| scholarly article | Q13442814 |
| P50 | author | Ruth Brenk | Q50638394 |
| P2093 | author name string | Brian K Shoichet | |
| Alan P Graves | |||
| P2860 | cites work | A Common Mechanism Underlying Promiscuous Inhibitors from Virtual and High-Throughput Screening | Q22251350 |
| Flexible ligand docking using conformational ensembles | Q24673137 | ||
| Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination | Q26778405 | ||
| Processing of X-ray diffraction data collected in oscillation mode | Q26778468 | ||
| A new target for shigellosis: rational design and crystallographic studies of inhibitors of tRNA-guanine transglycosylase | Q27629578 | ||
| Combinatorial computational method gives new picomolar ligands for a known enzyme | Q27637537 | ||
| PRO_SELECT: combining structure-based drug design and array-based chemistry for rapid lead discovery. 2. The development of a series of highly potent and selective factor Xa inhibitors | Q27638198 | ||
| Structure-based discovery of a novel, noncovalent inhibitor of AmpC beta-lactamase | Q27639372 | ||
| Combination of scoring functions improves discrimination in protein-protein docking | Q51794147 | ||
| SMall Molecule Growth 2001 (SMoG2001): an improved knowledge-based scoring function for protein-ligand interactions | Q52038712 | ||
| Scoring docked conformations generated by rigid-body protein-protein docking | Q52077262 | ||
| A general and fast scoring function for protein-ligand interactions: a simplified potential approach | Q52222006 | ||
| A fast flexible docking method using an incremental construction algorithm. | Q52298930 | ||
| Evaluation of protein models by atomic solvation preference | Q52421241 | ||
| The discovery of steroids and other novel FKBP inhibitors using a molecular docking program | Q57003698 | ||
| Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the Surface Generalized Born solvent model | Q57134711 | ||
| Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme | Q71881818 | ||
| Protein-protein docking. Generation and filtering of complexes | Q73206491 | ||
| Protein docking using continuum electrostatics and geometric fit | Q73739194 | ||
| Distance-dependent, pair potential for protein folding: results from linear optimization | Q74177419 | ||
| A model binding site for testing scoring functions in molecular docking | Q27639604 | ||
| A cavity-containing mutant of T4 lysozyme is stabilized by buried benzene | Q27643869 | ||
| Application of crystallographic and modeling methods in the design of purine nucleoside phosphorylase inhibitors | Q27646682 | ||
| UCSF Chimera--a visualization system for exploratory research and analysis | Q27860666 | ||
| Ab initio protein structure prediction of CASP III targets using ROSETTA | Q28145980 | ||
| Discovery of small-molecule inhibitors of Bcl-2 through structure-based computer screening | Q28208080 | ||
| Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors | Q28219491 | ||
| Modelling protein docking using shape complementarity, electrostatics and biochemical information | Q28249132 | ||
| Energy functions that discriminate X-ray and near native folds from well-constructed decoys | Q28278562 | ||
| Structure-based design of nonpeptide inhibitors specific for the human immunodeficiency virus 1 protease | Q28331230 | ||
| Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction | Q30327075 | ||
| How to generate improved potentials for protein tertiary structure prediction: a lattice model study. | Q30327152 | ||
| Discovery of novel aldose reductase inhibitors using a protein structure-based approach: 3D-database search followed by design and synthesis. | Q30328211 | ||
| How to derive a protein folding potential? A new approach to an old problem | Q30426274 | ||
| High-throughput docking for lead generation | Q30663788 | ||
| Structure-Based Generation of a New Class of Potent Cdk4 Inhibitors: Newde NovoDesign Strategy and Library Design | Q30777277 | ||
| Detailed analysis of scoring functions for virtual screening | Q30985789 | ||
| Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. | Q31057078 | ||
| Computer-assisted design of selective imidazole inhibitors for cytochrome p450 enzymes | Q31081174 | ||
| A specific mechanism of nonspecific inhibition | Q31166009 | ||
| Novel inhibitors of DNA gyrase: 3D structure based biased needle screening, hit validation by biophysical methods, and 3D guided optimization. A promising alternative to random screening | Q31406783 | ||
| A geometric approach to macromolecule-ligand interactions | Q34280176 | ||
| Testing a flexible-receptor docking algorithm in a model binding site | Q34309041 | ||
| Deciphering common failures in molecular docking of ligand-protein complexes. | Q38305525 | ||
| Context-dependent protein stabilization by methionine-to-leucine substitution shown in T4 lysozyme | Q39115801 | ||
| Modelling of factor Xa-inhibitor complexes: a computational flexible docking approach | Q41607225 | ||
| Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes | Q42602259 | ||
| Docking molecules by families to increase the diversity of hits in database screens: computational strategy and experimental evaluation | Q43512278 | ||
