Published in PLoS Comput Biol on January 12, 2012
On the binding affinity of macromolecular interactions: daring to ask why proteins interact. J R Soc Interface (2012) 1.16
Ubiquitin dynamics in complexes reveal molecular recognition mechanisms beyond induced fit and conformational selection. PLoS Comput Biol (2012) 1.04
Protein flexibility, not disorder, is intrinsic to molecular recognition. F1000 Biol Rep (2013) 1.01
Modeling protein association mechanisms and kinetics. Curr Opin Struct Biol (2013) 0.96
The scoring of poses in protein-protein docking: current capabilities and future directions. BMC Bioinformatics (2013) 0.95
Towards structural systems pharmacology to study complex diseases and personalized medicine. PLoS Comput Biol (2014) 0.87
Contacts-based prediction of binding affinity in protein-protein complexes. Elife (2015) 0.87
Spatial simulations in systems biology: from molecules to cells. Int J Mol Sci (2012) 0.83
Characterizing changes in the rate of protein-protein dissociation upon interface mutation using hotspot energy and organization. PLoS Comput Biol (2013) 0.80
The dataset for protein-RNA binding affinity. Protein Sci (2013) 0.77
Predicting Protein-protein Association Rates using Coarse-grained Simulation and Machine Learning. Sci Rep (2017) 0.75
A machine learning approach for ranking clusters of docked protein-protein complexes by pairwise cluster comparison. Proteins (2016) 0.75
CHARMM: the biomolecular simulation program. J Comput Chem (2009) 27.71
Effective energy function for proteins in solution. Proteins (1999) 9.44
Application of a Theory of Enzyme Specificity to Protein Synthesis. Proc Natl Acad Sci U S A (1958) 9.18
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci (2002) 7.40
The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol (2009) 7.36
Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol (1996) 6.81
Antibody multispecificity mediated by conformational diversity. Science (2003) 5.21
Folding funnels, binding funnels, and protein function. Protein Sci (1999) 4.22
Energy functions that discriminate X-ray and near native folds from well-constructed decoys. J Mol Biol (1996) 3.86
Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse. Proc Natl Acad Sci U S A (2002) 3.78
Fundamental aspects of protein-protein association kinetics. Chem Rev (2009) 3.43
Folding funnels and binding mechanisms. Protein Eng (1999) 3.25
Transition networks for modeling the kinetics of conformational change in macromolecules. Curr Opin Struct Biol (2008) 3.03
Induced fit, conformational selection and independent dynamic segments: an extended view of binding events. Trends Biochem Sci (2010) 2.97
FireDock: fast interaction refinement in molecular docking. Proteins (2007) 2.90
Structural systems biology: modelling protein interactions. Nat Rev Mol Cell Biol (2006) 2.61
A systematic study of low-resolution recognition in protein--protein complexes. Proc Natl Acad Sci U S A (1999) 2.36
Water in protein structure prediction. Proc Natl Acad Sci U S A (2004) 2.35
Prediction of protein conformational freedom from distance constraints. Proteins (1997) 2.30
Protein-protein binding affinity prediction on a diverse set of structures. Bioinformatics (2011) 2.29
Evaluation of a fast implicit solvent model for molecular dynamics simulations. Proteins (2002) 2.27
PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta. Bioinformatics (2010) 2.23
Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms. Proc Natl Acad Sci U S A (2008) 2.18
Assembly and function of a quaternary signal transduction complex monitored by surface plasmon resonance. Nature (1993) 2.16
Kinetic analysis of macromolecular interactions using surface plasmon resonance biosensors. Methods Enzymol (1998) 2.14
ProtorP: a protein-protein interaction analysis server. Bioinformatics (2008) 2.09
Conformational isomerism and the diversity of antibodies. Proc Natl Acad Sci U S A (1994) 1.99
Do we underestimate the importance of water in cell biology? Nat Rev Mol Cell Biol (2006) 1.91
Specific interactions for ab initio folding of protein terminal regions with secondary structures. Proteins (2008) 1.81
A structure-based benchmark for protein-protein binding affinity. Protein Sci (2011) 1.81
Selected-fit versus induced-fit protein binding: kinetic differences and mutational analysis. Proteins (2009) 1.80
Biomolecular diffusional association. Curr Opin Struct Biol (2002) 1.78
Mathematical modeling identifies Smad nucleocytoplasmic shuttling as a dynamic signal-interpreting system. Proc Natl Acad Sci U S A (2008) 1.75
