Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment

Marc F. Lensink, Guillaume Brysbaert, Nurul Nadzirin, +102

Proteins Structure Function and Bioinformatics

Structural BioinformaticsBiomolecular Structure PredictionMolecular BiologyCapri Round 46Protein Folding +14

Prediction of protein assemblies, the next frontier: The <scp>CASP14‐CAPRI</scp> experiment

Marc F. Lensink, Guillaume Brysbaert, Théo Mauri, +106

Proteins Structure Function and Bioinformatics

Protein–Protein and Protein–Peptide Docking with ClusPro Server

Andrey Alekseenko, Mikhail Ignatov, George Jones, +2

Methods in molecular biology

Molecular DockingMolecular BiologyCluspro Server

High Accuracy Prediction of PROTAC Complex Structures

Mikhail Ignatov, Akhil Jindal, Sergei Kotelnikov, +11

Journal of the American Chemical Society

Light-mediated multi-target protein degradation using arylazopyrazole photoswitchable PROTACs (AP-PROTACs)

Qisi Zhang, Cyrille S. Kounde, Milon Mondal, +13

Chemical Communications

PhotobiologyMolecular BiologyUnique Photoswitchable ProtacChemical BiologyOptogenetics +14

ClusPro LigTBM: Automated Template-based Small Molecule Docking

Andrey Alekseenko, Sergei Kotelnikov, Mikhail Ignatov, +4

Journal of Molecular Biology

Natural SciencesCluspro LigtbmMolecular BiologySmall Molecule LibraryMolecular Docking +2

Template‐based modeling by ClusPro in CASP13 and the potential for using co‐evolutionary information in docking

Kathryn A. Porter, Dzmitry Padhorny, Israel Desta, +11

Proteins Structure Function and Bioinformatics

Co‐evolutionary InformationEngineeringMolecular BiologyCluspro ServerComputer-aided Design +21

ClusPro FMFT-SAXS: Ultra-fast Filtering Using Small-Angle X-ray Scattering Data in Protein Docking

Mikhail Ignatov, Andrey Kazennov, Dima Kozakov

Journal of Molecular Biology

X-ray CrystallographyProtein AssemblyProtein FoldingMedicineNatural Sciences +7

Improved prediction of MHC-peptide binding using protein language models

Nasser Hashemi, Boran Hao, Mikhail Ignatov, +4

Frontiers in Bioinformatics

Convolutional Neural NetworkEngineeringMachine LearningImmunologyProtein Language Models +18

Monte Carlo on the manifold and MD refinement for binding pose prediction of protein–ligand complexes: 2017 D3R Grand Challenge

Mikhail Ignatov, Cong Liu, Andrey Alekseenko, +10

Journal of Computer-Aided Molecular Design

EngineeringBiomolecular Structure PredictionPose PredictionMedicineMonte Carlo +12