| Inhibitors of dihydrodipicolinate reductase, a key enzyme of the diaminopimelate pathway of Mycobacterium tuberculosis. | Q43600476 | ||
| Comparative evaluation of 11 scoring functions for molecular docking | Q44457437 | ||
| Discovery of a potent and selective protein kinase CK2 inhibitor by high-throughput docking | Q44474542 | ||
| Matching chemistry and shape in molecular docking | Q44625089 | ||
| MOPED: method for optimizing physical energy parameters using decoys. | Q46021752 | ||
| Orientational sampling and rigid-body minimization in molecular docking revisited: on-the-fly optimization and degeneracy removal | Q46841895 | ||
| A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance | Q47307422 | ||
| Assessing scoring functions for protein-ligand interactions | Q47429905 | ||
| P433 | issue | 11 | |
| P407 | language of work or name | English | Q1860 |
| P304 | page(s) | 3714-3728 | |
| P577 | publication date | 2005-06-01 | |
| P1433 | published in | Journal of Medicinal Chemistry | Q900316 |
| P1476 | title | Decoys for docking | |
| P478 | volume | 48 |
| Q48063202 | Absolute Binding Free Energies between T4 Lysozyme and 141 Small Molecules: Calculations Based on Multiple Rigid Receptor Configurations. |
| Q30427576 | Alchemical free energy methods for drug discovery: progress and challenges |
| Q28256939 | Automated docking screens: a feasibility study |
| Q37348271 | Automated site preparation in physics-based rescoring of receptor ligand complexes |
| Q29619637 | Benchmarking sets for molecular docking |
| Q37372747 | Binding of small-molecule ligands to proteins: "what you see" is not always "what you get". |
| Q30362300 | Bringing Clarity to the Prediction of Protein-Ligand Binding Free Energies via "Blurring" |
| Q40616404 | Cheminformatics meets molecular mechanics: a combined application of knowledge-based pose scoring and physical force field-based hit scoring functions improves the accuracy of structure-based virtual screening |
| Q28268675 | Community benchmarks for virtual screening |
| Q35748554 | DOCK 6: Impact of new features and current docking performance |
| Q42189457 | Density functional theory calculations on entire proteins for free energies of binding: application to a model polar binding site |
| Q33323614 | Differentiation of AmpC beta-lactamase binders vs. decoys using classification kNN QSAR modeling and application of the QSAR classifier to virtual screening |
| Q42251037 | Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking |
| Q30380679 | Docking screens: right for the right reasons? |
| Q33250369 | Electrostatic evaluation of isosteric analogues |
| Q41680386 | Ergot alkaloids: From witchcraft till in silico analysis. Multi-receptor analysis of ergotamine metabolites. |
| Q24656051 | Identification of xenoestrogens in food additives by an integrated in silico and in vitro approach |
| Q30409188 | Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics |
| Q33850040 | Improving VEGFR-2 Docking-Based Screening by Pharmacophore Postfiltering and Similarity Search Postprocessing |
| Q37565924 | Lessons Learned over Four Benchmark Exercises from the Community Structure-Activity Resource |
| Q42106721 | On the use of orientational restraints and symmetry corrections in alchemical free energy calculations |
| Q58846278 | POSE SCALING: GEOMETRICAL ASSESSMENT OF LIGAND BINDING POSES |
| Q30422862 | Perspective: Alchemical free energy calculations for drug discovery |
| Q39235195 | Predicting Binding Free Energies: Frontiers and Benchmarks |
| Q27657572 | Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site |
| Q24683618 | Predicting absolute ligand binding free energies to a simple model site |
| Q34516171 | Probing molecular docking in a charged model binding site |
| Q28536035 | Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information |
| Q36243073 | Recent theoretical and computational advances for modeling protein-ligand binding affinities |
| Q48050957 | Relative Binding Free Energy Calculations Applied to Protein Homology Models |
| Q27649874 | Rescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing |
| Q27679166 | Roles for Ordered and Bulk Solvent in Ligand Recognition and Docking in Two Related Cavities |
| Q41081254 | Sensitivity in Binding Free Energies Due to Protein Reorganization |
| Q35794917 | Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition |
| Q35635713 | Statistical potential for modeling and ranking of protein-ligand interactions |
| Q42958865 | Synthesis and preliminary evaluation of the antimicrobial activity of selected 3-benzofurancarboxylic acid derivatives. |
| Q64251177 | Synthesis of New Derivatives of Benzofuran as Potential Anticancer Agents |
| Q34352706 | The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities |
| Q38782563 | The Development of Target-Specific Pose Filter Ensembles To Boost Ligand Enrichment for Structure-Based Virtual Screening. |
| Q47261847 | Using the fast fourier transform in binding free energy calculations |
| Q33247681 | Virtual ligand screening: strategies, perspectives and limitations |
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