| review article | Q7318358 |
| scholarly article | Q13442814 |
| P50 | author | Philip Bourne | Q7183255 |
| Li Xie | Q60541176 | ||
| Lei Xie | Q28969662 | ||
| P2860 | cites work | Use of data-biased random walks on graphs for the retrieval of context-specific networks from genomic data | Q21145334 |
| I-TASSER server for protein 3D structure prediction | Q21284202 | ||
| Advances in Homology Protein Structure Modeling | Q22241408 | ||
| Kinase-dead BRAF and oncogenic RAS cooperate to drive tumor progression through CRAF | Q24298749 | ||
| Lessons learned from the development of an abl tyrosine kinase inhibitor for chronic myelogenous leukemia | Q24599829 | ||
| Core signaling pathways in human pancreatic cancers revealed by global genomic analyses | Q24606006 | ||
| Genomic-scale prioritization of drug targets: the TDR Targets database | Q24635333 | ||
| An integrated genomic analysis of human glioblastoma multiforme | Q24648860 | ||
| A cholesterol biosynthesis inhibitor blocks Staphylococcus aureus virulence | Q24650591 | ||
| Global reconstruction of the human metabolic network based on genomic and bibliomic data | Q24677060 | ||
| Predicting absolute ligand binding free energies to a simple model site | Q24683618 | ||
| Protein function prediction using local 3D templates | Q47606217 | ||
| Genetic modification of flux for flux prediction of mutants | Q47728960 | ||
| A robustness-based approach to systems-oriented drug design. | Q51062307 | ||
| Multiple weak hits confuse complex systems: a transcriptional regulatory network as an example. | Q51374935 | ||
| Ensemble Docking from Homology Models. | Q51902480 | ||
| Systems biology and combination therapy in the quest for clinical efficacy. | Q51934858 | ||
| Homology model-based virtual screening for GPCR ligands using docking and target-biased scoring. | Q53037530 | ||
| Data completeness—the Achilles heel of drug-target networks | Q57012660 | ||
| Network pharmacology | Q57932497 | ||
| Structure-based drug discovery using GPCR homology modeling: successful virtual screening for antagonists of the alpha1A adrenergic receptor | Q81409742 | ||
| An old target revisited: two new privileged skeletons and an unexpected binding mode for HIV-protease inhibitors | Q81635476 | ||
| Network-based prediction of human tissue-specific metabolism | Q81798711 | ||
| In silico search of putative adverse drug reaction related proteins as a potential tool for facilitating drug adverse effect prediction | Q82965636 | ||
| Mechanisms of drug combinations: interaction and network perspectives | Q83265745 | ||
| Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation | Q24794109 | ||
| The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema | Q24794858 | ||
| Functional coverage of the human genome by existing structures, structural genomics targets, and homology models | Q24814930 | ||
| Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data | Q27136634 | ||
| SuperTarget and Matador: resources for exploring drug-target relationships | Q27136964 | ||
| Harvesting candidate genes responsible for serious adverse drug reactions from a chemical-protein interactome | Q27335598 | ||
| Unexpected nanomolar inhibition of carbonic anhydrase by COX-2-selective celecoxib: new pharmacological opportunities due to related binding site recognition | Q27643006 | ||
| A class of selective antibacterials derived from a protein kinase inhibitor pharmacophore | Q27653498 | ||
| RAF inhibitors prime wild-type RAF to activate the MAPK pathway and enhance growth | Q27659493 | ||
| A global protein kinase and phosphatase interaction network in yeast. | Q27932206 | ||
| A quantitative analysis of kinase inhibitor selectivity | Q28264038 | ||
| Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia | Q28274064 | ||
| Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches | Q28290933 | ||
| In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators | Q28471679 | ||
| A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology | Q28472464 | ||
| Drug discovery using chemical systems biology: identification of the protein-ligand binding network to explain the side effects of CETP inhibitors | Q28475474 | ||
| FINDSITE: a threading-based approach to ligand homology modeling | Q28475563 | ||
| Drug discovery using chemical systems biology: repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis | Q28475676 | ||
| Drug off-target effects predicted using structural analysis in the context of a metabolic network model | Q28475693 | ||
