| review article | Q7318358 |
| scholarly article | Q13442814 |
| P356 | DOI | 10.1002/PROT.21082 |
| P8608 | Fatcat ID | release_iprk2g6avvfo3migaay7dfgu24 |
| P698 | PubMed publication ID | 16862531 |
| P50 | author | Pedro Alexandrino Fernandes | Q45563685 |
| Sérgio F. Sousa | Q47701889 | ||
| Maria J. Ramos | Q42932234 | ||
| P2860 | cites work | GROMACS 3.0: a package for molecular simulation and trajectory analysis | Q57082068 |
| The Protein Data Bank: a computer-based archival file for macromolecular structures | Q27860989 | ||
| Binding site characteristics in structure-based virtual screening: evaluation of current docking tools | Q31135121 | ||
| Targeting the HIV-protease in AIDS therapy: a current clinical perspective | Q33857482 | ||
| P433 | issue | 1 | |
| P407 | language of work or name | English | Q1860 |
| P304 | page(s) | 15-26 | |
| P577 | publication date | 2006-10-01 | |
| P1433 | published in | Proteins | Q7251514 |
| P1476 | title | Protein-ligand docking: current status and future challenges | |
| P478 | volume | 65 |
| Q42917188 | 3D-QSAR studies on triclosan derivatives as Plasmodium falciparum enoyl acyl carrier reductase inhibitors |
| Q40276857 | 3D-RISM-Dock: A New Fragment-Based Drug Design Protocol |
| Q28831094 | A Flow Cytometric and Computational Approaches to Carbapenems Affinity to the Different Types of Carbapenemases |
| Q45777298 | A Fragment-Based Scoring Function to Re-rank ATP Docking Results |
| Q92589923 | A Structure-Based Drug Discovery Paradigm |
| Q42174979 | A comparative molecular docking study of curcumin and methotrexate to dihydrofolate reductase |
| Q83298882 | A critical cross-validation of high throughput structural binding prediction methods for pMHC |
| Q51785467 | A fast protein-ligand docking algorithm based on hydrogen bond matching and surface shape complementarity. |
| Q40496890 | A flexible docking scheme to explore the binding selectivity of PDZ domains |
| Q51070839 | A fragment-based docking simulation for investigating peptide-protein bindings. |
| Q41788143 | A nonredundant structure dataset for benchmarking protein-RNA computational docking |
| Q34054190 | A possible structural model of members of the CPF family of cuticular proteins implicating binding to components other than chitin. |
| Q34402706 | ALiBERO: evolving a team of complementary pocket conformations rather than a single leader |
| Q30353037 | Accidental interaction between PDZ domains and diclofenac revealed by NMR-assisted virtual screening. |
| Q34377911 | Advances and challenges in protein-ligand docking |
| Q28542829 | Adverse drug reaction prediction using scores produced by large-scale drug-protein target docking on high-performance computing machines |
| Q34052154 | Affinity of aporphines for the human 5-HT2A receptor: insights from homology modeling and molecular docking studies |
| Q55385594 | An Efficient Implementation of the Nwat-MMGBSA Method to Rescore Docking Results in Medium-Throughput Virtual Screenings. |
| Q36087541 | An Improved Weighted-Residue Profile Based Method of Using Protein-Ligand Interaction Information in Increasing Hits Selection from Virtual Screening: A Study on Virtual Screening of Human GPCR A2A Receptor Antagonists |
| Q39017913 | An Integrated In Silico Approach for the Structural and Functional Exploration of Lipocalin 2 and its Functional Insights with Metalloproteinase 9 and Lipoprotein Receptor-Related Protein 2. |
| Q36838120 | An improved relaxed complex scheme for receptor flexibility in computer-aided drug design |
| Q51867361 | An improved scoring function for suboptimal polar ligand complexes. |
| Q33594934 | An interaction-motif-based scoring function for protein-ligand docking |
| Q27702054 | Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock |
| Q38076321 | Approaches for identification of HIV-1 entry inhibitors targeting gp41 pocket |
| Q52844449 | Apta-nanosensor preparation and in vitro assay for rapid Diazinon detection using a computational molecular approach. |
| Q51127935 | Assessing protein-ligand docking for the binding of organometallic compounds to proteins. |
| Q41935814 | Attracting cavities for docking. Replacing the rough energy landscape of the protein by a smooth attracting landscape |