A physical reference state unifies the structure-derived potential of mean force for protein folding and binding. Proteins (2004) 1.60
Targeting the human cancer pathway protein interaction network by structural genomics. Mol Cell Proteomics (2008) 1.54
From induced fit to conformational selection: a continuum of binding mechanism controlled by the timescale of conformational transitions. Biophys J (2010) 1.49
OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing. J Mol Biol (2007) 1.48
Antigen recognition by conformational selection. FEBS Lett (1999) 1.42
OPUS-Ca: a knowledge-based potential function requiring only Calpha positions. Protein Sci (2007) 1.33
Analyzing protein interaction networks using structural information. Annu Rev Biochem (2008) 1.32
Protein fragment reconstruction using various modeling techniques. J Comput Aided Mol Des (2003) 1.26
Pushing structural information into the yeast interactome by high-throughput protein docking experiments. PLoS Comput Biol (2009) 1.22
Three-dimensional modeling of protein interactions and complexes is going 'omics. Curr Opin Struct Biol (2011) 1.21
Refined models for computer simulation of protein folding. Applications to the study of conserved secondary structure and flexible hinge points during the folding of pancreatic trypsin inhibitor. J Mol Biol (1979) 1.20
Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys. Proteins (2007) 1.19
Structures in systems biology. Curr Opin Struct Biol (2007) 1.11
Fasciculin 2 binds to the peripheral site on acetylcholinesterase and inhibits substrate hydrolysis by slowing a step involving proton transfer during enzyme acylation. J Biol Chem (1995) 1.09
Bridging from molecular simulation to biochemical networks. Curr Opin Struct Biol (2007) 1.04
Binding of 125I-fasciculin to rat brain acetylcholinesterase. The complex still binds diisopropyl fluorophosphate. J Biol Chem (1993) 1.04
Spectroscopic, calorimetric, and kinetic demonstration of conformational adaptation in peptide-antibody recognition. Biochemistry (1995) 1.03
Water and proteins: a love-hate relationship. Proc Natl Acad Sci U S A (2004) 1.01
Adhesive water networks facilitate binding of protein interfaces. Nat Commun (2011) 1.00
Structure-based thermodynamic analysis of the dissociation of protein phosphatase-1 catalytic subunit and microcystin-LR docked complexes. Protein Sci (2000) 0.95
Quantitative prediction of protein-protein binding affinity with a potential of mean force considering volume correction. Protein Sci (2009) 0.93
Lack of significant differences in association rates and affinities of antibodies from short-term and long-term responses to hen egg lysozyme. J Immunol (1999) 0.89
Predicting kinetic constants of protein-protein interactions based on structural properties. Proteins (2010) 0.89
Fast predictions of thermodynamics and kinetics of protein-protein recognition from structures: from molecular design to systems biology. Mol Biosyst (2009) 0.88
New measures for estimating surface complementarity and packing at protein-protein interfaces. FEBS Lett (2010) 0.85
Potentials 'R' Us web-server for protein energy estimations with coarse-grained knowledge-based potentials. BMC Bioinformatics (2010) 0.85
A systematic study of the energetics involved in structural changes upon association and connectivity in protein interaction networks. Structure (2011) 0.83
Global topological features of cancer proteins in the human interactome. Bioinformatics (2006) 4.17
Reversal of DNA alkylation damage by two human dioxygenases. Proc Natl Acad Sci U S A (2002) 3.62
Transmission of cutaneous leishmaniasis by sand flies is enhanced by regurgitation of fPPG. Nature (2004) 2.36
Repair of alkylated DNA: recent advances. DNA Repair (Amst) (2006) 2.34
Protein-protein binding affinity prediction on a diverse set of structures. Bioinformatics (2011) 2.29
Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania. Genome Res (2011) 1.90
Matrix geometry determines optimal cancer cell migration strategy and modulates response to interventions. Nat Cell Biol (2013) 1.84
Planar polarization of the atypical myosin Dachs orients cell divisions in Drosophila. Genes Dev (2011) 1.82
A structure-based benchmark for protein-protein binding affinity. Protein Sci (2011) 1.81
OPCML at 11q25 is epigenetically inactivated and has tumor-suppressor function in epithelial ovarian cancer. Nat Genet (2003) 1.77
Mathematical modeling identifies Smad nucleocytoplasmic shuttling as a dynamic signal-interpreting system. Proc Natl Acad Sci U S A (2008) 1.75