| The Mycobacterium tuberculosis drugome and its polypharmacological implications | Q28476004 | ||
| The Connectivity Map: a new tool for biomedical research | Q28530408 | ||
| Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry | Q28766803 | ||
| The druggable genome | Q29547361 | ||
| The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease | Q29547614 | ||
| Twilight zone of protein sequence alignments | Q29614388 | ||
| Drug-target network | Q29614447 | ||
| Drug target identification using side-effect similarity | Q29615103 | ||
| Global mapping of pharmacological space | Q29615876 | ||
| Reconstruction of biochemical networks in microorganisms | Q29616018 | ||
| Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models | Q29616389 | ||
| Genome-scale models of microbial cells: evaluating the consequences of constraints | Q29616789 | ||
| RAF inhibitors transactivate RAF dimers and ERK signalling in cells with wild-type BRAF | Q29616828 | ||
| Relating protein pharmacology by ligand chemistry | Q29617492 | ||
| Diversity and complexity in DNA recognition by transcription factors | Q29619632 | ||
| Protein structure similarity as guiding principle for combinatorial library design. | Q30336116 | ||
| Teaching old receptors new tricks: biasing seven-transmembrane receptors | Q33985759 | ||
| On the calculation of absolute macromolecular binding free energies | Q34074487 | ||
| Evidence that fold-change, and not absolute level, of beta-catenin dictates Wnt signaling | Q34087711 | ||
| The incoherent feedforward loop can provide fold-change detection in gene regulation | Q34087717 | ||
| In silico prediction of binding sites on proteins | Q34099513 | ||
| Cross-reactivity virtual profiling of the human kinome by X-react(KIN): a chemical systems biology approach | Q34384664 | ||
| Multicomponent therapeutics for networked systems | Q34390417 | ||
| Extensive in vivo metabolite-protein interactions revealed by large-scale systematic analyses | Q34421346 | ||
| Application of drug repositioning strategy to TOFISOPAM. | Q34601815 | ||
| A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation | Q34731493 | ||
| Algorithmic and analytical methods in network biology | Q34921401 | ||
| Dynamic modularity in protein interaction networks predicts breast cancer outcome | Q34934057 | ||
| Medicinal chemistry of target family-directed masterkeys | Q35202868 | ||
| Systems biology in drug discovery | Q35911464 | ||
| Anti-inflammatory effects of statins: clinical evidence and basic mechanisms | Q36337932 | ||
| Creating more effective antidepressants: clues from the clinic | Q36515807 | ||
| Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening | Q36638820 | ||
| Structure selection for protein kinase docking and virtual screening: homology models or crystal structures? | Q36638823 | ||
| Innovative lead discovery strategies for tropical diseases | Q36642049 | ||
| Multi-target therapeutics: when the whole is greater than the sum of the parts | Q36697412 | ||
| Calculation of protein-ligand binding affinities. | Q36698596 | ||
| An improved relaxed complex scheme for receptor flexibility in computer-aided drug design | Q36838120 | ||
| Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei | Q36960711 | ||
| Executable cell biology | Q36996114 | ||
| Identifying the proteins to which small-molecule probes and drugs bind in cells | Q37114227 | ||
| Predicting protein function and binding profile via matching of local evolutionary and geometric surface patterns | Q37162894 | ||
| Toward accurate reconstruction of functional protein networks | Q37166062 | ||
| Model structure of APOBEC3C reveals a binding pocket modulating ribonucleic acid interaction required for encapsidation | Q37274403 | ||
| Binding of small-molecule ligands to proteins: "what you see" is not always "what you get". | Q37372747 | ||
| Computational evaluation of protein-small molecule binding. | Q37375373 | ||
| Protein promiscuity and its implications for biotechnology | Q37389046 | ||
| Cracking the phosphatase code: docking interactions determine substrate specificity | Q37649281 | ||
| Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls | Q38343206 | ||
| Signaling motifs and Weber's law. | Q39764209 | ||
| Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model | Q39866153 | ||
| Gaining insight into off-target mediated effects of drug candidates with a comprehensive systems chemical biology analysis. | Q39884541 | ||