| Q27860652 | AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading |
| Q29547658 | AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility |
| Q33407671 | AutoGrow: a novel algorithm for protein inhibitor design |
| Q44988568 | Automated docking studies provide insights into molecular determinants of ligand recognition by N-acetyl-1-D-myo-inosityl-2-amino-2-deoxy-α-D-glucopyranoside deacetylase (MshB). |
| Q37348271 | Automated site preparation in physics-based rescoring of receptor ligand complexes |
| Q34040043 | BSP-SLIM: a blind low-resolution ligand-protein docking approach using predicted protein structures |
| Q51555332 | BetaDock: shape-priority docking method based on beta-complex. |
| Q37372747 | Binding of small-molecule ligands to proteins: "what you see" is not always "what you get". |
| Q42004787 | Binding site and affinity prediction of general anesthetics to protein targets using docking |
| Q27690137 | Binding to large enzyme pockets: small-molecule inhibitors of trypanothione reductase |
| Q42637708 | Blind docking of pharmaceutically relevant compounds using RosettaLigand |
| Q45961158 | CScore: a simple yet effective scoring function for protein-ligand binding affinity prediction using modified CMAC learning architecture. |
| Q51914537 | Calculations of protein-ligand binding entropy of relative and overall molecular motions. |
| Q30398145 | Coarse-Grained Models for Protein-Cell Membrane Interactions |
| Q35252046 | Combined docking, molecular dynamics simulations and spectroscopic studies for the rational design of a dipeptide ligand for affinity chromatography separation of human serum albumin. |
| Q56979676 | Combining ligand-based and structure-based drug design in the virtual screening arena |
| Q58578302 | Comparative in vitro/theoretical studies on the anti-angiogenic activity of date pollen hydro-alcoholic extract: Highlighting the important roles of its hot polyphenols |
| Q52649574 | Comparative modeling and virtual screening for the identification of novel inhibitors for myo-inositol-1-phosphate synthase. |
| Q34607003 | Competitive molecular docking approach for predicting estrogen receptor subtype α agonists and antagonists |
| Q35676823 | Computational Optimization of Bioanalytical Parameters for the Evaluation of the Toxicity of the Phytomarker 1,4 Napthoquinone and its Metabolite 1,2,4-trihydroxynapththalene |
| Q30391368 | Computational Prediction of DrugTarget Interactions Using Chemical, Biological, and Network Features |
| Q30380431 | Computational analysis of membrane proteins: the largest class of drug targets. |
| Q47236264 | Computational and experimental investigation of DNA repair protein photolyase interactions with low molecular weight drugs. |
| Q37375373 | Computational evaluation of protein-small molecule binding. |
| Q26997089 | Computational methods in drug discovery |
| Q36900683 | Computational models of protein kinematics and dynamics: beyond simulation |
| Q36633020 | Computational molecular modeling for evaluating the toxicity of environmental chemicals: prioritizing bioassay requirements |
| Q35136550 | Computational tools for rational protein engineering of aldolases |
| Q47889903 | Computer aided drug design and its application to the development of potential drugs for neurodegenerative disorders |
| Q53460992 | Computer based screening for novel inhibitors against Vibrio cholerae using NCI diversity set-II: an alternative approach by targeting transcriptional activator ToxT. |
| Q33926210 | Conformational study on cyclic melanocortin ligands and new insight into their binding mode at the MC4 receptor |
| Q41382543 | Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes |
| Q36954036 | CovalentDock Cloud: a web server for automated covalent docking |
| Q43816076 | CovalentDock: automated covalent docking with parameterized covalent linkage energy estimation and molecular geometry constraints |
| Q34673409 | Curcumin binds in silico to anti-cancer drug target enzyme MMP-3 (human stromelysin-1) with affinity comparable to two known inhibitors of the enzyme |
| Q53203835 | Current insights into computer-aided immunotherapeutic design strategies. |
| Q38366025 | Current status and future challenges in T-cell receptor/peptide/MHC molecular dynamics simulations |
