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ClusPro: Performance in CAPRI rounds 6–11 and the new server

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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)1097-0134(19990515)35:3<364::aid-prot11>3.0.co;2-4openalex-snapshot

Use of pair potentials across protein interfaces in screening predicted docked complexes

inferredcites →https://doi.org/10.1002/(sici)1097-0134(20000501)39:2<178::aid-prot8>3.0.co;2-6openalex-snapshot

Protein docking using spherical polar Fourier correlations

inferredcites →https://doi.org/10.1002/(sici)1097-0282(199609)39:3<455::aid-bip16>3.0.co;2-aopenalex-snapshot

Low-resolution docking: Prediction of complexes for underdetermined structures

inferredcites →https://doi.org/10.1002/1097-0134(20000815)40:3<525::aid-prot190>3.0.co;2-fopenalex-snapshot

Scoring docked conformations generated by rigid-body protein-protein docking

inferredcites →https://doi.org/10.1002/jcc.540040211openalex-snapshot

CHARMM : A program for macromolecular energy, minimization, and dynamics calculations

inferredcites →https://doi.org/10.1002/prot.10389openalex-snapshot

ZDOCK: An initial‐stage protein‐docking algorithm

inferredcites →https://doi.org/10.1002/prot.10394openalex-snapshot

Successful discrimination of protein interactions

inferredcites →https://doi.org/10.1002/prot.20564openalex-snapshot

Performance of the first protein docking server ClusPro in CAPRI rounds 3–5

inferredcites →https://doi.org/10.1002/prot.21117openalex-snapshot

PIPER: An FFT‐based protein docking program with pairwise potentials

inferredcites →https://doi.org/10.1006/jmbi.1996.0859openalex-snapshot

Determination of atomic desolvation energies from the structures of crystallized proteins

inferredcites →https://doi.org/10.1006/jmbi.1997.1203openalex-snapshot

Modelling protein docking using shape complementarity, electrostatics and biochemical information 1 1Edited by J. Thornton

inferredcites →https://doi.org/10.1006/jmbi.1997.1519openalex-snapshot

Rapid refinement of protein interfaces incorporating solvation: application to the docking problem

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Structural Basis for the Bifunctionality of the U5 snRNP 52K Protein (CD2BP2)

inferredcites →https://doi.org/10.1016/j.jsb.2005.03.006openalex-snapshot

Predicting oligomeric assemblies: N-mers a primer

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Molecular Basis for Bacterial Class I Release Factor Methylation by PrmC

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Molecular Mimicry Enables Competitive Recruitment by a Natively Disordered Protein

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How guanylate-binding proteins achieve assembly-stimulated processive cleavage of GTP to GMP

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Structural basis for ARF1‐mediated recruitment of ARHGAP21 to Golgi membranes

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Structural basis of the Sir1–origin recognition complex interaction in transcriptional silencing

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Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques.

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ClusPro: an automated docking and discrimination method for the prediction of protein complexes

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Consensus alignment server for reliable comparative modeling with distant templates

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Protein docking using continuum electrostatics and geometric fit

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Comparative Protein Structure Modeling of Genes and Genomes

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Optimal Clustering for Detecting Near-Native Conformations in Protein Docking

What points at this work

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