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Gaussian 03, Revision E.01.
ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers
This paper presents a user-friendly protein docking server, based on the rigid-body docking programs ZDOCK and M-ZDOCK, to predict structures of protein-protein complexes and symmetric multimers, and provides options for users to guide the scoring and the selection of output models. Expand
Protein–protein docking benchmark version 4.0
The protein–protein docking benchmark is updated to include complexes that became available since the previous release, and provides 176 unbound–unbound cases that can be used for protein– protein docking method development and assessment. Expand
Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.
The number of antibody-antigen complexes has increased significantly, by 67% and 74% in the docking and affinity benchmarks, respectively, which now contain 230 and 179 entries. Expand
The HP1 Homolog Rhino Anchors a Nuclear Complex that Suppresses piRNA Precursor Splicing
It is proposed that Rhino anchors a nuclear complex that suppresses cluster transcript splicing and speculate that stalled splicing differentiates piRNA precursors from mRNAs. Expand
UAP56 Couples piRNA Clusters to the Perinuclear Transposon Silencing Machinery
A charge-substitution mutation that alters a conserved surface residue in UAP56 disrupts colocalization with Rhino, germline piRNA production, transposon silencing, and perinuclear localization of Vasa, and is proposed to function in a piRNA-processing compartment that spans the nuclear envelope. Expand
Combining Quantum Mechanics Methods with Molecular Mechanics Methods in ONIOM.
The potential surface can be discontinuous when there is bond breaking and forming closer than three bonds from the MM region and the behavior of ONIOM with electronic embedding can be more stable than QM/MM with electronicembedding. Expand
Integrating atom‐based and residue‐based scoring functions for protein–protein docking
Combination of residue‐based and atom‐based potentials into a scoring function can improve performance for protein–protein docking. Expand
Community-wide assessment of protein-interface modeling suggests improvements to design methodology.
A number of designed protein-protein interfaces with very favorable computed binding energies but which do not appear to be formed in experiments are generated, suggesting that there may be important physical chemistry missing in the energy calculations. Expand
On the application of the IMOMO (integrated molecular orbital + molecular orbital) method
The history of the method, a number of chemical problems that have studied, how to assess IMOMO combinations and partitionings, and the latest efforts that take the method beyond the conventional investigation of ground state energy surfaces are presented. Expand