| Q33833717 | Designing cyclic peptide inhibitor of dengue virus NS3-NS2B protease by using molecular docking approach |
| Q35864568 | Developing a comparative docking protocol for the prediction of peptide selectivity profiles: investigation of potassium channel toxins |
| Q36752033 | Diagnosis and therapy of oral squamous cell carcinoma. |
| Q46616542 | Discovering isozyme-selective inhibitor scaffolds of human carbonic anhydrases using structural alignment and de novo drug design approaches |
| Q34383248 | Discovering patterns in drug-protein interactions based on their fingerprints |
| Q58705939 | Discovery of (phenylureido)piperidinyl benzamides as prospective inhibitors of bacterial autolysin E from Staphylococcus aureus |
| Q46367039 | Discovery of NMDA glycine site inhibitors from the chemical universe database GDB. |
| Q82352030 | Docking and molecular dynamics study on the inhibitory activity of N, N-disubstituted-trifluoro-3-amino-2-propanols-based inhibitors of cholesteryl ester transfer protein |
| Q30607323 | Docking challenge: protein sampling and molecular docking performance |
| Q37296002 | Docking, virtual high throughput screening and in silico fragment-based drug design |
| Q54320660 | Docking-based CoMFA and CoMSIA studies on naphthyl-substituted diarylpyrimidines as NNRTIs. |
| Q55341853 | Docking-based inverse virtual screening: methods, applications, and challenges. |
| Q42022570 | DockoMatic: automated peptide analog creation for high throughput virtual screening |
| Q26745421 | Drug Design for CNS Diseases: Polypharmacological Profiling of Compounds Using Cheminformatic, 3D-QSAR and Virtual Screening Methodologies |
| Q57184141 | Dual-function triazole-pyridine derivatives as inhibitors of metal-induced amyloid-β aggregation |
| Q37479619 | Efficient algorithms to explore conformation spaces of flexible protein loops |
| Q47718677 | Enhancing Structure Prediction and Design of Soluble and Membrane Proteins with Explicit Solvent-Protein Interactions |
| Q34667464 | Enhancing protein-vitamin binding residues prediction by multiple heterogeneous subspace SVMs ensemble |
| Q48218323 | Ensemble-docking approach on BACE-1: pharmacophore perception and guidelines for drug design |
| Q48306226 | Fast NMR-Based Determination of the 3D Structure of the Binding Site of Protein-Ligand Complexes with Weak Affinity Binders. |
| Q31033753 | Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches. |
| Q38754277 | Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM |
| Q38035239 | From base pair to bedside: molecular simulation and the translation of genomics to personalized medicine. |
| Q88012078 | Functional and structural insights on self-assembled nanofiber-based novel antibacterial ointment from antimicrobial peptides, bacitracin and gramicidin S |
| Q47573321 | GalaxyDock2: protein-ligand docking using beta-complex and global optimization |
| Q91763848 | Getting Docking into Shape Using Negative Image-Based Rescoring |
| Q40689181 | Homology model, molecular dynamics simulation and novel pyrazole analogs design of Candida albicans CYP450 lanosterol 14 α-demethylase, a target enzyme for antifungal therapy |
| Q35050921 | Homology modeling, molecular docking, and molecular dynamics simulations elucidated α-fetoprotein binding modes |
| Q42185186 | Human structural proteome-wide characterization of Cyclosporine A targets |
| Q35608172 | Identification of binding sites and favorable ligand binding moieties by virtual screening and self-organizing map analysis |
| Q33976929 | Identification of small-molecule inhibitors of the XendoU endoribonucleases family |
| Q39902041 | Improved Homology Model of the Human all-trans Retinoic Acid Metabolizing Enzyme CYP26A1. |
| Q54963827 | Improving Docking Performance Using Negative Image-Based Rescoring. |
| Q89174818 | Improving Prediction Accuracy of Binding Free Energies and Poses of HIV Integrase Complexes Using the Binding Energy Distribution Analysis Method with Flattening Potentials |
| Q55669574 | In Silico Designed Axl Receptor Blocking Drug Candidates Against Zika Virus Infection. |
| Q92863081 | In silico Methods for Design of Kinase Inhibitors as Anticancer Drugs |
| Q37541732 | In silico analysis of the binding of anthelmintics to Caenorhabditis elegansP-glycoprotein 1. |
