Critical assessment of methods for predicting the 3D structure of proteins and protein complexes
SJ Wodak, S Vajda, MF Lensink… - Annual review of …, 2023 - annualreviews.org
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 …
Enhancing important fluctuations: Rare events and metadynamics from a conceptual viewpoint
Atomistic simulations play a central role in many fields of science. However, their usefulness
is often limited by the fact that many systems are characterized by several metastable states …
is often limited by the fact that many systems are characterized by several metastable states …
Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment
MF Lensink, G Brysbaert, T Mauri… - Proteins: Structure …, 2021 - Wiley Online Library
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 …
Classification and prediction of protein–protein interaction interface using machine learning algorithm
S Das, S Chakrabarti - Scientific reports, 2021 - nature.com
Structural insight of the protein–protein interaction (PPI) interface can provide knowledge
about the kinetics, thermodynamics and molecular functions of the complex while …
about the kinetics, thermodynamics and molecular functions of the complex while …
GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking
Protein-protein docking methods have been widely used to gain an atomic-level
understanding of protein interactions. However, docking methods that employ low-resolution …
understanding of protein interactions. However, docking methods that employ low-resolution …
Protein–protein docking: Past, present, and future
S Sunny, PB Jayaraj - The protein journal, 2022 - Springer
The biological significance of proteins attracted the scientific community in exploring their
characteristics. The studies shed light on the interaction patterns and functions of proteins in …
characteristics. The studies shed light on the interaction patterns and functions of proteins in …
Assessing exhaustiveness of stochastic sampling for integrative modeling of macromolecular structures
Modeling of macromolecular structures involves structural sampling guided by a scoring
function, resulting in an ensemble of good-scoring models. By necessity, the sampling is …
function, resulting in an ensemble of good-scoring models. By necessity, the sampling is …
[HTML][HTML] Computational modeling of protein assemblies
N Soni, MS Madhusudhan - Current opinion in structural biology, 2017 - Elsevier
Highlights•Template based protein complex modeling has gone beyond homology
modeling.•Protein docking methods have improved upon their sampling/scoring …
modeling.•Protein docking methods have improved upon their sampling/scoring …
Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles
Y Fukunishi, J Higo, K Kasahara - Biophysical Reviews, 2022 - Springer
Prediction of ligand-receptor complex structure is important in both the basic science and the
industry such as drug discovery. We report various computation molecular docking methods …
industry such as drug discovery. We report various computation molecular docking methods …
Distance‐based reconstruction of protein quaternary structures from inter‐chain contacts
Predicting the quaternary structure of protein complex is an important problem. Inter‐chain
residue‐residue contact prediction can provide useful information to guide the ab initio …
residue‐residue contact prediction can provide useful information to guide the ab initio …