Published in J Chem Inf Model on December 27, 2011
Druggable protein interaction sites are more predisposed to surface pocket formation than the rest of the protein surface. PLoS Comput Biol (2013) 0.98
Overcoming Chemical, Biological, and Computational Challenges in the Development of Inhibitors Targeting Protein-Protein Interactions. Chem Biol (2015) 0.91
Drug-Like Protein-Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology. Mol Inform (2014) 0.90
Pocket-based drug design: exploring pocket space. AAPS J (2012) 0.86
Molecular determinants of binding to the Plasmodium subtilisin-like protease 1. J Chem Inf Model (2013) 0.84
Rational design of small-molecule stabilizers of spermine synthase dimer by virtual screening and free energy-based approach. PLoS One (2014) 0.83
DrugScorePPI knowledge-based potentials used as scoring and objective function in protein-protein docking. PLoS One (2014) 0.81
Evidence of conformational selection driving the formation of ligand binding sites in protein-protein interfaces. PLoS Comput Biol (2014) 0.81
Contributions of the RAD51 N-terminal domain to BRCA2-RAD51 interaction. Nucleic Acids Res (2013) 0.80
HADDOCK(2P2I): a biophysical model for predicting the binding affinity of protein-protein interaction inhibitors. J Chem Inf Model (2014) 0.79
Predicting where small molecules bind at protein-protein interfaces. PLoS One (2013) 0.78
Structural basis of lantibiotic recognition by the nisin resistance protein from Streptococcus agalactiae. Sci Rep (2016) 0.78
Structure, dynamics, and interaction of Mycobacterium tuberculosis (Mtb) DprE1 and DprE2 examined by molecular modeling, simulation, and electrostatic studies. PLoS One (2015) 0.77
Complex long-distance effects of mutations that confer linezolid resistance in the large ribosomal subunit. Nucleic Acids Res (2015) 0.77
Molecular Mechanisms of Glutamine Synthetase Mutations that Lead to Clinically Relevant Pathologies. PLoS Comput Biol (2016) 0.77
Computational survey of peptides derived from disulphide-bonded protein loops that may serve as mediators of protein-protein interactions. BMC Bioinformatics (2014) 0.76
The origin of the cooperativity in the streptavidin-biotin system: A computational investigation through molecular dynamics simulations. Sci Rep (2016) 0.76
Resolving hot spots in the C-terminal dimerization domain that determine the stability of the molecular chaperone Hsp90. PLoS One (2014) 0.76
Of mice and men: Dissecting the interaction between Listeria monocytogenes Internalin A and E-cadherin. Comput Struct Biotechnol J (2013) 0.75
The Amber biomolecular simulation programs. J Comput Chem (2005) 28.84
Assessing scoring functions for protein-ligand interactions. J Med Chem (2004) 2.41
Target flexibility: an emerging consideration in drug discovery and design. J Med Chem (2008) 1.74
DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction. J Med Chem (2005) 1.68
A toolkit and benchmark study for FRET-restrained high-precision structural modeling. Nat Methods (2012) 1.56
Targeting protein-protein interactions with small molecules: challenges and perspectives for computational binding epitope detection and ligand finding. Curr Med Chem (2006) 1.37
Molecular basis for Kv1.5 channel block: conservation of drug binding sites among voltage-gated K+ channels. J Biol Chem (2003) 1.30
Ligand-supported homology modelling of protein binding-sites using knowledge-based potentials. J Mol Biol (2003) 1.13
Statics of the ribosomal exit tunnel: implications for cotranslational peptide folding, elongation regulation, and antibiotics binding. J Mol Biol (2009) 1.13
DrugScoreRNA--knowledge-based scoring function to predict RNA-ligand interactions. J Chem Inf Model (2007) 1.11
Scaffold diversity of natural products: inspiration for combinatorial library design. Nat Prod Rep (2008) 1.10
Structure of Aquifex aeolicus argonaute highlights conformational flexibility of the PAZ domain as a potential regulator of RNA-induced silencing complex function. J Biol Chem (2006) 1.10
DrugScorePPI webserver: fast and accurate in silico alanine scanning for scoring protein-protein interactions. Nucleic Acids Res (2010) 1.10
Molecular recognition of RNA: challenges for modelling interactions and plasticity. J Mol Recognit (2010) 1.10
Protein rigidity and thermophilic adaptation. Proteins (2011) 1.09
NMSim web server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins. Nucleic Acids Res (2012) 1.08
Analyzing the flexibility of RNA structures by constraint counting. Biophys J (2008) 1.07
Multiscale modeling of macromolecular conformational changes combining concepts from rigidity and elastic network theory. Proteins (2006) 1.03
Starting structure dependence of NMR order parameters derived from MD simulations: implications for judging force-field quality. Biophys J (2008) 1.01
A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins. J Chem Inf Model (2011) 0.95
Histone deacetylase (HDAC) inhibitors with a novel connecting unit linker region reveal a selectivity profile for HDAC4 and HDAC5 with improved activity against chemoresistant cancer cells. J Med Chem (2013) 0.95
Double-strand DNA end-binding and sliding of the toroidal CRISPR-associated protein Csn2. Nucleic Acids Res (2013) 0.95
Constraint counting on RNA structures: linking flexibility and function. Methods (2009) 0.93
Constraint Network Analysis (CNA): a Python software package for efficiently linking biomacromolecular structure, flexibility, (thermo-)stability, and function. J Chem Inf Model (2013) 0.90
The crystal structure of the CRISPR-associated protein Csn2 from Streptococcus agalactiae. J Struct Biol (2012) 0.90
Structure-based computational analysis of protein binding sites for function and druggability prediction. J Biotechnol (2011) 0.89
