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BSP‐SLIM: A blind low‐resolution ligand‐protein docking approach using predicted protein structures

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What this work says

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

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SPICKER: A clustering approach to identify near‐native protein folds

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UCSF Chimera—A visualization system for exploratory research and analysis

inferredcites →https://doi.org/10.1002/jcc.21256openalex-snapshot

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

inferredcites →https://doi.org/10.1002/jcc.21395openalex-snapshot

Q‐DockLHM: Low‐resolution refinement for ligand comparative modeling

inferredcites →https://doi.org/10.1002/jmr.984openalex-snapshot

Computational approaches to identifying and characterizing protein binding sites for ligand design

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Current topics in computer‐aided drug design

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Protein clefts in molecular recognition and function.

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Local energy landscape flattening: Parallel hyperbolic Monte Carlo sampling of protein folding

inferredcites →https://doi.org/10.1002/prot.20264openalex-snapshot

Scoring function for automated assessment of protein structure template quality

inferredcites →https://doi.org/10.1002/prot.21082openalex-snapshot

Protein–ligand docking: Current status and future challenges

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Template-based modeling and free modeling by I-TASSER in CASP7

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Assessment of CASP7 structure predictions for template free targets

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REMO: A new protocol to refine full atomic protein models from C‐alpha traces by optimizing hydrogen‐bonding networks

inferredcites →https://doi.org/10.1002/prot.22561openalex-snapshot

Evaluation of template‐based models in CASP8 with standard measures

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I‐TASSER: Fully automated protein structure prediction in CASP8

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Assessment of CASP8 structure predictions for template free targets

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Three-dimensional hydrogen-bond geometry and probability information from a crystal survey

inferredcites →https://doi.org/10.1007/s10822-006-9060-4openalex-snapshot

Development and validation of a modular, extensible docking program: DOCK 5

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Docking and chemoinformatic screens for new ligands and targets

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Virtual ligand screening: strategies, perspectives and limitations

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Blind docking of drug‐sized compounds to proteins with up to a thousand residues

inferredcites →https://doi.org/10.1016/j.sbi.2008.02.004openalex-snapshot

Progress and challenges in protein structure prediction

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Protein structure prediction: when is it useful?

inferredcites →https://doi.org/10.1021/ci700253hopenalex-snapshot

Lessons in Molecular Recognition. 2. Assessing and Improving Cross-Docking Accuracy

inferredcites →https://doi.org/10.1021/ci800324mopenalex-snapshot

Identifying and Characterizing Binding Sites and Assessing Druggability

inferredcites →https://doi.org/10.1021/ci9002365openalex-snapshot

Improving Virtual Screening Performance against Conformational Variations of Receptors by Shape Matching with Ligand Binding Pocket

inferredcites →https://doi.org/10.1021/jm0300330openalex-snapshot

Information Decay in Molecular Docking Screens against Holo, Apo, and Modeled Conformations of Enzymes

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Benchmarking Sets for Molecular Docking

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Diverse, High-Quality Test Set for the Validation of Protein−Ligand Docking Performance

inferredcites →https://doi.org/10.1038/nprot.2010.5openalex-snapshot

I-TASSER: a unified platform for automated protein structure and function prediction

inferredcites →https://doi.org/10.1073/pnas.0305695101openalex-snapshot

Automated structure prediction of weakly homologous proteins on a genomic scale

inferredcites →https://doi.org/10.1073/pnas.0707684105openalex-snapshot

A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation

inferredcites →https://doi.org/10.1093/bioinformatics/btq066openalex-snapshot

How significant is a protein structure similarity with TM-score = 0.5?

inferredcites →https://doi.org/10.1093/nar/gki070openalex-snapshot

The Universal Protein Resource (UniProt)

inferredcites →https://doi.org/10.1093/nar/gki524openalex-snapshot

TM-align: a protein structure alignment algorithm based on the TM-score

inferredcites →https://doi.org/10.1093/nar/gkm251openalex-snapshot

LOMETS: A local meta-threading-server for protein structure prediction

inferredcites →https://doi.org/10.1093/nar/gkm895openalex-snapshot

The Universal Protein Resource (UniProt)

inferredcites →https://doi.org/10.1110/ps.0202302openalex-snapshot

Efficient docking of peptides to proteins without prior knowledge of the binding site

inferredcites →https://doi.org/10.1126/science.1065659openalex-snapshot

Protein Structure Prediction and Structural Genomics

inferredcites →https://doi.org/10.1146/annurev.biophys.29.1.291openalex-snapshot

Comparative Protein Structure Modeling of Genes and Genomes

inferredcites →https://doi.org/10.1186/1471-2105-9-40openalex-snapshot

I-TASSER server for protein 3D structure prediction

inferredcites →https://doi.org/10.1186/1472-6807-6-19openalex-snapshot

LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation.

inferredcites →https://doi.org/10.1186/1741-7007-5-17openalex-snapshot

Ab initio modeling of small proteins by iterative TASSER simulations

inferredcites →https://doi.org/10.1371/journal.pcbi.0020013openalex-snapshot

Structure Modeling of All Identified G Protein–Coupled Receptors in the Human Genome

inferredcites →https://doi.org/10.1371/journal.pcbi.1000405openalex-snapshot

FINDSITELHM: A Threading-Based Approach to Ligand Homology Modeling

inferredcites →https://doi.org/10.1371/journal.pcbi.1000585openalex-snapshot

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure

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Additional file 1 of EDock: blind protein–ligand docking by replica-exchange monte carlo simulation

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