding site: a contraceptive drug target. Biol Reprod (2012) 0.77
A screen to identify small molecule inhibitors of protein-protein interactions in mycobacteria. Assay Drug Dev Technol (2011) 0.77
Beta-strand interfaces of non-dimeric protein oligomers are characterized by scattered charged residue patterns. PLoS One (2012) 0.76
ECMIS: computational approach for the identification of hotspots at protein-protein interfaces. BMC Bioinformatics (2014) 0.76
Infection of Beet necrotic yellow vein virus with RNA4-encoded P31 specifically up-regulates pathogenesis-related protein 10 in Nicotiana benthamiana. Virol J (2014) 0.75
Parallel synthesis of an oligomeric imidazole-4,5-dicarboxamide library. J Comb Chem (2010) 0.75
PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res (2005) 7.66
The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol (2009) 7.36
Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins (2002) 5.79
Is allostery an intrinsic property of all dynamic proteins? Proteins (2004) 4.99
A method for simultaneous alignment of multiple protein structures. Proteins (2004) 3.45
Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc Natl Acad Sci U S A (2003) 3.42
Allostery: absence of a change in shape does not imply that allostery is not at play. J Mol Biol (2008) 3.24
Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues. J Mol Biol (2004) 3.10
Stabilities and conformations of Alzheimer's beta -amyloid peptide oligomers (Abeta 16-22, Abeta 16-35, and Abeta 10-35): Sequence effects. Proc Natl Acad Sci U S A (2002) 3.06
Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci (2002) 3.01
Induced fit, conformational selection and independent dynamic segments: an extended view of binding events. Trends Biochem Sci (2010) 2.97
Principles of protein-protein interactions: what are the preferred ways for proteins to interact? Chem Rev (2008) 2.96
FireDock: fast interaction refinement in molecular docking. Proteins (2007) 2.90
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther (2013) 2.64
Close-range electrostatic interactions in proteins. Chembiochem (2002) 2.42
FireDock: a web server for fast interaction refinement in molecular docking. Nucleic Acids Res (2008) 2.39
The origin of allosteric functional modulation: multiple pre-existing pathways. Structure (2009) 2.33
Recognition of functional sites in protein structures. J Mol Biol (2004) 2.32
Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms. Mol Biosyst (2009) 2.18
Extended disordered proteins: targeting function with less scaffold. Trends Biochem Sci (2003) 2.12
A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications. Protein Sci (2004) 2.11
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
Relationship between ion pair geometries and electrostatic strengths in proteins. Biophys J (2002) 1.91
HingeProt: automated prediction of hinges in protein structures. Proteins (2008) 1.86
Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. Nat Protoc (2011) 1.84
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
Polymorphism in Alzheimer Abeta amyloid organization reflects conformational selection in a rugged energy landscape. Chem Rev (2010) 1.62
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
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
Modeling the Alzheimer Abeta17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities. Biophys J (2007) 1.44
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
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
The ARTS web server for aligning RNA tertiary structures. Nucleic Acids Res (2006) 1.37
Mechanisms of transcription factor selectivity. Trends Genet (2010) 1.35
Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35. Biophys J (2006) 1.33
Short peptide amyloid organization: stabilities and conformations of the islet amyloid peptide NFGAIL. Biophys J (2003) 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
Allostery and population shift in drug discovery. Curr Opin Pharmacol (2010) 1.32
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
Topological properties of protein interaction networks from a structural perspective. Biochem Soc Trans (2008) 1.28
The multiple common point set problem and its application to molecule binding pattern detection. J Comput Biol (2006) 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
Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets. Nucleic Acids Res (2007) 1.22
Spatial chemical conservation of hot spot interactions in protein-protein complexes. BMC Biol (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
SiteEngines: recognition and comparison of binding sites and protein-protein interfaces. Nucleic Acids Res (2005) 1.20
Modular architecture of protein structures and allosteric communications: potential implications for signaling proteins and regulatory linkages. Genome Biol (2007) 1.20
Analysis and classification of RNA tertiary structures. RNA (2008) 1.20
Allosteric effects in the marginally stable von Hippel-Lindau tumor suppressor protein and allostery-based rescue mutant design. Proc Natl Acad Sci U S A (2008) 1.20
Interaction of protegrin-1 with lipid bilayers: membrane thinning effect. Biophys J (2006) 1.18
Misfolded amyloid ion channels present mobile beta-sheet subunits in contrast to conventional ion channels. Biophys J (2009) 1.18
SiteLight: binding-site prediction using phage display libraries. Protein Sci (2003) 1.17
Antimicrobial protegrin-1 forms amyloid-like fibrils with rapid kinetics suggesting a functional link. Biophys J (2011) 1.17
From structure to function: methods and applications. Curr Protein Pept Sci (2005) 1.16
PharmaGist: a webserver for ligand-based pharmacophore detection. Nucleic Acids Res (2008) 1.16
Hollow core of Alzheimer's Abeta42 amyloid observed by cryoEM is relevant at physiological pH. Proc Natl Acad Sci U S A (2010) 1.14
Automatic prediction of protein interactions with large scale motion. Proteins (2007) 1.13
Polymorphism of Alzheimer's Abeta17-42 (p3) oligomers: the importance of the turn location and its conformation. Biophys J (2009) 1.13
Application of 1-aminocyclohexane carboxylic acid to protein nanostructure computer design. J Chem Inf Model (2008) 1.12
EMatch: discovery of high resolution structural homologues of protein domains in intermediate resolution cryo-EM maps. IEEE/ACM Trans Comput Biol Bioinform (2007) 1.12
Favorable scaffolds: proteins with different sequence, structure and function may associate in similar ways. Protein Eng Des Sel (2005) 1.12
Approaching the CAPRI challenge with an efficient geometry-based docking. Proteins (2005) 1.12
Protein structure prediction via combinatorial assembly of sub-structural units. Bioinformatics (2003) 1.11
Atomic force microscopy and MD simulations reveal pore-like structures of all-D-enantiomer of Alzheimer's β-amyloid peptide: relevance to the ion channel mechanism of AD pathology. J Phys Chem B (2012) 1.11
The hydrophobic effect: a new insight from cold denaturation and a two-state water structure. Crit Rev Biochem Mol Biol (2002) 1.10
Annular structures as intermediates in fibril formation of Alzheimer Abeta17-42. J Phys Chem B (2008) 1.10
MolAxis: a server for identification of channels in macromolecules. Nucleic Acids Res (2008) 1.10