Published in BMC Bioinformatics on December 14, 2005
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Novel knowledge-based mean force potential at the profile level. BMC Bioinformatics (2006) 0.93
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Artefacts and biases affecting the evaluation of scoring functions on decoy sets for protein structure prediction. Bioinformatics (2009) 0.88
Fast structure similarity searches among protein models: efficient clustering of protein fragments. Algorithms Mol Biol (2012) 0.80
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High-resolution x-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein. Proc Natl Acad Sci U S A (2005) 2.37
Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing. Biopolymers (2003) 2.35
The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology. J Mol Recognit (2002) 2.20
The victor/FRST function for model quality estimation. J Comput Biol (2005) 2.16
Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction. Protein Sci (2000) 2.10
Free-energy landscape of the villin headpiece in an all-atom force field. Structure (2005) 1.89
An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state. Protein Sci (2004) 1.74
Free energy determinants of tertiary structure and the evaluation of protein models. Protein Sci (2000) 1.71
Folding of the villin headpiece subdomain from random structures. Analysis of the charge distribution as a function of pH. J Mol Biol (2004) 1.58
Composites of local structure propensities: evidence for local encoding of long-range structure. Protein Sci (2002) 1.33
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Amino acid empirical contact energy definitions for fold recognition in the space of contact maps. BMC Bioinformatics (2003) 1.24
Protocol for MM/PBSA molecular dynamics simulations of proteins. Biophys J (2003) 1.22
Study of the Villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics. Proteins (2005) 1.18
Improved protein structure selection using decoy-dependent discriminatory functions. BMC Struct Biol (2004) 1.15
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A consistent set of statistical potentials for quantifying local side-chain and backbone interactions. Proteins (2005) 1.08
Protein refinement: a new challenge for CASP in its 10th anniversary. Bioinformatics (2005) 0.92
Application of MM/PBSA colony free energy to loop decoy discrimination: toward correlation between energy and root mean square deviation. Protein Sci (2005) 0.91
MM/PBSA analysis of molecular dynamics simulations of bovine beta-lactoglobulin: free energy gradients in conformational transitions? Proteins (2005) 0.86
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QMEAN: A comprehensive scoring function for model quality assessment. Proteins (2008) 3.90
Swe1Wee1-dependent tyrosine phosphorylation of Hsp90 regulates distinct facets of chaperone function. Mol Cell (2010) 2.24
The PASTA server for protein aggregation prediction. Protein Eng Des Sel (2007) 1.76
Rational design of shepherdin, a novel anticancer agent. Cancer Cell (2005) 1.74
Combinatorial drug design targeting multiple cancer signaling networks controlled by mitochondrial Hsp90. J Clin Invest (2009) 1.72
ESpritz: accurate and fast prediction of protein disorder. Bioinformatics (2011) 1.67
Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary-structure formation in peptides: a molecular dynamics study. Proc Natl Acad Sci U S A (2002) 1.64
LGI1 mutations in autosomal dominant and sporadic lateral temporal epilepsy. Hum Mutat (2009) 1.58
Exploiting the Burkholderia pseudomallei acute phase antigen BPSL2765 for structure-based epitope discovery/design in structural vaccinology. Chem Biol (2013) 1.45
Modeling signal propagation mechanisms and ligand-based conformational dynamics of the Hsp90 molecular chaperone full-length dimer. PLoS Comput Biol (2009) 1.43
Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines. Nucleic Acids Res (2006) 1.37
MobiDB: a comprehensive database of intrinsic protein disorder annotations. Bioinformatics (2012) 1.36
RING: networking interacting residues, evolutionary information and energetics in protein structures. Bioinformatics (2011) 1.25
Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust. Proteins (2009) 1.24
Decomposing protein networks into domain-domain interactions. Bioinformatics (2005) 1.22
Study of the Villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics. Proteins (2005) 1.18
Evolutionary and structural insights into the multifaceted glutathione peroxidase (Gpx) superfamily. Antioxid Redox Signal (2008) 1.15
CSpritz: accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs. Nucleic Acids Res (2011) 1.10
Structural insights into the function of human caveolin 1. Biochem Biophys Res Commun (2005) 1.10
Beta-hairpin conformation of fibrillogenic peptides: structure and alpha-beta transition mechanism revealed by molecular dynamics simulations. Proteins (2004) 1.09
Molecular simulation of multistate peptide dynamics: a comparison between microsecond timescale sampling and multiple shorter trajectories. J Comput Chem (2008) 1.07
