Taylor and Francis
No less than five full books on how to write papers are freely accessible online. To add to this there is audio advice from the editors, and section by section advice and comments on what not to do. This also contains links and email addresses for direct questions on grammar or journal style.
Young Hydrologic Society
In case the five books took too much time to read, this website provides presentation slides of how to write a paper, in minute detail. It also has three suggestions for referencing tools, which may not be free of charge but still a worthwhile organizational investment.
It's one thing to write down what you have done, it's another to write analytically, deciding which word goes where, what sentence needs to explain and what sentence needs to convince, and determining whether your message really comes across or not. As the abstract is among the first things to be read, getting this right will help reviewers decide to read the rest. To analytically write the abstract, look at this Nature guide to authors. Even if biological proteins are not your topic, the flow of the abstract of any scientific paper should ideally be roughly the same as this one. The trick will be to keep up this analytic writing style in the entire paper.
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