| Screening drug-like compounds by docking to homology models: a systematic study. | Q40356909 | ||
| Biospectra analysis: model proteome characterizations for linking molecular structure and biological response | Q40377787 | ||
| CGP 57148, a tyrosine kinase inhibitor, inhibits the growth of cells expressing BCR-ABL, TEL-ABL, and TEL-PDGFR fusion proteins | Q41073724 | ||
| Co-evolution of proteins with their interaction partners | Q41742351 | ||
| Binding mode of ecdysone agonists to the receptor: comparative modeling and docking studies | Q42048708 | ||
| High-order combination effects and biological robustness | Q42554339 | ||
| Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes | Q42602259 | ||
| Identifying functional modules in protein-protein interaction networks: an integrated exact approach | Q42646303 | ||
| Homology-modelling protein-ligand interactions: allowing for ligand-induced conformational change | Q43077696 | ||
| Capture compound mass spectrometry sheds light on the molecular mechanisms of liver toxicity of two Parkinson drugs | Q43270591 | ||
| Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule | Q43558049 | ||
| Homology modeling using multiple molecular dynamics simulations and docking studies of the human androgen receptor ligand binding domain bound to testosterone and nonsteroidal ligands. | Q43610076 | ||
| Inferring functional relationships of proteins from local sequence and spatial surface patterns | Q43749943 | ||
| Progress toward virtual screening for drug side effects. | Q44125156 | ||
| Protein-based virtual screening of chemical databases. II. Are homology models of G-Protein Coupled Receptors suitable targets? | Q44242205 | ||
| Closing the scientific loop: bridging correlation and causality in the petaflop age. | Q44824060 | ||
| Performance of 3D-database molecular docking studies into homology models | Q44887759 | ||
| Predicting polypharmacology by binding site similarity: from kinases to the protein universe | Q45763650 | ||
| Calculation of absolute protein-ligand binding free energy using distributed replica sampling | Q46221592 | ||
| Virtual screening approaches for the identification of non-lipid autotaxin inhibitors | Q46883500 | ||
| 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 | Q47600844 | ||
| Progress of structural genomics initiatives: an analysis of solved target structures. | Q30350633 | ||
| Charting biologically relevant chemical space: a structural classification of natural products (SCONP) | Q30351855 | ||
| A nonsynonymous SNP in human cytosolic sialidase in a small Asian population results in reduced enzyme activity: potential link with severe adverse reactions to oseltamivir. | Q30361021 | ||
| Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. | Q30368616 | ||
| Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. | Q30370020 | ||
| Structural relationships among proteins with different global topologies and their implications for function annotation strategies | Q30381353 | ||
| Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling. | Q30381629 | ||
| Protein interface conservation across structure space | Q30390154 | ||
| Computational chemogenomics approaches to systematic knowledge-based drug discovery. | Q30832795 | ||
| Nuclear hormone receptor targeted virtual screening | Q30952756 | ||
| Chemogenomic data analysis: prediction of small-molecule targets and the advent of biological fingerprint | Q31138061 | ||
| Kinases, Homology Models, and High Throughput Docking | Q33193967 | ||
| Finding new tricks for old drugs: an efficient route for public-sector drug discovery | Q33229063 | ||
| Protein and small molecule microarrays: powerful tools for high-throughput proteomics | Q33252427 | ||
| Generalized modeling of enzyme-ligand interactions using proteochemometrics and local protein substructures | Q33256084 | ||
| Evaluation of the utility of homology models in high throughput docking | Q33284018 | ||
| Discovery of antiandrogen activity of nonsteroidal scaffolds of marketed drugs | Q33289718 | ||
| Combination chemical genetics | Q33378070 | ||
| Mycobacterium tuberculosis interactome analysis unravels potential pathways to drug resistance | Q33395486 | ||
| Bioactivity-guided mapping and navigation of chemical space. | Q33475595 | ||
| Interactive exploration of chemical space with Scaffold Hunter | Q33475598 | ||
| Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks | Q33488155 | ||