| Q34176063 | In silico approach to screen compounds active against parasitic nematodes of major socio-economic importance |
| Q79448420 | In silico drug discovery: solving the "target-rich and lead-poor" imbalance using the genome-to-drug-lead paradigm |
| Q94932863 | In silico fight against novel coronavirus by finding chromone derivatives as inhibitor of coronavirus main proteases enzyme |
| Q38029118 | In silico fragment-based drug design |
| Q30353814 | In silico study on multidrug resistance conferred by I223R/H275Y double mutant neuraminidase. |
| Q30407436 | Informatics resources for tuberculosis--towards drug discovery. |
| Q38814898 | Innovative computer-aided methods for the discovery of new kinase ligands |
| Q26773062 | Insights into Protein-Ligand Interactions: Mechanisms, Models, and Methods |
| Q51921245 | Insights into catalytic activity of industrial enzyme Co-nitrile hydratase. Docking studies of nitriles and amides. |
| Q40087112 | Interstitial contacts in an RNA-dependent RNA polymerase lattice |
| Q86755941 | Intramolecular hydrogen-bonding in aqueous carbohydrates as a cause or consequence of conformational preferences: a molecular dynamics study of cellobiose stereoisomers |
| Q36252541 | Investigating metabolite-protein interactions: an overview of available techniques |
| Q38168995 | Ionic channels as targets for drug design: a review on computational methods |
| Q35885354 | Lack of aquaporin-4 water transport inhibition by antiepileptics and arylsulfonamides |
| Q47579891 | LigDockCSA: protein-ligand docking using conformational space annealing. |
| Q51891908 | Ligand-specific scoring functions: improved ranking of docking solutions. |
| Q34331455 | MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters. |
| Q28740672 | Mastering the canonical loop of serine protease inhibitors: enhancing potency by optimising the internal hydrogen bond network |
| Q37484837 | Modeling small molecule-compound binding to G-protein-coupled receptors |
| Q58919546 | Molecular Docking Study on the Interaction of Riboflavin (VitaminB2) and Cyanocobalamin (VitaminB12) Coenzymes |
| Q89870017 | Molecular Docking: From Lock and Key to Combination Lock |
| Q57044313 | Molecular Dynamics Simulations of Kir2.2 Interactions with an Ensemble of Cholesterol Molecules |
| Q47362097 | Molecular Modeling of Multidrug Properties of Resistance Nodulation Division (RND) Transporters. |
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| Q44735021 | Molecular docking characterization of a four-domain segment of human fibronectin encompassing the RGD loop with hydroxyapatite. |
| Q35696275 | Molecular docking simulations for macromolecularly imprinted polymers |
| Q37285667 | Molecular docking studies for the identification of novel melatoninergic inhibitors for acetylserotonin-O-methyltransferase using different docking routines |
| Q39494960 | Molecular dynamics simulations and in silico peptide ligand screening of the Elk-1 ETS domain. |
| Q54577952 | Molecular modeling study of checkpoint kinase 1 inhibitors by multiple docking strategies and prime/MM-GBSA calculation. |
| Q37843834 | Molecular motions in drug design: the coming age of the metadynamics method |
| Q58691705 | Multi-Body Interactions in Molecular Docking Program Devised with Key Water Molecules in Protein Binding Sites |
| Q34775341 | Multi-haem cytochromes in Shewanella oneidensis MR-1: structures, functions and opportunities |
| Q42080735 | Multilevel Parallelization of AutoDock 4.2. |
| Q35096124 | Multipose binding in molecular docking. |
| Q34053706 | NNScore 2.0: a neural-network receptor-ligand scoring function |
| Q37058812 | Nanovehicular intracellular delivery systems |
| Q57714456 | New dihydropyridine derivatives: anti-inflammatory, analgesic and docking studies |
| Q37377130 | New functional aspects of the atypical protein tyrosine phosphatase VHZ. |
| Q35163073 | Non-bisphosphonate inhibitors of isoprenoid biosynthesis identified via computer-aided drug design. |
| Q28547170 | Novel Penicillin Analogues as Potential Antimicrobial Agents; Design, Synthesis and Docking Studies |
| Q35048610 | Novel natural inhibitors of CYP1A2 identified by in silico and in vitro screening |