Antileukemic activity of shepherdin and molecular diversity of hsp90 inhibitors. J Natl Cancer Inst (2006) 1.06
Sequence dependence of amyloid fibril formation: insights from molecular dynamics simulations. J Mol Biol (2005) 1.04
Small-molecule targeting of heat shock protein 90 chaperone function: rational identification of a new anticancer lead. J Med Chem (2006) 1.03
REPETITA: detection and discrimination of the periodicity of protein solenoid repeats by discrete Fourier transform. Bioinformatics (2009) 1.02
Corresponding functional dynamics across the Hsp90 Chaperone family: insights from a multiscale analysis of MD simulations. PLoS Comput Biol (2012) 1.01
The thioredoxin specificity of Drosophila GPx: a paradigm for a peroxiredoxin-like mechanism of many glutathione peroxidases. J Mol Biol (2006) 1.00
Simple consensus procedures are effective and sufficient in secondary structure prediction. Protein Eng (2003) 1.00
Understanding the determinants of stability and folding of small globular proteins from their energetics. Protein Sci (2004) 1.00
Dynamic diagnosis of familial prion diseases supports the β2-α2 loop as a universal interference target. PLoS One (2011) 0.98
Effect of hexafluoroisopropanol alcohol on the structure of melittin: a molecular dynamics simulation study. Protein Sci (2005) 0.97
Molecular mechanism of allosteric communication in Hsp70 revealed by molecular dynamics simulations. PLoS Comput Biol (2012) 0.97
RepeatsDB: a database of tandem repeat protein structures. Nucleic Acids Res (2013) 0.97
Relationship between energy distribution and fold stability: Insights from molecular dynamics simulations of native and mutant proteins. Proteins (2008) 0.96
Targeting tumor angiogenesis with TSP-1-based compounds: rational design of antiangiogenic mimetics of endogenous inhibitors. Oncotarget (2010) 0.96
Investigating the mechanism of peptide aggregation: insights from mixed monte carlo-molecular dynamics simulations. Biophys J (2008) 0.95
Predicting interaction sites from the energetics of isolated proteins: a new approach to epitope mapping. Biophys J (2010) 0.95
The structural intolerance of the PrP alpha-fold for polar substitution of the helix-3 methionines. Cell Mol Life Sci (2010) 0.95
Exploiting antigenic diversity for vaccine design: the chlamydia ArtJ paradigm. J Biol Chem (2010) 0.94
Misfolding of the amyloid beta-protein: a molecular dynamics study. Proteins (2006) 0.94
NeEMO: a method using residue interaction networks to improve prediction of protein stability upon mutation. BMC Genomics (2014) 0.94
The SSEA server for protein secondary structure alignment. Bioinformatics (2004) 0.93
Low density lipoprotein misfolding and amyloidogenesis. FASEB J (2008) 0.92
Fly cryptochrome and the visual system. Proc Natl Acad Sci U S A (2013) 0.91
MOBI: a web server to define and visualize structural mobility in NMR protein ensembles. Bioinformatics (2010) 0.91
Molecular recognition and drug-lead identification: what can molecular simulations tell us? Curr Med Chem (2010) 0.91
Application of MM/PBSA colony free energy to loop decoy discrimination: toward correlation between energy and root mean square deviation. Protein Sci (2005) 0.91
Immunogenic and structural properties of the Asn-Gly-Arg (NGR) tumor neovasculature-homing motif. Mol Immunol (2005) 0.90
Pharmacological enhancement of α-glucosidase by the allosteric chaperone N-acetylcysteine. Mol Ther (2012) 0.89
Improving the quality of protein structure models by selecting from alignment alternatives. BMC Bioinformatics (2006) 0.89
A multiscale approach to characterize the early aggregation steps of the amyloid-forming peptide GNNQQNY from the yeast prion sup-35. PLoS Comput Biol (2011) 0.89
Structural determinants of the unusual helix stability of a de novo engineered vascular endothelial growth factor (VEGF) mimicking peptide. Chemistry (2008) 0.89
Linear motifs in the C-terminus of D. melanogaster cryptochrome. Biochem Biophys Res Commun (2007) 0.89
Determinants of protein stability and folding: comparative analysis of beta-lactoglobulins and liver basic fatty acid binding protein. Proteins (2005) 0.87
Inhibitory interaction of the 14-3-3 proteins with ubiquitous (PMCA1) and tissue-specific (PMCA3) isoforms of the plasma membrane Ca2+ pump. Cell Calcium (2007) 0.87
Probing the hirudin-thrombin interaction by incorporation of noncoded amino acids and molecular dynamics simulation. Biochemistry (2002) 0.87
Synthesis, structure and conformation of partially-modified retro- and retro-inverso psi[NHCH(CF3)]Gly peptides. Chemistry (2003) 0.87
Molecular dynamics simulations of proteins and peptides: from folding to drug design. Curr Protein Pept Sci (2008) 0.86
FRASS: the web-server for RNA structural comparison. BMC Bioinformatics (2010) 0.86
3D-QSAR Assisted Design, Synthesis and Evaluation of Novobiocin Analogues. ACS Med Chem Lett (2012) 0.86
A novel WT1 gene mutation in a three-generation family with progressive isolated focal segmental glomerulosclerosis. Clin J Am Soc Nephrol (2010) 0.86
Modeling the alpha-helix to beta-hairpin transition mechanism and the formation of oligomeric aggregates of the fibrillogenic peptide Abeta(12-28): insights from all-atom molecular dynamics simulations. J Mol Graph Model (2004) 0.86