| Molecular docking screens using comparative models of proteins | Q33511631 | ||
| An integrative -omics approach to identify functional sub-networks in human colorectal cancer | Q33525505 | ||
| Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery | Q33649365 | ||
| Blueprint for antimicrobial hit discovery targeting metabolic networks | Q33667030 | ||
| Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction | Q33668279 | ||
| Three-dimensional structural view of the central metabolic network of Thermotoga maritima | Q33707860 | ||
| Interaction between Ras(V12) and scribbled clones induces tumour growth and invasion | Q33715310 | ||
| A chemical and phosphoproteomic characterization of dasatinib action in lung cancer | Q33742159 | ||
| Calculation of absolute protein-ligand binding free energy from computer simulations | Q33784404 | ||
| Targeting the cancer kinome through polypharmacology | Q33893019 | ||
| Quantitative proteomics approach for identifying protein-drug interactions in complex mixtures using protein stability measurements. | Q33927283 | ||
| Prediction of protein function from protein sequence and structure | Q33976748 | ||
| P433 | issue | 2 | |
| P304 | page(s) | 189-199 | |
| P577 | publication date | 2011-02-01 | |
| P1433 | published in | Current Opinion in Structural Biology | Q15758416 |
| P1476 | title | Structure-based systems biology for analyzing off-target binding | |
| P478 | volume | 21 |
| Q28553224 | A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism |
| Q28534683 | A comprehensive survey of small-molecule binding pockets in proteins |
| Q35332572 | A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors |
| Q37691954 | A strategy based on protein-protein interface motifs may help in identifying drug off-targets |
| Q30353037 | Accidental interaction between PDZ domains and diclofenac revealed by NMR-assisted virtual screening. |
| Q28649519 | Achievements and challenges in structural bioinformatics and computational biophysics |
| Q30372092 | Algorithmic approaches to protein-protein interaction site prediction. |
| Q92702841 | Allosteric Binding Sites On Nuclear Receptors: Focus On Drug Efficacy and Selectivity |
| Q42238354 | Anti-infectious drug repurposing using an integrated chemical genomics and structural systems biology approach. |
| Q36859642 | Are predicted protein structures of any value for binding site prediction and virtual ligand screening? |
| Q57047335 | Bergenin: a computationally proven promising scaffold for novel galectin-3 inhibitors |
| Q38243624 | Biological networks and drug discovery--where do we stand? |
| Q30430641 | Catalytic site identification--a web server to identify catalytic site structural matches throughout PDB. |
| Q34507683 | Clarifying off-target effects for torcetrapib using network pharmacology and reverse docking approach |
| Q57038529 | Computational approaches for drug target identification in pathogenic diseases |
| Q33847906 | Computational discovery and experimental verification of tyrosine kinase inhibitor pazopanib for the reversal of memory and cognitive deficits in rat model neurodegeneration. |
| Q24672143 | Delineation of Polypharmacology across the Human Structural Kinome Using a Functional Site Interaction Fingerprint Approach |
| Q41002933 | Detecting similar binding pockets to enable systems polypharmacology |
| Q36088280 | Differential Virtual Screening (DVS) with Active and Inactive Molecular Models for Finding and Profiling GPCR Modulators: Case of the CCK1 Receptor |
| Q55341853 | Docking-based inverse virtual screening: methods, applications, and challenges. |
| Q35926542 | Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology |
| Q36924343 | Elucidating common structural features of human pathogenic variations using large-scale atomic-resolution protein networks |
| Q39343644 | Essential gene identification and drug target prioritization in Leishmania species |
| Q34646772 | Finding novel pharmaceuticals in the systems biology era using multiple effective drug targets, phenotypic screening and knowledge of transporters: where drug discovery went wrong and how to fix it. |
| Q27693375 | Heterogeneity of glycolysis in cancers and therapeutic opportunities |
| Q34556651 | High-throughput virtual screening of phloroglucinol derivatives against HIV-reverse transcriptase. |
| Q42185186 | Human structural proteome-wide characterization of Cyclosporine A targets |
| Q27902352 | Improving protein-ligand binding site prediction accuracy by classification of inner pocket points using local features |