Leishmania manipulation of sand fly feeding behavior results in enhanced transmission. PLoS Pathog (2007) 1.72
Agent-based simulation of notch-mediated tip cell selection in angiogenic sprout initialisation. J Theor Biol (2007) 1.60
Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasis. BMC Bioinformatics (2006) 1.57
The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking. J Mol Biol (2005) 1.41
Tipping the balance: robustness of tip cell selection, migration and fusion in angiogenesis. PLoS Comput Biol (2009) 1.40
Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J Mol Biol (2011) 1.40
Two separate growth phases during the development of Leishmania in sand flies: implications for understanding the life cycle. Int J Parasitol (2003) 1.39
SwarmDock: a server for flexible protein-protein docking. Bioinformatics (2013) 1.32
Leishmania chitinase facilitates colonization of sand fly vectors and enhances transmission to mice. Cell Microbiol (2008) 1.27
Evidence incriminating midges (Diptera: Ceratopogonidae) as potential vectors of Leishmania in Australia. Int J Parasitol (2011) 1.25
Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins (2013) 1.20
Different Smad2 partners bind a common hydrophobic pocket in Smad2 via a defined proline-rich motif. EMBO J (2002) 1.20
Synthetic glycovaccine protects against the bite of leishmania-infected sand flies. J Infect Dis (2006) 1.18
Implicit flexibility in protein docking: cross-docking and local refinement. Proteins (2007) 1.10
In silico protein recombination: enhancing template and sequence alignment selection for comparative protein modelling. J Mol Biol (2003) 1.07
Recognition of phosphorylated-Smad2-containing complexes by a novel Smad interaction motif. Mol Cell Biol (2004) 1.06
A dyad of lymphoblastic lysosomal cysteine proteases degrades the antileukemic drug L-asparaginase. J Clin Invest (2009) 1.05
Inhibition of trypsin expression in Lutzomyia longipalpis using RNAi enhances the survival of Leishmania. Parasit Vectors (2009) 1.03
SwarmDock and the use of normal modes in protein-protein docking. Int J Mol Sci (2010) 1.01
A real-time PCR assay to estimate Leishmania chagasi load in its natural sand fly vector Lutzomyia longipalpis. Trans R Soc Trop Med Hyg (2008) 1.01
A Markov-chain model description of binding funnels to enhance the ranking of docked solutions. Proteins (2013) 1.01
Gene silencing in phlebotomine sand flies: Xanthine dehydrogenase knock down by dsRNA microinjections. Insect Biochem Mol Biol (2008) 1.00
Leishmania donovani and cutaneous leishmaniasis, Sri Lanka. Emerg Infect Dis (2007) 0.99
Molecular characterization, expression, and in vivo analysis of LmexCht1: the chitinase of the human pathogen, Leishmania mexicana. J Biol Chem (2004) 0.99
Stage-specific adhesion of Leishmania promastigotes to sand fly midguts assessed using an improved comparative binding assay. PLoS Negl Trop Dis (2010) 0.98
Modeling protein association mechanisms and kinetics. Curr Opin Struct Biol (2013) 0.96
Flexible relaxation of rigid-body docking solutions. Proteins (2007) 0.96
Rational engineering of L-asparaginase reveals importance of dual activity for cancer cell toxicity. Blood (2010) 0.96
Colonisation resistance in the sand fly gut: Leishmania protects Lutzomyia longipalpis from bacterial infection. Parasit Vectors (2014) 0.96
Can MM-PBSA calculations predict the specificities of protein kinase inhibitors? J Comput Chem (2006) 0.95
The scoring of poses in protein-protein docking: current capabilities and future directions. BMC Bioinformatics (2013) 0.95
Investigation of the bacterial communities associated with females of Lutzomyia sand fly species from South America. PLoS One (2012) 0.95
Evidence to support two conspecific cytological races on Anopheles aconitus in Thailand. J Vector Ecol (2005) 0.95
Blood meal identification and parasite detection in laboratory-fed and field-captured Lutzomyia longipalpis by PCR using FTA databasing paper. Acta Trop (2008) 0.95
Novel use of a genetic algorithm for protein structure prediction: searching template and sequence alignment space. Proteins (2003) 0.94
Development of synchronous VHL syndrome tumors reveals contingencies and constraints to tumor evolution. Genome Biol (2014) 0.92
Alternating evolutionary pressure in a genetic algorithm facilitates protein model selection. BMC Struct Biol (2008) 0.92
Detection and refinement of encounter complexes for protein-protein docking: taking account of macromolecular crowding. Proteins (2010) 0.92
A link between sequence conservation and domain motion within the AAA+ family. J Struct Biol (2004) 0.91
