2021 Research Highlights

Evaluating local and directional resolution of cryo-EM density maps

Methods are presented for evaluating and improving cryo-EM maps.

Aiyer S, Zhang C, Baldwin PR, Lyumkis D. Methods Mol Biol. 2021;2215:161-187.

PubMed PMID: 33368004

Tools for visualizing and analyzing Fourier space sampling in Cryo-EM

Tools are presented for understanding how molecular orientation impacts structure determination by cryoelectron microscopy.

Baldwin PR, Lyumkis D. Prog Biophys Mol Biol. 2021 Mar;160:53-65.

PubMed PMID: 32645314

PubMedCentral PMCID: PMC7785567 (available on )

Mi3-GPU: MCMC-based Inverse Ising Inference on GPUs for protein covariation analysis

HIVE Center members improve methods for predicting interactions between amino acids based on observed mutational covariations.

Haldane A, Levy RM. Comput Phys Commun. 2021 Mar;260:107312.

PubMed PMID: 33716309

PubMedCentral PMCID: PMC7944406 (available on 2022-03-01)

Sec24C is an HIV-1 host dependency factor crucial for virus replication

Integrase strand transfer inhibitors are effective anti-HIV drugs

Clinically-useful inhibitors that block the active site of HIV-1 integrase are reviewed.

Smith SJ, Zhao XZ, Passos DO, Lyumkis D, Burke TR Jr, Hughes SH.  Viruses. 2021 Jan 29;13(2):205.

PubMed PMID: 33572956

PubMedCentral PMCID: PMC7912079

Computational design of small molecular modulators of protein-protein interactions with a novel thermodynamic cycle: Allosteric inhibitors of HIV-1 integrase

A new method for targeting protein-protein interfaces is applied to design of integrase inhibitors

Sun Q, Ramaswamy VSK, Levy R, Deng N. Protein Sci. 2021 Feb;30(2):438-447.

PubMed PMID: 33244804

PubMedCentral PMCID: PMC7784772