| Q28536904 | In silico mechanistic profiling to probe small molecule binding to sulfotransferases |
| Q39185205 | In silico target fishing for the potential targets and molecular mechanisms of baicalein as an antiparkinsonian agent: discovery of the protective effects on NMDA receptor-mediated neurotoxicity |
| Q26775404 | Individuality, phenotypic differentiation, dormancy and 'persistence' in culturable bacterial systems: commonalities shared by environmental, laboratory, and clinical microbiology |
| Q28534051 | Insights into an original pocket-ligand pair classification: a promising tool for ligand profile prediction |
| Q34436688 | Investigating drug repositioning opportunities in FDA drug labels through topic modeling |
| Q55691227 | Ligand Selectivity between the ADP-Ribosylating Toxins: An Inverse-Docking Study for Multitarget Drug Discovery. |
| Q64462266 | Ligand-Binding-Site Structure Shapes Allosteric Signal Transduction and the Evolution of Allostery in Protein Complexes |
| Q37996185 | Merging systems biology with pharmacodynamics |
| Q38149723 | Minireview: applied structural bioinformatics in proteomics |
| Q26743663 | Molecular docking as a popular tool in drug design, an in silico travel |
| Q33917845 | Molecular mechanisms involved in the side effects of fatty acid amide hydrolase inhibitors: a structural phenomics approach to proteome-wide cellular off-target deconvolution and disease association. |
| Q38093187 | Network pharmacology strategies toward multi-target anticancer therapies: from computational models to experimental design principles |
| Q37384418 | Non-clinical studies required for new drug development - Part I: early in silico and in vitro studies, new target discovery and validation, proof of principles and robustness of animal studies |
| Q35765830 | On the translocation of bacteria and their lipopolysaccharides between blood and peripheral locations in chronic, inflammatory diseases: the central roles of LPS and LPS-induced cell death |
| Q57009474 | P2RANK: Knowledge-Based Ligand Binding Site Prediction Using Aggregated Local Features |
| Q57009477 | P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure |
| Q42565777 | Pharmacologic efficacy of PU.1 inhibition by heterocyclic dications: a mechanistic analysis |
| Q61795686 | Potent Antitrypanosomal Activities of 3-Aminosteroids against African Trypanosomes: Investigation of Cellular Effects and of Cross-Resistance with Existing Drugs |
| Q34008437 | Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. |
| Q36936203 | Profiling 976 ToxCast chemicals across 331 enzymatic and receptor signaling assays |
| Q31033184 | Providing data science support for systems pharmacology and its implications to drug discovery |
| Q40786545 | Relating Essential Proteins to Drug Side-Effects Using Canonical Component Analysis: A Structure-Based Approach |
| Q35797482 | SInCRe-structural interactome computational resource for Mycobacterium tuberculosis. |
| Q36917998 | SM-TF: A structural database of small molecule-transcription factor complexes |
| Q54982220 | Sequence-based prediction of physicochemical interactions at protein functional sites using a function-and-interaction-annotated domain profile database. |
| Q30363264 | Structural bioinformatics of the interactome. |
| Q39025002 | Structural bioinformatics-based identification of EGFR inhibitor gefitinib as a putative lead compound for BACE. |
| Q27008867 | Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review |
| Q38287400 | Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently |
| Q46245245 | TIBLE: a web-based, freely accessible resource for small-molecule binding data for mycobacterial species. |
| Q34626974 | Target identification and mechanism of action in chemical biology and drug discovery |
| Q39204077 | Targeting the off-targets: a computational bioinformatics approach to understanding the polypharmacology of nelfinavir |
| Q36482177 | Toward a three-dimensional view of protein networks between species |
| Q28538838 | Towards structural systems pharmacology to study complex diseases and personalized medicine |
| Q39531365 | eFindSite: Enhanced Fingerprint-Based Virtual Screening Against Predicted Ligand Binding Sites in Protein Models |
| Q36088437 | idTarget: a web server for identifying protein targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach |
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