Bluues server: electrostatic properties of wild-type and mutated protein structures. Bioinformatics (2012) 0.85
Identification and in silico analysis of novel von Hippel-Lindau (VHL) gene variants from a large population. Ann Hum Genet (2011) 0.85
RAPHAEL: recognition, periodicity and insertion assignment of solenoid protein structures. Bioinformatics (2012) 0.85
Rational epitope design for protein targeting. ACS Chem Biol (2012) 0.85
A structure-based strategy for epitope discovery in Burkholderia pseudomallei OppA antigen. Structure (2012) 0.84
Functional interaction of phospholipid hydroperoxide glutathione peroxidase with sperm mitochondrion-associated cysteine-rich protein discloses the adjacent cysteine motif as a new substrate of the selenoperoxidase. J Biol Chem (2005) 0.84
CDKN2A unclassified variants in familial malignant melanoma: combining functional and computational approaches for their assessment. Hum Mutat (2014) 0.84
MANIFOLD: protein fold recognition based on secondary structure, sequence similarity and enzyme classification. Protein Eng (2003) 0.83
A computational model of the LGI1 protein suggests a common binding site for ADAM proteins. PLoS One (2011) 0.83
Analysis and consensus of currently available intrinsic protein disorder annotation sources in the MobiDB database. BMC Bioinformatics (2013) 0.83
A cry from the krill. Chronobiol Int (2010) 0.83
Computational study of the resistance shown by the subtype B/HIV-1 protease to currently known inhibitors. Biochemistry (2010) 0.83
Mechanism of helix nucleation and propagation: microscopic view from microsecond time scale MD simulations. J Phys Chem B (2005) 0.83
TESE: generating specific protein structure test set ensembles. Bioinformatics (2008) 0.82
Cardiomyopathy in patients with POMT1-related congenital and limb-girdle muscular dystrophy. Eur J Hum Genet (2012) 0.82
Direct and allosteric inhibition of the FGF2/HSPGs/FGFR1 ternary complex formation by an antiangiogenic, thrombospondin-1-mimic small molecule. PLoS One (2012) 0.82
RUBI: rapid proteomic-scale prediction of lysine ubiquitination and factors influencing predictor performance. Amino Acids (2013) 0.81
Deforestation and the structure of frog communities in the Humedale Terraba-Sierpe, Costa Rica. Zoolog Sci (2009) 0.81
Fast three dimensional pharmacophore virtual screening of new potent non-steroid aromatase inhibitors. J Med Chem (2009) 0.81
Exploiting conformational dynamics in drug discovery: design of C-terminal inhibitors of Hsp90 with improved activities. J Chem Inf Model (2014) 0.81
Selecting sequences that fold into a defined 3D structure: A new approach for protein design based on molecular dynamics and energetics. Biophys Chem (2009) 0.81
Updated management of non-st-segment elevation acute coronary syndromes: selection of patients for low-cost care: an analysis of outcome and cost effectiveness. Med Sci Monit (2005) 0.81
Energetic and dynamic aspects of the affinity maturation process: characterizing improved variants from the bevacizumab antibody with molecular simulations. J Chem Inf Model (2013) 0.81
PANADA: protein association network annotation, determination and analysis. PLoS One (2013) 0.81
Identification of domains in protein structures from the analysis of intramolecular interactions. J Phys Chem B (2012) 0.81
Investigating dynamic and energetic determinants of protein nucleic acid recognition: analysis of the zinc finger zif268-DNA complexes. BMC Struct Biol (2010) 0.80
A molecular dynamics study of the interaction of D-peptide amyloid inhibitors with their target sequence reveals a potential inhibitory pharmacophore conformation. J Mol Biol (2008) 0.80
Structural and computational biology of the molecular chaperone Hsp90: from understanding molecular mechanisms to computer-based inhibitor design. Curr Top Med Chem (2009) 0.80
Two amino acid substitutions within the first external loop of CCR5 induce human immunodeficiency virus-blocking antibodies in mice and chickens. J Virol (2008) 0.80
Cost utility and budget impact of third-generation aromatase inhibitors for advanced breast cancer: a literature-based model analysis of costs in the Italian National Health Service. Clin Ther (2004) 0.80
Combining computational and biochemical studies for a rationale on the anti-aromatase activity of natural polyphenols. ChemMedChem (2007) 0.80
Why is a protective antigen protective? Hum Vaccin (2009) 0.80
Inactivation of TEM-1 by avibactam (NXL-104): insights from quantum mechanics/molecular mechanics metadynamics simulations. Biochemistry (2014) 0.80
An efficient steroid pharmacophore-based strategy to identify new aromatase inhibitors. Eur J Med Chem (2009) 0.79
Investigating allostery in molecular recognition: insights from a computational study of multiple antibody-antigen complexes. J Phys Chem B (2013) 0.79
Deletions and mutations in the acidic lipid-binding region of the plasma membrane Ca2+ pump: a study on different splicing variants of isoform 2. J Biol Chem (2010) 0.79
Similar folds with different stabilization mechanisms: the cases of Prion and Doppel proteins. BMC Struct Biol (2006) 0.79