Dimer-tetramer transition controls RUNX1/ETO leukemogenic activity. Blood (2010) 0.89
FEW: a workflow tool for free energy calculations of ligand binding. J Comput Chem (2013) 0.88
CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function. Nucleic Acids Res (2013) 0.88
Large-scale comparison of protein essential dynamics from molecular dynamics simulations and coarse-grained normal mode analyses. Proteins (2010) 0.87
6,8-Difluoro-4-methylumbiliferyl phosphate: a fluorogenic substrate for protein tyrosine phosphatases. Anal Biochem (2005) 0.87
Global and local indices for characterizing biomolecular flexibility and rigidity. J Comput Chem (2012) 0.86
Solution structure of the 30 kDa polysulfide-sulfur transferase homodimer from Wolinella succinogenes. Biochemistry (2004) 0.86
Pocket-space maps to identify novel binding-site conformations in proteins. J Chem Inf Model (2011) 0.85
Modulating protein-protein interactions: from structural determinants of binding to druggability prediction to application. Curr Pharm Des (2012) 0.84
Thermostabilizing mutations preferentially occur at structural weak spots with a high mutation ratio. J Biotechnol (2012) 0.84
Arg149 is involved in switching the low affinity, open state of the binding protein AfProX into its high affinity, closed state. J Mol Biol (2011) 0.83
How good are state-of-the-art docking tools in predicting ligand binding modes in protein-protein interfaces? J Chem Inf Model (2012) 0.83
Determinants of the unexpected stability of RNA fluorobenzene self pairs. Chembiochem (2008) 0.82
HIV-1 TAR RNA spontaneously undergoes relevant apo-to-holo conformational transitions in molecular dynamics and constrained geometrical simulations. J Chem Inf Model (2010) 0.81
Steering protein-ligand docking with quantitative NMR chemical shift perturbations. J Chem Inf Model (2009) 0.81
Scaffold-hopping potential of fragment-based de novo design: the chances and limits of variation. Comb Chem High Throughput Screen (2009) 0.80
Design, synthesis, and biological evaluation of simplified side chain hybrids of the potent actin binding polyketides rhizopodin and bistramide. ChemMedChem (2015) 0.80
From determinants of RUNX1/ETO tetramerization to small-molecule protein-protein interaction inhibitors targeting acute myeloid leukemia. J Chem Inf Model (2013) 0.80
Efficient and robust analysis of biomacromolecular flexibility using ensembles of network topologies based on fuzzy noncovalent constraints. Structure (2013) 0.80
Aromatic N versus aromatic F: bioisosterism discovered in RNA base pairing interactions leads to a novel class of universal base analogs. Nucleic Acids Res (2010) 0.80
Determinants of the species selectivity of oxazolidinone antibiotics targeting the large ribosomal subunit. Biol Chem (2013) 0.79
Predicting transmembrane helix pair configurations with knowledge-based distance-dependent pair potentials. Proteins (2008) 0.79
A membrane-proximal, C-terminal α-helix is required for plasma membrane localization and function of the G Protein-coupled receptor (GPCR) TGR5. J Biol Chem (2013) 0.79
Elastic potential grids: accurate and efficient representation of intermolecular interactions for fully flexible docking. ChemMedChem (2009) 0.79
Quality matters: extension of clusters of residues with good hydrophobic contacts stabilize (hyper)thermophilic proteins. J Chem Inf Model (2014) 0.79
Understanding the inhibitory effect of highly potent and selective archazolides binding to the vacuolar ATPase. J Chem Inf Model (2012) 0.78
Activation of integrins by urea in perfused rat liver. J Biol Chem (2010) 0.78
Targeting dynamic pockets of HIV-1 protease by structure-based computational screening for allosteric inhibitors. J Chem Inf Model (2014) 0.78
Development of in silico filters to predict activation of the pregnane X receptor (PXR) by structurally diverse drug-like molecules. Bioorg Med Chem (2012) 0.77
Docking into knowledge-based potential fields: a comparative evaluation of DrugScore. J Med Chem (2002) 0.77
Consensus adaptation of fields for molecular comparison (AFMoC) models incorporate ligand and receptor conformational variability into tailor-made scoring functions. J Chem Inf Model (2007) 0.77
Design, synthesis, and conformational analysis of trispyrimidonamides as α-helix mimetics. J Org Chem (2014) 0.76
Influence of the solvent representation on vibrational entropy calculations: generalized born versus distance-dependent dielectric model. J Comput Chem (2012) 0.76
Failure of the IDA in FRET Systems at Close Inter-Dye Distances Is Moderated by Frequent Low κ(2) Values. J Phys Chem B (2016) 0.75
Improving binding mode predictions by docking into protein-specifically adapted potential fields. J Med Chem (2005) 0.75
Alignment-independent comparison of binding sites based on DrugScore potential fields encoded by 3D Zernike descriptors. J Chem Inf Model (2012) 0.75
Alkoxyurea-based Histone Deacetylase Inhibitors Increase Cisplatin Potency in Chemoresistant Cancer Cell Lines. J Med Chem (2017) 0.75
Flexibility analysis of biomacromolecules with application to computer-aided drug design. Methods Mol Biol (2012) 0.75
Design, multicomponent synthesis and anticancer activity of a focused histone deacetylase (HDAC) inhibitor library with peptoid-based cap groups. J Med Chem (2017) 0.75
Corrigendum: Trading off stability against activity in extremophilic aldolases. Sci Rep (2016) 0.75
Tertiary interactions in the unbound guanine-sensing riboswitch focus functional conformational variability on the binding site. J Chem Inf Model (2017) 0.75
Is computer-assisted rescaffolding the future in lead generation? Future Med Chem (2013) 0.75
Erratum: Fractal Dimensions of Macromolecular Structures. Mol Inform (2014) 0.75