| Q27655956 | One Scaffold, Three Binding Modes: Novel and Selective Pteridine Reductase 1 Inhibitors Derived from Fragment Hits Discovered by Virtual Screening |
| Q36931811 | Overcoming the inadequacies or limitations of experimental structures as drug targets by using computational modeling tools and molecular dynamics simulations |
| Q34358460 | PL-PatchSurfer: a novel molecular local surface-based method for exploring protein-ligand interactions |
| Q51373396 | PRL-Dock: protein-ligand docking based on hydrogen bond matching and probabilistic relaxation labeling. |
| Q39026290 | PSOVina: The hybrid particle swarm optimization algorithm for protein-ligand docking |
| Q59328919 | Paradigm Shift in Drug Re-purposing From Phenalenone to Phenaleno-Furanone to Combat Multi-Drug Resistant Serovar Typhi |
| Q38179927 | Pharmacoinformatic approaches to understand complexation of dendrimeric nanoparticles with drugs |
| Q37665888 | Physiologically based pharmacokinetic models: integration of in silico approaches with micro cell culture analogues |
| Q99578694 | Plant Antimicrobial Peptides: State of the Art, In Silico Prediction and Perspectives in the Omics Era |
| Q30377334 | PoLi: A Virtual Screening Pipeline Based on Template Pocket and Ligand Similarity. |
| Q37380059 | Polymer-drug interactions in tyrosine-derived triblock copolymer nanospheres: a computational modeling approach |
| Q39647348 | Pose prediction and virtual screening performance of GOLD scoring functions in a standardized test. |
| Q34669773 | Predicting the accuracy of protein-ligand docking on homology models. |
| Q47957867 | Prediction of Drug-Target Interaction Networks from the Integration of Protein Sequences and Drug Chemical Structures |
| Q41968137 | Prediction of HIV-1 protease/inhibitor affinity using RosettaLigand |
| Q41849790 | Prediction of sub-cavity binding preferences using an adaptive physicochemical structure representation |
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| Q30002405 | Protein-protein interactions: analysis and prediction |
| Q30381629 | Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling. |
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| Q47396971 | Rational and Semirational Protein Design |
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| Q42081112 | Recipes for the selection of experimental protein conformations for virtual screening |
| Q40475389 | Recognizing drug targets using evolutionary information: implications for repurposing FDA-approved drugs against Mycobacterium tuberculosis H37Rv. |
| Q34267214 | Response surface methodology in docking study of small molecule BACE-1 inhibitors |
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| Q33295083 | Setting up a large set of protein-ligand PDB complexes for the development and validation of knowledge-based docking algorithms |
| Q45892090 | Shape and pharmacophore-based virtual screening to identify potential cytochrome P450 sterol 14α-demethylase inhibitors |
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| Q27014744 | Specific binding of lacosamide to collapsin response mediator protein 2 (CRMP2) and direct impairment of its canonical function: implications for the therapeutic potential of lacosamide |
| Q37469096 | Structural features of mammalian histidine decarboxylase reveal the basis for specific inhibition. |
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| Q39512241 | Target Flexibility in RNA-Ligand Docking Modeled by Elastic Potential Grids |
| Q30406909 | The VSGB 2.0 model: a next generation energy model for high resolution protein structure modeling |
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| Q39038790 | The importance of employing computational resources for the automation of drug discovery |
| Q42155548 | The measured and calculated affinity of methyl- and methoxy-substituted benzoquinones for the Q(A) site of bacterial reaction centers |
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| Q42278847 | VB-MK-LMF: fusion of drugs, targets and interactions using variational Bayesian multiple kernel logistic matrix factorization. |
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| Q57991078 | vsLab-An implementation for virtual high-throughput screening using AutoDock and VMD |
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