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Towards in silico lead optimization: Scores from ensembles of protein/ligand conformations reliably correlate with biological activity

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/(sici)1097-461x(1999)72:1<73::aid-qua7>3.0.co;2-oopenalex-snapshot

Computer simulations of ligand-protein binding with ensembles of protein conformations: A Monte Carlo study of HIV-1 protease binding energy landscapes

inferredcites →https://doi.org/10.1002/bip.10231openalex-snapshot

Discovery of nonpeptide, peptidomimetic peptidase inhibitors that target alternate enzyme active site conformations

inferredcites →https://doi.org/10.1002/jhet.5570330665openalex-snapshot

Brominated trimetrexate analogues as inhibitors of pneumocystis carinii and toxoplasma gondii dihydrofolate reductase

inferredcites →https://doi.org/10.1002/prot.10028openalex-snapshot

Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock

inferredcites →https://doi.org/10.1002/prot.1168openalex-snapshot

Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM

inferredcites →https://doi.org/10.1006/jmbi.1996.0776openalex-snapshot

Molecular docking to ensembles of protein structures 1 1Edited by B. Honig

inferredcites →https://doi.org/10.1006/jmbi.1999.3328openalex-snapshot

Three-dimensional structure of M. tuberculosis dihydrofolate reductase reveals opportunities for the design of novel tuberculosis drugs

inferredcites →https://doi.org/10.1006/jmbi.2001.4551openalex-snapshot

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inferredcites →https://doi.org/10.1016/j.jmb.2004.02.015openalex-snapshot

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Ligand-Induced Conformational Changes: Improved Predictions of Ligand Binding Conformations and Affinities

inferredcites →https://doi.org/10.1016/s0969-2126(94)00093-xopenalex-snapshot

The structure of Pneumocystis carinii dihydrofolate reductase to 1.9 å resolution

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Incorporating Protein Flexibility in Structure-Based Drug Discovery: Using HIV-1 Protease as a Test Case

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Prediction of Drug Binding Affinities by Comparative Binding Energy Analysis

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A New Concept for Multidimensional Selection of Ligand Conformations (MultiSelect) and Multidimensional Scoring (MultiScore) of Protein−Ligand Binding Affinities

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Receptor Flexibility in the in Silico Screening of Reagents in the S1‘ Pocket of Human Collagenase

inferredcites →https://doi.org/10.1021/jm040153nopenalex-snapshot

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Structure-Based Design of Selective Inhibitors of Dihydrofolate Reductase: Synthesis and Antiparasitic Activity of 2,4-Diaminopteridine Analogues with a Bridged Diarylamine Side Chain

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inferredcites →https://doi.org/10.1089/cmb.2005.12.740openalex-snapshot

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inferredcites →https://doi.org/10.1107/s090744490200505xopenalex-snapshot

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inferredcites →https://doi.org/10.1109/robot.2002.1014221openalex-snapshot

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inferredcites →https://doi.org/10.1110/ps.21302openalex-snapshot

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inferredcites →https://doi.org/10.1128/aac.37.9.1914openalex-snapshot

Identification of highly potent and selective inhibitors of Toxoplasma gondii dihydrofolate reductase

inferredcites →https://doi.org/10.1128/aac.44.4.1019-1028.2000openalex-snapshot

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inferredcites →https://doi.org/10.1128/aac.45.12.3293-3303.2001openalex-snapshot

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/ardp.200800042openalex-snapshot

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inferred← citeshttps://doi.org/10.1002/ejoc.201100832openalex-snapshot

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inferred← citeshttps://doi.org/10.1002/prot.22081openalex-snapshot

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inferred← citeshttps://doi.org/10.1002/prot.22115openalex-snapshot

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inferred← citeshttps://doi.org/10.1002/prot.22214openalex-snapshot

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inferred← citeshttps://doi.org/10.1007/978-3-7091-1562-6_11openalex-snapshot

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inferred← citeshttps://doi.org/10.1007/s11095-008-9807-9openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.cbpa.2007.08.033openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.ejmech.2015.02.019openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.ejmech.2023.115885openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.jmb.2007.12.068openalex-snapshot

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inferred← citeshttps://doi.org/10.1017/s0033583512000066openalex-snapshot

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inferred← citeshttps://doi.org/10.1021/acs.jcim.2c01115openalex-snapshot

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inferred← citeshttps://doi.org/10.1021/ci9003078openalex-snapshot

Scoring Ensembles of Docked Protein:Ligand Interactions for Virtual Lead Optimization

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Recipes for the Selection of Experimental Protein Conformations for Virtual Screening

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Highly Efficient Ligands for Dihydrofolate Reductase from Cryptosporidium hominis and Toxoplasma gondii Inspired by Structural Analysis

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inferred← citeshttps://doi.org/10.1186/1471-2105-9-184openalex-snapshot

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inferred← citeshttps://doi.org/10.1186/1471-2105-9-438openalex-snapshot

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inferred← citeshttps://doi.org/10.1517/13543776.2012.668886openalex-snapshot

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inferred← citeshttps://doi.org/10.2174/138161211795428966openalex-snapshot

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inferred← citeshttps://doi.org/10.2174/138161211796355056openalex-snapshot

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inferred← citeshttps://doi.org/10.5114/bta.2011.46542openalex-snapshot

REVIEW PAPER Virtual screening strategies in drug design – methods and applications

inferred← citeshttps://doi.org/10.5935/1984-6835.20120055openalex-snapshot

Virtual Screening Strategies in Drug Design

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