Caspar-like gene depletion reduces Leishmania infection in sand fly host Lutzomyia longipalpis. J Biol Chem (2012) 0.91
Developmentally regulated expression of a cell surface class I nuclease in Leishmania mexicana. Int J Parasitol (2002) 0.91
Blind prediction of interfacial water positions in CAPRI. Proteins (2013) 0.90
Functional recycling of C2 domains throughout evolution: a comparative study of synaptotagmin, protein kinase C and phospholipase C by sequence, structural and modelling approaches. J Mol Biol (2003) 0.90
Comparative modelling: an essential methodology for protein structure prediction in the post-genomic era. Appl Bioinformatics (2002) 0.87
A structural systems biology approach for quantifying the systemic consequences of missense mutations in proteins. PLoS Comput Biol (2012) 0.87
Cancer networks and beyond: interpreting mutations using the human interactome and protein structure. Semin Cancer Biol (2013) 0.86
Detailed analysis of an experimental challenge model for Leishmania infantum (JPC strain) in dogs. Vet Parasitol (2005) 0.86
Incorporation of flexibility into rigid-body docking: applications in rounds 3-5 of CAPRI. Proteins (2005) 0.86
Susceptibility of two karyotypic forms of Anopheles aconitus (Diptera: Culicidae) to Plasmodium falciparum and P. vivax. Rev Inst Med Trop Sao Paulo (2006) 0.86
Guided docking: first step to locate potential binding sites. Proteins (2003) 0.85
Production and characterization of stable amphotericin-resistant amastigotes and promastigotes of Leishmania mexicana. Antimicrob Agents Chemother (2005) 0.85
Comparative morphometry and morphology of Anopheles aconitus Form B and C eggs under scanning electron microscope. Rev Inst Med Trop Sao Paulo (2004) 0.83
Structural context of exons in protein domains: implications for protein modelling and design. J Mol Biol (2003) 0.83
Chicken blood provides a suitable meal for the sand fly Lutzomyia longipalpis and does not inhibit Leishmania development in the gut. Parasit Vectors (2010) 0.83
Understanding cancer mechanisms through network dynamics. Brief Funct Genomics (2012) 0.83
The structural basis for enhancer-dependent assembly and activation of the AAA transcriptional activator NorR. Mol Microbiol (2014) 0.82
A glycine- and glutamate-rich protein is female salivary gland-specific and abundant in the malaria vector Anopheles dirus B (Diptera: Culicidae). J Med Entomol (2006) 0.82
Probability-based model of protein-protein interactions on biological timescales. Algorithms Mol Biol (2006) 0.81
Flagellar attachment of Leishmania promastigotes to plastic film in vitro. Exp Parasitol (2004) 0.81
The role of surface glycoconjugates in Leishmania midgut attachment examined by competitive binding assays and experimental development in sand flies. Parasitology (2013) 0.81
Salivary gland proteins of the human malaria vector, Anopheles dirus B (Diptera: Culicidae). Rev Inst Med Trop Sao Paulo (2007) 0.80
Salivary gland of Toxorhynchites splendens Wiedemann (Diptera: Culicidae): ultrastructural morphology and electrophoretic protein profiles. J Med Entomol (2004) 0.80
Salivary gland proteome of the human malaria vector, Anopheles campestris-like (Diptera: Culicidae). Parasitol Res (2012) 0.80
Mechanism of cohesin loading onto chromosomes: a conformational dynamics study. Biophys J (2010) 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
C-reactive protein-mediated phagocytosis of Leishmania donovani promastigotes does not alter parasite survival or macrophage responses. Parasite Immunol (2003) 0.79
Predicting the structure of protein-protein complexes using the SwarmDock Web Server. Methods Mol Biol (2014) 0.78
A unique, highly conserved secretory invertase is differentially expressed by promastigote developmental forms of all species of the human pathogen, Leishmania. Mol Cell Biochem (2015) 0.78
Developing a move-set for protein model refinement. Bioinformatics (2006) 0.77
Sequence analyses of three nuclear ribosomal loci and a mitochondrial locus in cytologically different forms of Thai Anopheles aconitus mosquitoes. Southeast Asian J Trop Med Public Health (2005) 0.77
RaTrav: a tool for calculating mean first-passage times on biochemical networks. BMC Syst Biol (2013) 0.76
C-reactive protein initiates transformation of Leishmania donovani and L. mexicana through binding to lipophosphoglycan. Mol Biochem Parasitol (2006) 0.75
MIDGUT ULTRASTRUCTURE OF FOURTH INSTAR OCHLEROTATUS TOGOI (DIPTERA: CULICIDAE). Southeast Asian J Trop Med Public Health (2014) 0.75