We believe that a solution of the docking problem may be achieved by matching a simple model of molecular recognition with an efficient search procedure. The necessary ingredients of a molecular recognition model include only steric and hydrogen-bond interaction terms. Although these terms are not necessarily sufficient to predict binding affinity, they describe ligand-protein interactions faithfully enough to enable a docking program to predict the structure of the bound ligand. This docking strategy thus provides an important tool for the interdisciplinary field of rational drug design.

A new computational method for the in situ generation of small molecules within the binding site of a protein is described. The method has been evaluated using two well-studied systems, dihydrofolate reductase and thymidylate synthase. The method has also been used to guide improvements to inhibitors of HIV-1 protease. One such improvement resulted in a compound selected for preclinical studies as an antiviral agent against AIDS.

BackgroundOur study aimed to describe the concordance of chlamydia infections of the rectum and urethra in men who have sex with men (MSM) and their male partners.MethodsThis was a cross-sectional study of chlamydia in MSM and their male sexual partners both attending Melbourne Sexual Health Centre (MSHC), Australia, between February 2011 and March 2015. We excluded partnerships where testing for chlamydia at both the rectum and urethra were not undertaken.ResultsOur study included 473 partnerships (946 men). 30 men had urethral chlamydia, of whom 14 (47%, 95% CI 28 to 66) had a partner with rectal chlamydia. 46 men had rectal chlamydia, of whom 14 (30%, 95% CI 18 to 46) had a partner with urethral chlamydia. The proportion of men with rectal chlamydia when their partner had urethral chlamydia was significantly higher than the proportion of men with urethral chlamydia when their partner had rectal chlamydia (McNemar’s p = 0.02).ConclusionsThis is the first study of chlamydia concordance in male sexual partnerships and suggests that transmission of chlamydia between the urethra and rectum may be less efficient than has been reported for transmission between the urethra and cervix in heterosexual couples. It also suggests that transmission from the urethra to the rectum may be more efficient than in the opposite direction.Electronic supplementary materialThe online version of this article (doi:10.1186/s12879-016-2141-7) contains supplementary material, which is available to authorized users.

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