Critical assessment of methods for predicting the 3D structure of proteins and protein complexes
Advances in a scientific discipline are often measured by small, incremental steps. In this
review, we report on two intertwined disciplines in the protein structure prediction field …
review, we report on two intertwined disciplines in the protein structure prediction field …
Molecular docking as a popular tool in drug design, an in silico travel
New molecular modeling approaches, driven by rapidly improving computational platforms,
have allowed many success stories for the use of computer-assisted drug design in the …
have allowed many success stories for the use of computer-assisted drug design in the …
Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment
We present the results for CAPRI Round 50, the fourth joint CASP‐CAPRI protein assembly
prediction challenge. The Round comprised a total of twelve targets, including six dimers …
prediction challenge. The Round comprised a total of twelve targets, including six dimers …
Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment
We present the results for CAPRI Round 54, the 5th joint CASP‐CAPRI protein assembly
prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo …
prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo …
Modeling protein–protein and protein–peptide complexes: CAPRI 6th edition
MF Lensink, S Velankar… - … : Structure, Function, and …, 2017 - Wiley Online Library
We present the sixth report evaluating the performance of methods for predicting the atomic
resolution structures of protein complexes offered as targets to the community‐wide initiative …
resolution structures of protein complexes offered as targets to the community‐wide initiative …
Modeling protein‐protein, protein‐peptide, and protein‐oligosaccharide complexes: CAPRI 7th edition
MF Lensink, N Nadzirin, S Velankar… - Proteins: Structure …, 2020 - Wiley Online Library
We present the seventh report on the performance of methods for predicting the atomic
resolution structures of protein complexes offered as targets to the community‐wide initiative …
resolution structures of protein complexes offered as targets to the community‐wide initiative …
Docking, scoring, and affinity prediction in CAPRI
MF Lensink, SJ Wodak - Proteins: Structure, Function, and …, 2013 - Wiley Online Library
We present the fifth evaluation of docking and related scoring methods used in the
community‐wide experiment on the Critical Assessment of Predicted Interactions (CAPRI) …
community‐wide experiment on the Critical Assessment of Predicted Interactions (CAPRI) …
GalaxyWater-CNN: Prediction of water positions on the protein structure by a 3D-convolutional neural network
S Park, C Seok - Journal of Chemical Information and Modeling, 2022 - ACS Publications
Proteins interact with numerous water molecules to perform their physiological functions in
biological organisms. Most water molecules act as solvent media; hence, their roles may be …
biological organisms. Most water molecules act as solvent media; hence, their roles may be …
Blind prediction of homo‐and hetero‐protein complexes: The CASP13‐CAPRI experiment
We present the results for CAPRI Round 46, the third joint CASP‐CAPRI protein assembly
prediction challenge. The Round comprised a total of 20 targets including 14 homo …
prediction challenge. The Round comprised a total of 20 targets including 14 homo …
Addressing recent docking challenges: A hybrid strategy to integrate template‐based and free protein‐protein docking
Protein–protein docking is an important computational tool for predicting protein–protein
interactions. With the rapid development of proteomics projects, more and more …
interactions. With the rapid development of proteomics projects, more and more …