Inactivation of cell-free HIV-1 by designing potent peptides based on mutations in the CD4 binding site

Urtica dioica agglutinin (UDA) as a potential candidate for inhibition of SARS-CoV-2 Omicron variants: In silico prediction and experimental validation

(2023) Fatemeh Sabzian-Molaei et al.   PHYTOMEDICINE

ToxIBTL: prediction of peptide toxicity based on information bottleneck and transfer learning

(2022) Lesong Wei et al.   BIOINFORMATICS

Urtica dioica Agglutinin: A plant protein candidate for inhibition of SARS-COV-2 receptor-binding domain for control of Covid19 Infection

(2022) Fatemeh Sabzian-Molaei et al.   PLoS One

Antiviral Effect of Saffron Compounds on the GP120 of HIV‐1: an In Silico Study

(2022) Fatemeh Sabzian‐Molaei et al.   ChemistrySelect

HLPpred-Fuse: improved and robust prediction of hemolytic peptide and its activity by fusing multiple feature representation

(2020) Md Mehedi Hasan et al.   BIOINFORMATICS

Protein- and Peptide-Based Virus Inactivators: Inactivating Viruses Before Their Entry Into Cells

(2020) Xiaojie Su et al.   Frontiers in Microbiology

Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD:KRas protein-protein interface

(2020) Anna U. Lowegard et al.   PLoS Computational Biology

Opening the HIV envelope: potential of CD4 mimics as multifunctional HIV entry inhibitors

(2020) Annemarie Laumaea et al.   Current Opinion in HIV and AIDS

A Peptide-Based HIV-1 Fusion Inhibitor with Two Tail-Anchors and Palmitic Acid Exhibits Substantially Improved In Vitro and Ex Vivo Anti-HIV-1 Activity and Prolonged In Vivo Half-Life

(2019) Shan Su et al.   MOLECULES

Development of Protein- and Peptide-Based HIV Entry Inhibitors Targeting gp120 or gp41

(2019) Pu et al.   Viruses-Basel

In Silico Identification of Novel Aromatic Compounds as Potential HIV-1 Entry Inhibitors Mimicking Cellular Receptor CD4

(2019) Alexander M. Andrianov et al.   Viruses-Basel

Structural and Functional Characterization of Membrane Fusion Inhibitors with Extremely Potent Activity against Human Immunodeficiency Virus Type 1 (HIV-1), HIV-2, and Simian Immunodeficiency Virus

(2018) Huihui Chong et al.   JOURNAL OF VIROLOGY

Engineering multi-specific antibodies against HIV-1

(2018) Neal N. Padte et al.   Retrovirology

OSPREY 3.0: Open-source protein redesign for you, with powerful new features

(2018) Mark A. Hallen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Small-molecule HIV-1 entry inhibitors targeting gp120 and gp41: a patent review (2010-2015)

(2017) Wen Li et al.   EXPERT OPINION ON THERAPEUTIC PATENTS

Enfuvirtide (T20)-Based Lipopeptide Is a Potent HIV-1 Cell Fusion Inhibitor: Implications for Viral Entry and Inhibition

(2017) Xiaohui Ding et al.   JOURNAL OF VIROLOGY

PDBsum: Structural summaries of PDB entries

(2017) Roman A. Laskowski et al.   PROTEIN SCIENCE

PRODIGY: a web server for predicting the binding affinity of protein–protein complexes

(2016) Li C. Xue et al.   BIOINFORMATICS

Engineered Bispecific Antibodies with Exquisite HIV-1-Neutralizing Activity

(2016) Yaoxing Huang et al.   CELL

Creating an Artificial Tail Anchor as a Novel Strategy To Enhance the Potency of Peptide-Based HIV Fusion Inhibitors

(2016) Shan Su et al.   JOURNAL OF VIROLOGY

Fusion peptide of HIV-1 as a site of vulnerability to neutralizing antibody

(2016) R. Kong et al.   SCIENCE

Identification and characterization of a subpocket on the N-trimer of HIV-1 Gp41

(2015) Zonglin Qiu et al.   AIDS

MAESTRO - multi agent stability prediction upon point mutations

(2015) Josef Laimer et al.   BMC BIOINFORMATICS

The I-TASSER Suite: protein structure and function prediction

(2015) Jianyi Yang et al.   NATURE METHODS

g_mmpbsa—A GROMACS Tool for High-Throughput MM-PBSA Calculations

(2014) Rashmi Kumari et al.   Journal of Chemical Information and Modeling

AllerTOP v.2—a server for in silico prediction of allergens

(2014) Ivan Dimitrov et al.   JOURNAL OF MOLECULAR MODELING

Broad and potent HIV-1 neutralization by a human antibody that binds the gp41–gp120 interface

(2014) Jinghe Huang et al.   NATURE

An engineered HIV-1 gp41 trimeric coiled coil with increased stability and anti-HIV-1 activity: implication for developing anti-HIV microbicides

(2013) P. Tong et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Computational analysis of anti-HIV-1 antibody neutralization panel data to identify potential functional epitope residues

(2013) A. P. West et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Generation of HIV-1 potent and broad neutralizing antibodies by immunization with postfusion HR1/HR2 complex

(2012) Reham Dawood et al.   AIDS

Broad and potent neutralization of HIV-1 by a gp41-specific human antibody

(2012) Jinghe Huang et al.   NATURE

Characterization of HIV-1 resistance to a fusion inhibitor, N36, derived from the gp41 amino-terminal heptad repeat

(2010) Kazuki Izumi et al.   ANTIVIRAL RESEARCH

Identification of a gp41 Core-Binding Molecule with Homologous Sequence of Human TNNI3K-Like Protein as a Novel Human Immunodeficiency Virus Type 1 Entry Inhibitor

(2010) Y. Zhu et al.   JOURNAL OF VIROLOGY

Novel approaches to inhibiting HIV-1 replication

(2009) Catherine S. Adamson et al.   ANTIVIRAL RESEARCH

Addition of a cholesterol group to an HIV-1 peptide fusion inhibitor dramatically increases its antiviral potency

(2009) P. Ingallinella et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details

(2009) V. Potapov et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Reviews Of Anti‐infective Agents: Maraviroc: The First of a New Class of Antiretroviral Agents

(2008) Rodger D. MacArthur et al.   CLINICAL INFECTIOUS DISEASES